Merge remote-tracking branch 'unstable/master'

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,53 @@
+### Instructions
+
+- Use a **concise** yet **descriptive** title;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;
+- If the issue will be added to the public tracker (using the `public` label), it must conform to [these guidelines](http://gatkforums.broadinstitute.org/dsde/discussion/6801/guidelines-for-tagging-issues-with-the-public-tag#latest);
+- Delete the other template blocks and this header.
+
+----
+
+## Bug Report
+
+### Affected tool(s)
+_Tool name(s), special parameters?_
+
+### Affected version(s)
+- [ ] Latest public release version [version?]
+- [ ] Latest development/master branch as of [date of test?]
+
+### Description 
+_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._
+
+#### Steps to reproduce
+_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem on a test case on one of the gsa* servers._
+
+#### Expected behavior
+_Tell us what should happen_
+
+#### Actual behavior
+_Tell us what happens instead_
+
+----
+
+## Feature request
+
+### Tool(s) involved
+_Tool name(s), special parameters?_
+
+### Description
+_Specify whether you want a modification of an existing behavior or addition of a new capability._
+_Provide **examples**, **screenshots**, where appropriate._
+
+----
+
+## Documentation request
+
+### Tool(s) involved
+_Tool name(s), parameters?_
+
+### Description 
+_Describe what needs to be added or modified._
+
+----

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,30 @@
+### Description
+
+_Please explain the changes you made here._
+_Explain the **motivation** for making this change. What existing problem does the pull request solve?_
+_Mention any issues fixed, addressed or otherwise related to this pull request, including issue numbers or hard links for issues in other repos._
+
+----
+
+### Checklist (never delete this)
+
+Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below. 
+
+#### Content
+- [ ] Added or modified tests to cover changes and any new functionality
+- [ ] All tests passing on Bamboo (including license tests!)
+
+#### Form
+- [ ] Rebased, squashed and reworded to produce a single commit (exemptions may be made -- sparingly) that is _uncluttered by excess lines_ (lines that just say "addressed review", "fixed" etc left over from squashing)
+- [ ] Both the PR and the final rebased commit have a **concise** yet **descriptive** title (they are used when we compile version notes)
+- [ ] Edited the README / documentation accordingly and got sign-off from support team (private code is exempt)
+
+#### Review
+- [ ] Suggest a reviewer or ask your team lead to suggest one
+- [ ] Final (thumbsup) from the reviewer(s)
+
+#### GATK4 Implications
+- [ ] If your fix/change is applicable to GATK4 as well, and is reasonably small and self-contained (< ~50 lines or so), port the change to GATK4 and open a PR against https://github.com/broadinstitute/gatk or https://github.com/broadinstitute/gatk-protected as appropriate, or at least make a "best effort" attempt to do so.
+- [ ] If your fix/change cannot yet be ported to GATK4 because the tool in question hasn't been ported yet, or has only been partially ported, or it would be difficult/burdensome to port the change, or you tried to port the change and failed, then add the ticket to our list of [GATK3 PRs to be eventually ported to GATK4](https://docs.google.com/document/d/1DjEHw57k5h0i8MZRGYPlQA3InvURKwQ7pCoi_Eigc4M/edit)
+
+Once everything is checked off, you can go ahead and merge the PR. Don't forget to also delete the branch.

.gitignore

@@ -1,3 +1,5 @@
+.idea/
+.queue/
 /*.bam
 /*.bai
 /*.bed
@@ -5,7 +7,6 @@
 /*.vcf
 /*.txt
 /*.csh
-/.*
 /*.pdf
 /*.eval
 *.ipr
@@ -13,11 +14,9 @@
 *.iml
 *.pyc
 .DS_Store
-queueScatterGather
 /foo*
 /bar*
 integrationtests/
-public/testdata/onTheFlyOutputTest.vcf
 build/
 dist/
 dump/

licensing/private_license.txt

@@ -4,7 +4,7 @@ BROAD INSTITUTE
 SOFTWARE LICENSE AGREEMENT
 FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 
-This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 
 WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th
 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 
 3. PHONE-HOME FEATURE
-LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 
 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-Copyright 2012-2015 Broad Institute, Inc.
+Copyright 2012-2016 Broad Institute, Inc.
 Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 

licensing/protected_license.txt

@@ -4,7 +4,7 @@ BROAD INSTITUTE
 SOFTWARE LICENSE AGREEMENT
 FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 
-This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 
 WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th
 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 
 3. PHONE-HOME FEATURE
-LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 
 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-Copyright 2012-2015 Broad Institute, Inc.
+Copyright 2012-2016 Broad Institute, Inc.
 Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 

licensing/public_license.txt

@@ -1,4 +1,4 @@
-Copyright 2012-2015 Broad Institute, Inc.
+Copyright 2012-2016 Broad Institute, Inc.
 
 Permission is hereby granted, free of charge, to any person
 obtaining a copy of this software and associated documentation

pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-root</artifactId>
-        <version>3.5</version>
+        <version>3.6-SNAPSHOT</version>
         <relativePath>public/gatk-root</relativePath>
     </parent>
 
@@ -32,6 +32,7 @@
         <resource.bundle.skip>false</resource.bundle.skip>
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
+        <gatkdocs.extension>html</gatkdocs.extension>
         <gatk.shell.directory>${gatk.basedir}/public/src/main/scripts/shell</gatk.shell.directory>
         <gatk.assembly.directory>${gatk.basedir}/public/src/main/assembly</gatk.assembly.directory>
 
@@ -768,7 +769,7 @@
                             <useStandardDocletOptions>false</useStandardDocletOptions>
                             <quiet>true</quiet>
                             <show>private</show>
-                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs</additionalparam>
+                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs -output-file-extension ${gatkdocs.extension}</additionalparam>
                         </configuration>
                     </reportSet>
                 </reportSets>

protected/gatk-package-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.5</version>
+        <version>3.6-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
@@ -61,6 +61,11 @@
             <groupId>commons-httpclient</groupId>
             <artifactId>commons-httpclient</artifactId>
         </dependency>
+        <!-- Used in ONE unit test (grr) -->
+        <dependency>
+            <groupId>colt</groupId>
+            <artifactId>colt</artifactId>
+        </dependency>
         <!--
         Some cofoja annotations (ex: PreconditionError) are ONLY in used tests.
         They are not picked up by shade, not required during normal runs, but are important for tests to avoid

protected/gatk-queue-extensions-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.5</version>
+        <version>3.6-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -109,7 +109,8 @@ class ExampleUnifiedGenotyperQueueTest {
   }
 
   @DataProvider(name="resMemReqParams")
-  def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
+  //mem_free no longer works on GridEngine8 configuration; UGER will require "m_mem_free" instead of "virtual_free"
+  def getResMemReqParam = Array(Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
 
   @Test(dataProvider = "resMemReqParams", timeOut=36000000)
   def testUnifiedGenotyperResMemReqParam(reqParam: String) {

protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-queue-package-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.5</version>
+        <version>3.6-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-tools-protected/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.5</version>
+        <version>3.6-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.engine.arguments;
 
+import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator;
 import org.broadinstitute.gatk.utils.commandline.Advanced;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
@@ -60,6 +61,9 @@ import java.util.List;
 
 public class GenotypeCalculationArgumentCollection implements Cloneable{
 
+
+    public static final String MAX_ALTERNATE_ALLELES_SHORT_NAME = "maxAltAlleles";
+
     /**
      * Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
      * Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.
@@ -113,7 +117,7 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
     public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
 
     /**
-     * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
+     * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN_ALLELES),
      * then only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
      * scales exponentially based on the number of alternate alleles.  Unless there is a good reason to change the default value, we highly recommend
      * that you not play around with this parameter.
@@ -121,9 +125,18 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
      * As of GATK 2.2 the genotyper can handle a very large number of events, so the default maximum has been increased to 6.
      */
     @Advanced
-    @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
+    @Argument(fullName = "max_alternate_alleles", shortName = MAX_ALTERNATE_ALLELES_SHORT_NAME, doc = "Maximum number of alternate alleles to genotype", required = false)
     public int MAX_ALTERNATE_ALLELES = 6;
 
+    /**
+     * Determines the maximum number of PL values that will be logged in the output.  If the number of genotypes
+     * (which is determined by the ploidy and the number of alleles) exceeds the value provided by this argument,
+     * then output of all of the PL values will be suppressed.
+     */
+    @Advanced
+    @Argument(fullName = "max_num_PL_values", shortName = "maxNumPLValues", doc = "Maximum number of PL values to output", required = false)
+    public int MAX_NUM_PL_VALUES = AFCalculator.MAX_NUM_PL_VALUES_DEFAULT;
+
     /**
      * By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model,
      * see e.g. Waterson (1975) or Tajima (1996).

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java

@@ -1,138 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration;
-
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.log4j.Logger;
-import org.broadinstitute.gatk.utils.commandline.Gatherer;
-import org.broadinstitute.gatk.utils.report.GATKReport;
-import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
-import org.broadinstitute.gatk.utils.exceptions.UserException;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
-import java.util.*;
-
-/**
- * User: carneiro
- * Date: 3/29/11
- */
-
-
-public class BQSRGatherer extends Gatherer  {
-
-    private static final Logger logger = Logger.getLogger(BQSRGatherer.class);
-    private static final String EMPTY_INPUT_LIST = "list of inputs files is empty or there is no usable data in any input file";
-    private static final String MISSING_OUTPUT_FILE = "missing output file name";
-    private static final String MISSING_READ_GROUPS = "Missing read group(s)";
-
-    @Override
-    public void gather(final List<File> inputs, final File output) {
-        final PrintStream outputFile;
-        try {
-            outputFile = new PrintStream(output);
-        } catch(FileNotFoundException e) {
-            throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE);
-        }
-        final GATKReport report = gatherReport(inputs);
-        report.print(outputFile);
-    }
-
-    /**
-     * Gathers the input recalibration reports into a single report.
-     *
-     * @param inputs Input recalibration GATK reports
-     * @return gathered recalibration GATK report
-     */
-    public static GATKReport gatherReport(final List<File> inputs) {
-        final SortedSet<String> allReadGroups = new TreeSet<String>();
-        final LinkedHashMap<File, Set<String>> inputReadGroups = new LinkedHashMap<File, Set<String>>();
-
-        // Get the read groups from each input report
-        for (final File input : inputs) {
-            final Set<String> readGroups = RecalibrationReport.getReadGroups(input);
-            inputReadGroups.put(input, readGroups);
-            allReadGroups.addAll(readGroups);
-        }
-
-        // Log the read groups that are missing from specific inputs
-        for (Map.Entry<File, Set<String>> entry: inputReadGroups.entrySet()) {
-            final File input = entry.getKey();
-            final Set<String> readGroups = entry.getValue();
-            if (allReadGroups.size() != readGroups.size()) {
-                // Since this is not completely unexpected, more than debug, but less than a proper warning.
-                logger.info(MISSING_READ_GROUPS + ": " + input.getAbsolutePath());
-                for (final Object readGroup: CollectionUtils.subtract(allReadGroups, readGroups)) {
-                    logger.info("  " + readGroup);
-                }
-            }
-        }
-
-        RecalibrationReport generalReport = null;
-        for (File input : inputs) {
-            final RecalibrationReport inputReport = new RecalibrationReport(input, allReadGroups);
-            if( inputReport.isEmpty() ) { continue; }
-
-            if (generalReport == null)
-                generalReport = inputReport;
-            else
-                generalReport.combine(inputReport);
-        }
-        if (generalReport == null)
-            throw new ReviewedGATKException(EMPTY_INPUT_LIST);
-
-        generalReport.calculateQuantizedQualities();
-
-        return generalReport.createGATKReport();
-    }
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java

@@ -1,104 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration;
-
-import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
-import org.broadinstitute.gatk.engine.WalkerManager;
-import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
-import org.broadinstitute.gatk.engine.walkers.Walker;
-import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-
-/**
- * A ReadTransformer that applies BQSR on the fly to reads
- *
- * User: rpoplin
- * Date: 2/13/12
- */
-public class BQSRReadTransformer extends ReadTransformer {
-    private boolean enabled;
-    private BaseRecalibration bqsr = null;
-
-    @Override
-    public OrderingConstraint getOrderingConstraint() { return OrderingConstraint.MUST_BE_FIRST; }
-
-    @Override
-    public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) {
-        this.enabled = engine.hasBQSRArgumentSet();
-        if ( enabled ) {
-            // TODO -- See important note below about applying BQSR to a reduced BAM file:
-            // If it is important to make sure that BQSR is not applied (as opposed to having the covariates computed) against a reduced bam file,
-            // we need to figure out how to make this work.  The problem is that the ReadTransformers are initialized before the ReadDataSource
-            // inside the GenomeAnalysisEngine, so we generate a NPE when trying to retrieve the SAMFileHeaders.  Ultimately, I don't think this is
-            // a necessary check anyways since we disallow running BaseRecalibrator on reduced bams (so we can't generate the recal tables to use here).
-            // Although we could add this check to the apply() method below, it's kind of ugly and inefficient.
-            // The call here would be: RecalUtils.checkForInvalidRecalBams(engine.getSAMFileHeaders(), engine.getArguments().ALLOW_BQSR_ON_REDUCED_BAMS);
-            final BQSRArgumentSet args = engine.getBQSRArgumentSet();
-            this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals(), args.getGlobalQScorePrior(), args.getStaticQuantizedQuals(), args.getRoundDown());
-        }
-        final BQSRMode mode = WalkerManager.getWalkerAnnotation(walker, BQSRMode.class);
-        return mode.ApplicationTime();
-    }
-
-    @Override
-    public boolean enabled() {
-        return enabled;
-    }
-
-    /**
-     * initialize a new BQSRReadTransformer that applies BQSR on the fly to incoming reads.
-     */
-    @Override
-    public GATKSAMRecord apply(GATKSAMRecord read) {
-        bqsr.recalibrateRead(read);
-        return read;
-    }
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java

@@ -1,151 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration;
-
-import org.broadinstitute.gatk.utils.report.GATKReportTable;
-import org.broadinstitute.gatk.utils.MathUtils;
-import org.broadinstitute.gatk.utils.QualityUtils;
-import org.broadinstitute.gatk.utils.collections.NestedIntegerArray;
-
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * Class that encapsulates the information necessary for quality score quantization for BQSR
- *
- * @author carneiro
- * @since 3/26/12
- */
-public class QuantizationInfo {
-    private List<Byte> quantizedQuals;
-    private List<Long> empiricalQualCounts;
-    private int quantizationLevels;
-
-    private QuantizationInfo(List<Byte> quantizedQuals, List<Long> empiricalQualCounts, int quantizationLevels) {
-        this.quantizedQuals = quantizedQuals;
-        this.empiricalQualCounts = empiricalQualCounts;
-        this.quantizationLevels = quantizationLevels;
-    }
-
-    public QuantizationInfo(List<Byte> quantizedQuals, List<Long> empiricalQualCounts) {
-        this(quantizedQuals, empiricalQualCounts, calculateQuantizationLevels(quantizedQuals));
-    }
-    
-    public QuantizationInfo(final RecalibrationTables recalibrationTables, final int quantizationLevels) {
-        final Long [] qualHistogram = new Long[QualityUtils.MAX_SAM_QUAL_SCORE +1]; // create a histogram with the empirical quality distribution
-        for (int i = 0; i < qualHistogram.length; i++)
-            qualHistogram[i] = 0L;
-
-        final NestedIntegerArray<RecalDatum> qualTable = recalibrationTables.getQualityScoreTable(); // get the quality score table
-
-        for (final RecalDatum value : qualTable.getAllValues()) {
-            final RecalDatum datum = value;
-            final int empiricalQual = MathUtils.fastRound(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL )
-            qualHistogram[empiricalQual] += (long) datum.getNumObservations(); // add the number of observations for every key
-        }
-        empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities
-        quantizeQualityScores(quantizationLevels);
-
-        this.quantizationLevels = quantizationLevels;
-    }
-
-
-    public void quantizeQualityScores(int nLevels) {
-        QualQuantizer quantizer = new QualQuantizer(empiricalQualCounts, nLevels, QualityUtils.MIN_USABLE_Q_SCORE); // quantize the qualities to the desired number of levels
-        quantizedQuals = quantizer.getOriginalToQuantizedMap(); // map with the original to quantized qual map (using the standard number of levels in the RAC)
-    }
-
-    public void noQuantization() {
-        this.quantizationLevels = QualityUtils.MAX_SAM_QUAL_SCORE;
-        for (int i = 0; i < this.quantizationLevels; i++)
-            quantizedQuals.set(i, (byte) i);
-    }
-
-    public List<Byte> getQuantizedQuals() {
-        return quantizedQuals;
-    }
-
-    public int getQuantizationLevels() {
-        return quantizationLevels;
-    }
-
-    public GATKReportTable generateReportTable(boolean sortByCols) {
-        GATKReportTable quantizedTable;
-        if(sortByCols) {
-            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
-        }   else {
-            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);
-        }
-        quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME);
-        quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME);
-        quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME);
-
-        for (int qual = 0; qual <= QualityUtils.MAX_SAM_QUAL_SCORE; qual++) {
-            quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual);
-            quantizedTable.set(qual, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual));
-            quantizedTable.set(qual, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual));
-        }
-        return quantizedTable;
-    }
-
-    private static int calculateQuantizationLevels(List<Byte> quantizedQuals) {
-        byte lastByte = -1;
-        int quantizationLevels = 0;
-        for (byte q : quantizedQuals) {
-            if (q != lastByte) {
-                quantizationLevels++;
-                lastByte = q;
-            }
-        }
-        return quantizationLevels;
-    }
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java

@@ -1,176 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration;
-
-import org.apache.log4j.Logger;
-import org.broadinstitute.gatk.utils.LRUCache;
-import org.broadinstitute.gatk.utils.recalibration.EventType;
-
-/**
- * The object temporarily held by a read that describes all of it's covariates.
- *
- * In essence, this is an array of CovariateValues, but it also has some functionality to deal with the optimizations of the NestedHashMap
- *
- * @author Mauricio Carneiro
- * @since 2/8/12
- */
-public class ReadCovariates {
-    private final static Logger logger = Logger.getLogger(ReadCovariates.class);
-
-    /**
-     * How big should we let the LRU cache grow
-     */
-    private static final int LRU_CACHE_SIZE = 500;
-
-    /**
-     * Use an LRU cache to keep cache of keys (int[][][]) arrays for each read length we've seen.
-     * The cache allows us to avoid the expense of recreating these arrays for every read.  The LRU
-     * keeps the total number of cached arrays to less than LRU_CACHE_SIZE.
-     *
-     * This is a thread local variable, so the total memory required may grow to N_THREADS x LRU_CACHE_SIZE
-     */
-    private final static ThreadLocal<LRUCache<Integer, int[][][]>> keysCache = new ThreadLocal<LRUCache<Integer, int[][][]>>() {
-        @Override protected LRUCache<Integer, int[][][]> initialValue() {
-            return new LRUCache<Integer, int[][][]>(LRU_CACHE_SIZE);
-        }
-    };
-
-    /**
-     * The keys cache is only valid for a single covariate count.  Normally this will remain constant for the analysis.
-     * If running multiple analyses (or the unit test suite), it's necessary to clear the cache.
-     */
-    public static void clearKeysCache() {
-        keysCache.remove();
-    }
-
-    /**
-     * Our keys, indexed by event type x read length x covariate
-     */
-    private final int[][][] keys;
-
-    /**
-     * The index of the current covariate, used by addCovariate
-     */
-    private int currentCovariateIndex = 0;
-
-    public ReadCovariates(final int readLength, final int numberOfCovariates) {
-        final LRUCache<Integer, int[][][]> cache = keysCache.get();
-        final int[][][] cachedKeys = cache.get(readLength);
-        if ( cachedKeys == null ) {
-            // There's no cached value for read length so we need to create a new int[][][] array
-            if ( logger.isDebugEnabled() ) logger.debug("Keys cache miss for length " + readLength + " cache size " + cache.size());
-            keys = new int[EventType.values().length][readLength][numberOfCovariates];
-            cache.put(readLength, keys);
-        } else {
-            keys = cachedKeys;
-        }
-    }
-
-    public void setCovariateIndex(final int index) {
-        currentCovariateIndex = index;
-    }
-
-    /**
-     * Update the keys for mismatch, insertion, and deletion for the current covariate at read offset
-     *
-     * NOTE: no checks are performed on the number of covariates, for performance reasons.  If the count increases
-     * after the keysCache has been accessed, this method will throw an ArrayIndexOutOfBoundsException.  This currently
-     * only occurs in the testing harness, and we don't anticipate that it will become a part of normal runs.
-     *
-     * @param mismatch the mismatch key value
-     * @param insertion the insertion key value
-     * @param deletion the deletion key value
-     * @param readOffset the read offset, must be >= 0 and <= the read length used to create this ReadCovariates
-     */
-    public void addCovariate(final int mismatch, final int insertion, final int deletion, final int readOffset) {
-        keys[EventType.BASE_SUBSTITUTION.ordinal()][readOffset][currentCovariateIndex] = mismatch;
-        keys[EventType.BASE_INSERTION.ordinal()][readOffset][currentCovariateIndex] = insertion;
-        keys[EventType.BASE_DELETION.ordinal()][readOffset][currentCovariateIndex] = deletion;
-    }
-
-    /**
-     * Get the keys for all covariates at read position for error model
-     *
-     * @param readPosition
-     * @param errorModel
-     * @return
-     */
-    public int[] getKeySet(final int readPosition, final EventType errorModel) {
-        return keys[errorModel.ordinal()][readPosition];
-    }
-
-    public int[][] getKeySet(final EventType errorModel) {
-        return keys[errorModel.ordinal()];
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // routines for testing
-    //
-    // ----------------------------------------------------------------------
-
-    protected int[][] getMismatchesKeySet() { return getKeySet(EventType.BASE_SUBSTITUTION); }
-    protected int[][] getInsertionsKeySet() { return getKeySet(EventType.BASE_INSERTION); }
-    protected int[][] getDeletionsKeySet() { return getKeySet(EventType.BASE_DELETION); }
-
-    protected int[] getMismatchesKeySet(final int readPosition) {
-        return getKeySet(readPosition, EventType.BASE_SUBSTITUTION);
-    }
-
-    protected int[] getInsertionsKeySet(final int readPosition) {
-        return getKeySet(readPosition, EventType.BASE_INSERTION);
-    }
-
-    protected int[] getDeletionsKeySet(final int readPosition) {
-        return getKeySet(readPosition, EventType.BASE_DELETION);
-    }
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java

@@ -1,169 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration;
-
-import com.google.java.contract.Ensures;
-import org.broadinstitute.gatk.utils.collections.LoggingNestedIntegerArray;
-import org.broadinstitute.gatk.utils.recalibration.EventType;
-import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate;
-import org.broadinstitute.gatk.utils.collections.NestedIntegerArray;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-
-/**
- * Utility class to facilitate on-the-fly base quality score recalibration.
- *
- * User: ebanks
- * Date: 6/20/12
- */
-
-public final class RecalibrationTables {
-    public enum TableType {
-        READ_GROUP_TABLE,
-        QUALITY_SCORE_TABLE,
-        OPTIONAL_COVARIATE_TABLES_START;
-    }
-
-    private final ArrayList<NestedIntegerArray<RecalDatum>> tables;
-    private final int qualDimension;
-    private final int eventDimension = EventType.values().length;
-    private final int numReadGroups;
-    private final PrintStream log;
-
-    public RecalibrationTables(final Covariate[] covariates) {
-        this(covariates, covariates[TableType.READ_GROUP_TABLE.ordinal()].maximumKeyValue() + 1, null);
-    }
-
-    public RecalibrationTables(final Covariate[] covariates, final int numReadGroups) {
-        this(covariates, numReadGroups, null);
-    }
-
-    public RecalibrationTables(final Covariate[] covariates, final int numReadGroups, final PrintStream log) {
-        tables = new ArrayList<NestedIntegerArray<RecalDatum>>(covariates.length);
-        for ( int i = 0; i < covariates.length; i++ )
-            tables.add(i, null); // initialize so we can set below
-
-        qualDimension = covariates[TableType.QUALITY_SCORE_TABLE.ordinal()].maximumKeyValue() + 1;
-        this.numReadGroups = numReadGroups;
-        this.log = log;
-
-        tables.set(TableType.READ_GROUP_TABLE.ordinal(),
-                log == null ? new NestedIntegerArray<RecalDatum>(numReadGroups, eventDimension) :
-                        new LoggingNestedIntegerArray<RecalDatum>(log, "READ_GROUP_TABLE", numReadGroups, eventDimension));
-
-        tables.set(TableType.QUALITY_SCORE_TABLE.ordinal(), makeQualityScoreTable());
-
-        for (int i = TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal(); i < covariates.length; i++)
-            tables.set(i,
-                    log == null ? new NestedIntegerArray<RecalDatum>(numReadGroups, qualDimension, covariates[i].maximumKeyValue()+1, eventDimension) :
-                            new LoggingNestedIntegerArray<RecalDatum>(log, String.format("OPTIONAL_COVARIATE_TABLE_%d", i - TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal() + 1),
-                                    numReadGroups, qualDimension, covariates[i].maximumKeyValue()+1, eventDimension));
-    }
-
-    @Ensures("result != null")
-    public NestedIntegerArray<RecalDatum> getReadGroupTable() {
-        return getTable(TableType.READ_GROUP_TABLE.ordinal());
-    }
-
-    @Ensures("result != null")
-    public NestedIntegerArray<RecalDatum> getQualityScoreTable() {
-        return getTable(TableType.QUALITY_SCORE_TABLE.ordinal());
-    }
-
-    @Ensures("result != null")
-    public NestedIntegerArray<RecalDatum> getTable(final int index) {
-        return tables.get(index);
-    }
-
-    @Ensures("result >= 0")
-    public int numTables() {
-        return tables.size();
-    }
-
-    /**
-     * @return true if all the tables contain no RecalDatums
-     */
-    public boolean isEmpty() {
-        for( final NestedIntegerArray<RecalDatum> table : tables ) {
-            if( !table.getAllValues().isEmpty() ) { return false; }
-        }
-        return true;
-    }
-
-    /**
-     * Allocate a new quality score table, based on requested parameters
-     * in this set of tables, without any data in it.  The return result
-     * of this table is suitable for acting as a thread-local cache
-     * for quality score values
-     * @return a newly allocated, empty read group x quality score table
-     */
-    public NestedIntegerArray<RecalDatum> makeQualityScoreTable() {
-        return log == null
-                ? new NestedIntegerArray<RecalDatum>(numReadGroups, qualDimension, eventDimension)
-                : new LoggingNestedIntegerArray<RecalDatum>(log, "QUALITY_SCORE_TABLE", numReadGroups, qualDimension, eventDimension);
-    }
-
-    /**
-     * Merge all of the tables from toMerge into into this set of tables
-     */
-    public void combine(final RecalibrationTables toMerge) {
-        if ( numTables() != toMerge.numTables() )
-            throw new IllegalArgumentException("Attempting to merge RecalibrationTables with different sizes");
-
-        for ( int i = 0; i < numTables(); i++ ) {
-            final NestedIntegerArray<RecalDatum> myTable = this.getTable(i);
-            final NestedIntegerArray<RecalDatum> otherTable = toMerge.getTable(i);
-            RecalUtils.combineTables(myTable, otherTable);
-        }
-    }
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java

@@ -1,144 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-import org.broadinstitute.gatk.engine.recalibration.ReadCovariates;
-import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection;
-import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Oct 30, 2009
- *
- * The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read.
- * In general most error checking and adjustments to the data are done before the call to the covariates getValue methods in order to speed up the code.
- * This unfortunately muddies the code, but most of these corrections can be done per read while the covariates get called per base, resulting in a big speed up.
- */
-
-public interface Covariate {
-
-    /**
-     * Initialize any member variables using the command-line arguments passed to the walker
-     *
-     * @param RAC the recalibration argument collection
-     */
-    public void initialize(final RecalibrationArgumentCollection RAC);
-
-    /**
-     * Calculates covariate values for all positions in the read.
-     *
-     * @param read   the read to calculate the covariates on.
-     * @param values the object to record the covariate values for every base in the read.
-     */
-    public void recordValues(final GATKSAMRecord read, final ReadCovariates values);
-
-    /**
-     * Used to get the covariate's value from input (Recalibration Report) file during on-the-fly recalibration
-     *
-     * @param str the key in string type (read from the csv)
-     * @return the key in it's correct type.
-     */
-    public Object getValue(final String str);
-
-    /**
-     * Converts the internal representation of the key to String format for file output.
-     *
-     * @param key the long representation of the key
-     * @return a string representation of the key
-     */
-    public String formatKey(final int key);
-
-    /**
-     * Converts an Object key into a long key using only the lowest numberOfBits() bits
-     *
-     * Only necessary for on-the-fly recalibration when you have the object, but need to store it in memory in long format. For counting covariates
-     * the getValues method already returns all values in long format.
-     *
-     * @param value the object corresponding to the covariate
-     * @return a long representation of the object
-     */
-    public int keyFromValue(final Object value);
-
-    /**
-     * Returns the maximum value possible for any key representing this covariate
-     *
-     * @return the maximum value possible for any key representing this covariate
-     */
-    public int maximumKeyValue();
-}
-

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java

@@ -1,81 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-/**
- * [Short one sentence description of this walker]
- * <p/>
- * <p>
- * [Functionality of this walker]
- * </p>
- * <p/>
- * <h3>Input</h3>
- * <p>
- * [Input description]
- * </p>
- * <p/>
- * <h3>Output</h3>
- * <p>
- * [Output description]
- * </p>
- * <p/>
- * <h3>Examples</h3>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T $WalkerName
- *  </pre>
- *
- * @author Your Name
- * @since Date created
- */
-public interface ExperimentalCovariate extends Covariate {}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java

@@ -1,190 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection;
-import org.broadinstitute.gatk.engine.recalibration.ReadCovariates;
-import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord;
-import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Oct 30, 2009
- *
- * The Read Group covariate.
- */
-
-public class ReadGroupCovariate implements RequiredCovariate {
-
-    private final HashMap<String, Integer> readGroupLookupTable = new HashMap<String, Integer>();
-    private final HashMap<Integer, String> readGroupReverseLookupTable = new HashMap<Integer, String>();
-    private int nextId = 0;
-    private String forceReadGroup;
-
-    // Initialize any member variables using the command-line arguments passed to the walkers
-    @Override
-    public void initialize(final RecalibrationArgumentCollection RAC) {
-        forceReadGroup = RAC.FORCE_READGROUP;
-    }
-
-    @Override
-    public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
-        final String readGroupId = readGroupValueFromRG(read.getReadGroup());
-        final int key = keyForReadGroup(readGroupId);
-
-        final int l = read.getReadLength();
-        for (int i = 0; i < l; i++)
-            values.addCovariate(key, key, key, i);
-    }
-
-    @Override
-    public final Object getValue(final String str) {
-        return str;
-    }
-
-    @Override
-    public synchronized String formatKey(final int key) {
-        // This method is synchronized so that we don't attempt to do a get()
-        // from the reverse lookup table while that table is being updated
-        return readGroupReverseLookupTable.get(key);
-    }
-
-    @Override
-    public int keyFromValue(final Object value) {
-        return keyForReadGroup((String) value);
-    }
-
-    /**
-     * Get the mapping from read group names to integer key values for all read groups in this covariate
-     * @return a set of mappings from read group names -> integer key values
-     */
-    public Set<Map.Entry<String, Integer>> getKeyMap() {
-        return readGroupLookupTable.entrySet();
-    }
-
-    private int keyForReadGroup(final String readGroupId) {
-        // Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
-        // synchronize only the table updates.
-
-        // Before entering the synchronized block, check to see if this read group is not in our tables.
-        // If it's not, either we will have to insert it, OR another thread will insert it first.
-        // This preliminary check avoids doing any synchronization most of the time.
-        if ( ! readGroupLookupTable.containsKey(readGroupId) ) {
-
-            synchronized ( this ) {
-
-                // Now we need to make sure the key is STILL not there, since another thread may have come along
-                // and inserted it while we were waiting to enter this synchronized block!
-                if ( ! readGroupLookupTable.containsKey(readGroupId) ) {
-                    readGroupLookupTable.put(readGroupId, nextId);
-                    readGroupReverseLookupTable.put(nextId, readGroupId);
-                    nextId++;
-                }
-            }
-        }
-
-        return readGroupLookupTable.get(readGroupId);
-    }
-
-    @Override
-    public synchronized int maximumKeyValue() {
-        // Synchronized so that we don't query table size while the tables are being updated
-        return readGroupLookupTable.size() - 1;
-    }
-
-    /**
-     * If the sample has a PU tag annotation, return that. If not, return the read group id.
-     *
-     * @param rg the read group record
-     * @return platform unit or readgroup id
-     */
-    private String readGroupValueFromRG(final GATKSAMReadGroupRecord rg) {
-        if ( forceReadGroup != null )
-            return forceReadGroup;
-
-        final String platformUnit = rg.getPlatformUnit();
-        return platformUnit == null ? rg.getId() : platformUnit;
-    }
-    
-}
-
-

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java

@@ -1,74 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-
-public class RepeatLengthCovariate extends RepeatCovariate {
-
-    @Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"})
-    @Ensures("result != null")
-    protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
-        return String.format("%d",repeatLength);
-    }
-
-    @Override
-    public synchronized int maximumKeyValue() {
-        // Synchronized so that we don't query table size while the tables are being updated
-        //return repeatLookupTable.size() - 1;
-        // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
-        // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
-        return (1+MAX_REPEAT_LENGTH);
-    }
-
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java

@@ -1,75 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-
-
-public class RepeatUnitAndLengthCovariate extends RepeatCovariate {
-
-    @Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"})
-    @Ensures("result != null")
-    protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
-        return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength);
-    }
-
-    @Override
-    public synchronized int maximumKeyValue() {
-        // Synchronized so that we don't query table size while the tables are being updated
-        //return repeatLookupTable.size() - 1;
-        // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
-        // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
-        return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1;
-    }
-
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java

@@ -1,78 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-/**
- * Created with IntelliJ IDEA.
- * User: rpoplin
- * Date: 11/3/12
- */
-
-public class RepeatUnitCovariate extends RepeatCovariate {
-
-    protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
-        return new String(repeatFromUnitAndLength);
-
-    }
-
-
-    @Override
-    public synchronized int maximumKeyValue() {
-        // Synchronized so that we don't query table size while the tables are being updated
-        //return repeatLookupTable.size() - 1;
-        // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
-        // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
-        return (1<<(2*MAX_STR_UNIT_LENGTH))  +1;
-    }
-
-
-}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java

@@ -1,81 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-/**
- * [Short one sentence description of this walker]
- * <p/>
- * <p>
- * [Functionality of this walker]
- * </p>
- * <p/>
- * <h3>Input</h3>
- * <p>
- * [Input description]
- * </p>
- * <p/>
- * <h3>Output</h3>
- * <p>
- * [Output description]
- * </p>
- * <p/>
- * <h3>Examples</h3>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T $WalkerName
- *  </pre>
- *
- * @author Your Name
- * @since Date created
- */
-public interface RequiredCovariate extends Covariate {}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java

@@ -1,81 +0,0 @@
-/*
-* By downloading the PROGRAM you agree to the following terms of use:
-* 
-* BROAD INSTITUTE
-* SOFTWARE LICENSE AGREEMENT
-* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
-* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
-* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
-* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
-* 1. DEFINITIONS
-* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
-* 2. LICENSE
-* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
-* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
-* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
-* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
-* 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
-* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
-* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
-* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
-* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
-* 5. INDEMNIFICATION
-* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
-* 6. NO REPRESENTATIONS OR WARRANTIES
-* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
-* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
-* 7. ASSIGNMENT
-* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
-* 8. MISCELLANEOUS
-* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
-* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
-* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
-* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
-* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
-* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
-* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
-*/
-
-package org.broadinstitute.gatk.engine.recalibration.covariates;
-
-/**
- * [Short one sentence description of this walker]
- * <p/>
- * <p>
- * [Functionality of this walker]
- * </p>
- * <p/>
- * <h3>Input</h3>
- * <p>
- * [Input description]
- * </p>
- * <p/>
- * <h3>Output</h3>
- * <p>
- * [Output description]
- * </p>
- * <p/>
- * <h3>Examples</h3>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T $WalkerName
- *  </pre>
- *
- * @author Your Name
- * @since Date created
- */
-public interface StandardCovariate extends Covariate {}

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/GatherBqsrReports.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_BaseQualityRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_FisherStrand.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeff.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -49,39 +49,39 @@
 * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.gatk.tools.walkers.indels;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import htsjdk.samtools.reference.IndexedFastaSequenceFile;
-import htsjdk.samtools.SAMFileHeader;
-import org.broadinstitute.gatk.utils.BaseTest;
-import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
+import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
 
-import java.io.File;
-import java.io.FileNotFoundException;
+import java.util.Arrays;
+import java.util.List;
 
-public class IndelRealignerUnitTest extends BaseTest {
+/**
+ * Allele specific Rank Sum Test for insert sizes of REF versus ALT reads
+ *
+ * <p>
+ *     This annotation tests whether the insert sizes of reads supporting the REF allele and ALT allele are roughly equal.
+ *     In case of multiple alternate alleles, each alternate allele is considered separately.
+ *
+ * </p>
+ * <h3>Statistical notes</h3>
+ * <p> See the <a href="http://www.broadinstitute.org/gatk/guide/article?id=4732">method document</a> for a more detailed explanation of the rank sum test. </p>
+ *
+ * */
 
-    private SAMFileHeader header;
+public class AS_InsertSizeRankSum extends AS_RankSumTest implements ExperimentalAnnotation, BetaTestingAnnotation {
+    @Override
+    public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_INSERT_SIZE_RANK_SUM_KEY);}
 
-    @BeforeClass
-    public void setup() throws FileNotFoundException {
-        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
-        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
+    @Override
+    public String getRawKeyName() { return GATKVCFConstants.AS_RAW_INSERT_SIZE_RANK_SUM_KEY; }
+
+    @Override
+    protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
+        return (double)Math.abs(read.getInferredInsertSize());
     }
-
-    @Test
-    public void realignAtContigBorderTest() {
-        final int contigEnd = header.getSequence(0).getSequenceLength();
-        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "goodRead", 0, contigEnd - 1, 2);
-        read.setCigarString("2M");
-        Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), false);
-        read.setCigarString("1M1D1M");
-        Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), true);
-    }
-
 }

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -49,81 +49,54 @@
 * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.gatk.engine.recalibration.covariates;
+package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.gatk.engine.recalibration.ReadCovariates;
-import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection;
-import org.broadinstitute.gatk.utils.QualityUtils;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
 
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Nov 3, 2009
+ * Allele specific Rank Sum Test for mate's mapping qualities of REF versus ALT reads
  *
- * The Reported Quality Score covariate.
+ * <p>This allele specific variant-level annotation compares the mapping qualities of the reads' mates supporting the reference allele with the reads' mates supporting the alternative allele.  To be clear, it does so separately for each alternate allele. The Rank Sum Test is using the null hypothesis that the mapping qualities from the reads' mates in the reference allele come from the same distribution as the mapping qualities of the reads' mates in the alternative allele. The alternative hypothesis is that the mapping qualities of the alternative allele reads' mates are stochastically less than the reference allele reads' mates' mapping qualities. Therefore if the resulting Z-score is close to 0 (in other words it follows a standard normal distribution) then there isn't enough evidence to reject the null hypothesis. If you have a more extreme Z-score in the negative direction you know that this variant might have lower quality reads that support the alternative allele (or in this case at least their mates have lower mapping quality).</p>
+ * <p>This annotation can be used to evaluate confidence in a variant call and could be used as a covariate for variant recalibration (VQSR). Finding a statistically significant difference in quality either way suggests that the sequencing and/or mapping process may have been biased or affected by an artifact. In practice, we only filter out low negative values when evaluating variant quality because the idea is to filter out variants for which the quality of the data supporting the alternate allele is comparatively low. The reverse case, where it is the quality of data supporting the reference allele that is lower (resulting in positive ranksum scores), is not really informative for filtering variants.</p>
+ *
+ * <h3>Statistical notes</h3>
+ * <p>The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities of the read's mate See the <a href="http://www.broadinstitute.org/gatk/guide/article?id=4732">method document on statistical tests</a> for a more detailed explanation of the ranksum test.</p>
+ *
+ * * <h3>Caveats</h3>
+ * <ul><li>The mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.</li>
+ * <li>Uninformative reads are not used in these annotations.</li>
+ * </ul>
+ *
+ * <h3>Related annotations</h3>
+ * <ul>
+ *     <li><b><a href="https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_AS_MappingQualityRankSumTest.php">AS_MappingQualityRankSumTest</a></b> outputs the same rank sum test on the mapping quality of the reads themselves rather than their mates.</li>
+ * </ul>
  */
-
-public class QualityScoreCovariate implements RequiredCovariate {
-
-    // Initialize any member variables using the command-line arguments passed to the walkers
+public class AS_MQMateRankSumTest extends AS_RankSumTest implements BetaTestingAnnotation {
     @Override
-    public void initialize(final RecalibrationArgumentCollection RAC) {}
+    public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_MATE_MAP_QUAL_RANK_SUM_KEY); }
 
     @Override
-    public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
-        final byte[] baseQualities = read.getBaseQualities();
-        final byte[] baseInsertionQualities = read.getBaseInsertionQualities();
-        final byte[] baseDeletionQualities = read.getBaseDeletionQualities();
-
-        for (int i = 0; i < baseQualities.length; i++) {
-            values.addCovariate((int)baseQualities[i], (int)baseInsertionQualities[i], (int)baseDeletionQualities[i], i);
-        }
-    }
-
-    // Used to get the covariate's value from input csv file during on-the-fly recalibration
-    @Override
-    public final Object getValue(final String str) {
-        return Byte.parseByte(str);
-    }
+    public String getRawKeyName() { return GATKVCFConstants.AS_RAW_MATE_MAP_QUAL_RANK_SUM_KEY;}
 
     @Override
-    public String formatKey(final int key) {
-        return String.format("%d", key);
-    }
-
-    @Override
-    public int keyFromValue(final Object value) {
-        return (value instanceof String) ? (int)Byte.parseByte((String) value) : (int)(Byte) value;
-    }
-
-    @Override
-    public int maximumKeyValue() {
-        return QualityUtils.MAX_SAM_QUAL_SCORE;
+    protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
+        Integer mappingQuality = read.getMateMappingQuality();
+        return mappingQuality==null ? null : (double) mappingQuality;
     }
 }

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MappingQualityRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -172,6 +172,8 @@ public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnno
             return null;
 
         final List<Integer> standardDepth = getAlleleDepths(genotypes);
+        if (standardDepth == null) //all no-calls and homRefs
+            return null;
 
         //Parse the VC's allele-specific qual values
         List<Object> alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY);

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSAnnotation.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSMappingQuality.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -59,11 +59,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation;
-import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller;
-import org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs;
-import org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs;
 import org.broadinstitute.gatk.utils.MannWhitneyU;
-import org.broadinstitute.gatk.utils.collections.Pair;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.exceptions.GATKException;
@@ -298,14 +294,16 @@ public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnn
         for (final Allele alt : perAlleleValues.keySet()) {
             if (alt.equals(ref, false))
                 continue;
-            final MannWhitneyU mannWhitneyU = new MannWhitneyU(useDithering);
-            //load alts
+            final MannWhitneyU mannWhitneyU = new MannWhitneyU();
+            //load alts (series 1)
+            List<Double> alts = new ArrayList<>();
             for (final Number qual : perAlleleValues.get(alt)) {
-                mannWhitneyU.add(qual, MannWhitneyU.USet.SET1);
+                alts.add((double) qual.intValue());
             }
-            //load refs
+            //load refs (series 2)
+            List<Double> refs = new ArrayList<>();
             for (final Number qual : perAlleleValues.get(ref)) {
-                mannWhitneyU.add(qual, MannWhitneyU.USet.SET2);
+                refs.add((double) qual.intValue());
             }
 
             if (DEBUG) {
@@ -320,8 +318,8 @@ public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnn
 
             }
             // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases)
-            final Pair<Double, Double> testResults = mannWhitneyU.runOneSidedTest(MannWhitneyU.USet.SET1);
-            perAltRankSumResults.put(alt, testResults.first);
+            final MannWhitneyU.Result result = mannWhitneyU.test(convertToArray(alts), convertToArray(refs), MannWhitneyU.TestType.FIRST_DOMINATES);
+            perAltRankSumResults.put(alt, result.getZ());
         }
         return perAltRankSumResults;
     }

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_ReadPosRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandBiasTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandOddsRatio.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -66,6 +66,7 @@ import org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller;
+import org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 
 import java.util.ArrayList;
@@ -75,15 +76,15 @@ import java.util.Set;
 
 public class AnnotationUtils {
 
-    public static final String ANNOTATION_HC_WARN_MSG = " annotation will not be calculated, must be called from HaplotypeCaller";
+    public static final String ANNOTATION_HC_WARN_MSG = " annotation will not be calculated, must be called from HaplotypeCaller or MuTect2";
     public static final int WARNINGS_LOGGED_SIZE = 3;
 
     /**
-     * Helper function to parse the list into the annotation string
-     * @param valueList the ArrayList returned from StrandBiasBySample.annotate()
-     * @return the array used by the per-sample Strand Bias annotation
+     * Helper function to convert a List of Doubles to a comma-separated String
+     * @param valueList the ArrayList with Double data
+     * @return a comma-separated String
      */
-    protected static String encodeValueList( final List<Double> valueList, final String precisionFormat ) {
+    public static String encodeValueList( final List<Double> valueList, final String precisionFormat ) {
         List<String> outputList = new ArrayList<>();
         for (Double d : valueList) {
             outputList.add(String.format(precisionFormat, d));
@@ -91,6 +92,15 @@ public class AnnotationUtils {
         return StringUtils.join(outputList, ",");
     }
 
+    /**
+     * Helper function to convert a List of Strings to a comma-separated String
+     * @param stringList the ArrayList with String data
+     * @return a comma-separated String
+     */
+    public static String encodeStringList( final List<String> stringList) {
+        return StringUtils.join(stringList, ",");
+    }
+
     /**
      * Checks if the walker is compatible with allele-specific annotations
      */
@@ -145,7 +155,7 @@ public class AnnotationUtils {
             throw new ReviewedGATKException("Warnings logged array must have at least " + WARNINGS_LOGGED_SIZE + " elements, but has " + warningsLogged.length);
         }
 
-        if ( !(walker instanceof HaplotypeCaller) ) {
+        if ( !(walker instanceof HaplotypeCaller) && !(walker instanceof MuTect2)) {
             if ( !warningsLogged[0] ) {
                 logger.warn(annotation + ANNOTATION_HC_WARN_MSG + ", not " + walker.getClass().getSimpleName());
                 warningsLogged[0] = true;

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCountsBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -139,7 +139,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         final Set<Allele> alleles = new HashSet<>(vc.getAlleles());
 
         // make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
-        if ( ! perReadAlleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
+        if ( ! perReadAlleleLikelihoodMap.getAllelesSet().isEmpty() && ! perReadAlleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
             throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + perReadAlleleLikelihoodMap.getAllelesSet());
 
         final HashMap<Allele, Integer> alleleCounts = new HashMap<>();
@@ -148,7 +148,6 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
             final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
             if (! a.isInformative() ) continue; // read is non-informative
-            final GATKSAMRecord read = el.getKey();
             final int prevCount = alleleCounts.get(a.getMostLikelyAllele());
             alleleCounts.put(a.getMostLikelyAllele(), prevCount + 1);
         }

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHet.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -79,7 +79,7 @@ import java.util.*;
 /**
  * Phred-scaled p-value for exact test of excess heterozygosity
  *
- * This annotation estimates excess heterozygosity in a population of samples. It is related to but distinct from InbreedingCoeff, which estimates evidence for inbreeding in a population. ExcessHet scales more reliably to large cohort sizes.
+ * <p>This annotation estimates excess heterozygosity in a population of samples. It is related to but distinct from InbreedingCoeff, which estimates evidence for inbreeding in a population. ExcessHet scales more reliably to large cohort sizes.</p>
  *
  * <h3>Statistical notes</h3>
  * <p>This annotation is a one-sided phred-scaled p-value using an exact test of the Hardy-Weinberg Equilibrium. The null hypothesis is that the number of heterozygotes follows the Hardy-Weinberg Equilibrium. The p-value is the probability of getting the same or more heterozygotes as was observed, given the null hypothesis. </p>

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HeterozygosityUtils.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.annotator;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -83,7 +84,11 @@ import java.util.Map;
  */
 public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
+    private final static Logger logger = Logger.getLogger(HomopolymerRun.class);
+
     private boolean ANNOTATE_INDELS = true;
+    
+    private final static int BAD_RUN_LENGTH = -1;
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
@@ -103,6 +108,9 @@ public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalA
         } else {
             return null;
         }
+
+        if ( run == BAD_RUN_LENGTH )
+            return null;
         
         Map<String, Object> map = new HashMap<>();
         map.put(getKeyNames().get(0), String.format("%d", run));
@@ -149,15 +157,13 @@ public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalA
         GenomeLoc window = ref.getWindow();
         int refBasePos = (int) (locus.getStart() - window.getStart())+1;
         if ( vc.isSimpleDeletion() ) {
-            // check that deleted bases are the same
-            byte dBase = bases[refBasePos];
-            for ( int i = 0; i < vc.getReference().length(); i ++ ) {
-                if ( bases[refBasePos+i] != dBase ) {
-                    return 0;
-                }
+            if ( refBasePos + vc.getReference().length() - 1 >= bases.length ) {
+                logger.warn("Encountered a homopolymer at " + locus.toString() + " longer than the tool's default window size, so the position was skipped. " +
+                        "To process this position, add --reference_window_stop to your command with a value equal or greater than " + vc.getReference().length());
+                return BAD_RUN_LENGTH;
             }
 
-            return computeHomopolymerRun(dBase, ref);
+            return computeHomopolymerRun(bases[refBasePos], ref);
         } else {
             // check that inserted bases are the same
             byte insBase = vc.getAlternateAllele(0).getBases()[0];

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSAnnotation.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -212,8 +212,14 @@ public abstract class RMSAnnotation extends InfoFieldAnnotation implements Reduc
             numOfReads += Integer.parseInt(vc.getAttributeAsString(VCFConstants.DEPTH_KEY, "-1"));
             if(vc.hasGenotypes()) {
                 for(Genotype gt : vc.getGenotypes()) {
-                    if(gt.isHomRef() && gt.hasExtendedAttribute("MIN_DP")) //site-level DP contribution will come from MIN_DP for gVCF-called reference variants
-                        numOfReads -= Integer.parseInt(gt.getExtendedAttribute("MIN_DP").toString());
+                    if(gt.isHomRef()) {
+                        //site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution
+                        if (gt.hasExtendedAttribute("MIN_DP"))
+                            numOfReads -= Integer.parseInt(gt.getExtendedAttribute("MIN_DP").toString());
+                        else if (gt.hasDP())
+                            numOfReads -= gt.getDP();
+                    }
+
                 }
             }
             return numOfReads;

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,7 +51,6 @@
 
 package org.broadinstitute.gatk.tools.walkers.annotator;
 
-import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
@@ -61,8 +60,6 @@ import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.gatk.utils.MannWhitneyU;
 import org.broadinstitute.gatk.utils.QualityUtils;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.gatk.utils.collections.Pair;
 import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
 import htsjdk.variant.variantcontext.Allele;
@@ -79,7 +76,6 @@ import java.util.*;
 //TODO: will eventually implement ReducibleAnnotation in order to preserve accuracy for CombineGVCFs and GenotypeGVCFs -- see RMSAnnotation.java for an example of an abstract ReducibleAnnotation
 public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation {
     static final boolean DEBUG = false;
-    protected boolean useDithering = true;
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
@@ -122,13 +118,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
         if ( refQuals.isEmpty() && altQuals.isEmpty() )
             return null;
 
-        final MannWhitneyU mannWhitneyU = new MannWhitneyU(useDithering);
-        for (final Double qual : altQuals) {
-            mannWhitneyU.add(qual, MannWhitneyU.USet.SET1);
-        }
-        for (final Double qual : refQuals) {
-            mannWhitneyU.add(qual, MannWhitneyU.USet.SET2);
-        }
+        final MannWhitneyU mannWhitneyU = new MannWhitneyU();
 
         if (DEBUG) {
             System.out.format("%s, REF QUALS:", this.getClass().getName());
@@ -142,14 +132,26 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
 
         }
         // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases)
-        final Pair<Double, Double> testResults = mannWhitneyU.runOneSidedTest(MannWhitneyU.USet.SET1);
+        final MannWhitneyU.Result result = mannWhitneyU.test(convertToArray(altQuals), convertToArray(refQuals), MannWhitneyU.TestType.FIRST_DOMINATES);
+        final double zScore = result.getZ();
+
 
         final Map<String, Object> map = new HashMap<>();
-        if (!Double.isNaN(testResults.first))
-            map.put(getKeyNames().get(0), String.format("%.3f", testResults.first));
+        if (!Double.isNaN(zScore))
+            map.put(getKeyNames().get(0), String.format("%.3f", zScore));
         return map;
     }
 
+    public static double[] convertToArray(List<Double> list){
+        double[] ret = new double[list.size()];
+        Iterator<Double> iterator = list.iterator();
+        for (int i = 0; i < ret.length; i++)
+        {
+            ret[i] = iterator.next().doubleValue();
+        }
+        return ret;
+    }
+
     private void fillQualsFromPileup(final List<Allele> alleles,
                                      final ReadBackedPileup pileup,
                                      final List<Double> refQuals,
@@ -255,14 +257,4 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
                 read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE );
     }
 
-    /**
-     * Initialize the rank sum test annotation using walker and engine information. Right now this checks to see if
-     * engine randomization is turned off, and if so does not dither.
-     * @param walker            the walker
-     * @param toolkit           the GATK engine
-     * @param headerLines       the header lines
-     */
-    public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
-        useDithering = ! toolkit.getArguments().disableDithering;
-    }
 }

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -69,9 +69,7 @@ import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
 import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
 
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Number of forward and reverse reads that support each allele
@@ -142,11 +140,16 @@ public class StrandAlleleCountsBySample extends GenotypeAnnotation {
         if( stratifiedPerReadAlleleLikelihoodMap == null ) { throw new IllegalArgumentException("stratifiedPerReadAlleleLikelihoodMap cannot be null"); }
         if( vc == null ) { throw new IllegalArgumentException("input vc cannot be null"); }
 
+        final Set<Allele> alleles = new HashSet<>(vc.getAlleles());
+
         final int[] table = new int[vc.getNAlleles()*2];
 
         for (final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
+            // make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
+            if ( ! maps.getAllelesSet().isEmpty() && ! maps.getAllelesSet().containsAll(alleles) )
+                throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + maps.getAllelesSet());
             for (final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
-                final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
+                final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
                 final GATKSAMRecord read = el.getKey();
                 if (mostLikelyAllele.isInformative())
                     updateTable(table, vc.getAlleleIndex(mostLikelyAllele.getAlleleIfInformative()), read);

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtils.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardHCAnnotation.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -78,8 +78,8 @@ import java.util.Map;
 /**
  * Create plots to visualize base recalibration results
  *
- * <p/>
- * This tool generates plots for visualizing the quality of a recalibration run (effected by <a href='http://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php'>BaseRecalibrator</a>).
+ * <p>
+ * This tool generates plots for visualizing the quality of a recalibration run (effected by BaseRecalibrator).
  * </p>
  *
  * <h3>Input</h3>

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -86,7 +86,7 @@ import java.util.Arrays;
 import java.util.List;
 
 /**
- * Generate base recalibration table to compensate for systematic errors in basecalling confidences
+ * Detect systematic errors in base quality scores
  *
  * <p>
  * Variant calling algorithms rely heavily on the quality scores assigned to the individual base calls in each sequence

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/AssignSomaticStatus.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -54,6 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.cancer;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
 import org.broadinstitute.gatk.utils.commandline.Output;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
@@ -66,6 +67,8 @@ import org.broadinstitute.gatk.engine.SampleUtils;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.engine.GATKVCFUtils;
 import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -78,6 +81,7 @@ import java.util.*;
 /**
  * Assigns somatic status to a set of calls
  */
+@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class}, enable = false )
 public class AssignSomaticStatus extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/AnnotatePopulationAFWalker.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -52,6 +52,9 @@
 package org.broadinstitute.gatk.tools.walkers.cancer.contamination;
 
 
+import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.utils.commandline.Input;
 import org.broadinstitute.gatk.utils.commandline.Output;
@@ -78,6 +81,7 @@ import java.util.*;
 /**
  * Given a input VCF representing a collection of populations, split the input into each population, and annotate each record with population allele frequencies
  */
+@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class}, enable = false  )
 // @Requires(DataSource.SAMPLE) <- require the sample data when this works
 public class AnnotatePopulationAFWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
     // control the output

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEst.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -80,7 +80,7 @@ import java.util.*;
 /**
  * Estimate cross-sample contamination
  *
- * This tool determine the percent contamination of an input bam by sample, by lane, or in aggregate across all the input reads.
+ * <p>This tool determine the percent contamination of an input bam by sample, by lane, or in aggregate across all the input reads.</p>
  *
  * <h3>Usage examples</h3>
  * <p>These are example commands that show how to run ContEst for typical use cases. Square brackets ("[ ]")
@@ -264,14 +264,14 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
             useSequencingGenotypes = true;
             // if were not using arrays, we need to figure out what samples are what
             for(SAMReaderID id : getToolkit().getReadsDataSource().getReaderIDs()) {
-                if (id.getTags().getPositionalTags().size() == 0)
+                if (id.getTags().getPositionalTags().isEmpty())
                     throw new UserException.BadInput("BAMs must be tagged with " + GENOTYPE_BAM_TAG + " and " + EVAL_BAM_TAG + " when running in array-free mode. Please see the ContEst documentation for more details");
 
                 // now sort out what tags go with what bam
                 for (String tag : id.getTags().getPositionalTags()) {
                     if (GENOTYPE_BAM_TAG.equalsIgnoreCase(tag)) {
                         try {
-                            if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().size() == 0)
+                            if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().isEmpty())
                                 throw new RuntimeException("No Read Groups found for Genotyping BAM -- Read Groups are Required in sequencing genotype mode!");
                             genotypeSample = getToolkit().getReadsDataSource().getHeader(id).getReadGroups().get(0).getSample();
                         } catch (NullPointerException npe) {
@@ -279,7 +279,7 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
                         }
                     } else if (EVAL_BAM_TAG.equalsIgnoreCase(tag)) {
                         try {
-                            if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().size() == 0)
+                            if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().isEmpty())
                                 throw new RuntimeException("No Read Groups found for Genotyping BAM -- Read Groups are Required in sequencing genotype mode!");
                             evalSample = getToolkit().getReadsDataSource().getHeader(id).getReadGroups().get(0).getSample();
                         } catch (NullPointerException npe) {
@@ -410,7 +410,7 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
                                 namePair.getKey(),
                                 populationsToEvaluate);
 
-                if (results.size() > 0) {
+                if (!results.isEmpty()) {
                     countResults++;
                     stats.put(namePair.getKey(), results);
                 }
@@ -498,7 +498,7 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
     private static Genotype getGenotypeFromArray(RefMetaDataTracker tracker, RodBinding<VariantContext> genotypes, boolean verifiedSampleName, boolean verifySample, String sampleName) {
         // get the truthForSample and the hapmap information for this site; if either are null we can't move forward
         Collection<VariantContext> truths = tracker.getValues(genotypes);
-        if (truths == null || truths.size() == 0) return null;
+        if (truths == null || truths.isEmpty()) return null;
 
         VariantContext truthForSample = truths.iterator().next();
 
@@ -506,7 +506,7 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
         if (!verifiedSampleName && verifySample) {
             if (!truthForSample.getSampleNames().contains(sampleName))
                 throw new UserException.BadInput("The sample name was set to " + sampleName + " but this sample isn't in your genotypes file.  Please Verify your sample name");
-                verifiedSampleName = true;
+            verifiedSampleName = true;
         }
 
         GenotypesContext gt = truthForSample.getGenotypes();
@@ -622,6 +622,9 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
 
         for (String pop : pops) {
             PopulationFrequencyInfo info = parsePopulationFrequencyInfo(popVC, pop);
+            if ( info == null )
+                throw new RuntimeException("No population frequency annotation for " + pop + " in " + popVC.toString());
+
             double alleleFreq = info.getMinorAlleleFrequency();
             if (alleleFreq > 0.5) {
                 throw new RuntimeException("Minor allele frequency is greater than 0.5, this is an error; we saw AF of " + alleleFreq);
@@ -708,7 +711,7 @@ public class ContEst extends RodWalker<Map<String, Map<String, ContaminationStat
             }
 
 
-            if (newMap.size() > 0)
+            if (!newMap.isEmpty())
                 cleanedMap.put(entry.getKey(), newMap);
             else
                 out.println("Warning: We're throwing out lane " + entry.getKey() + " since it has fewer than " + minBaseCount +

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationEstimate.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationResults.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationStats.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2ArgumentCollection.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -62,30 +62,32 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
 
     /**
      * Artifact detection mode is used to prepare a panel of normals. This maintains the specified tumor LOD threshold,
-     * but disables the remaining pragmatic filters. See M2 usage examples for more information.
+     * but disables the remaining pragmatic filters. See usage examples above for more information.
      */
     @Advanced
     @Argument(fullName = "artifact_detection_mode", required = false, doc="Enable artifact detection for creating panels of normals")
     public boolean ARTIFACT_DETECTION_MODE = false;
 
     /**
-     * This is the tumor LOD threshold to output the variant in the VCF, although it may be filtered
+     * This is the LOD threshold that a variant must pass in the tumor to be emitted to the VCF. Note that the variant may pass this threshold yet still be annotated as FILTERed based on other criteria.
      */
     @Argument(fullName = "initial_tumor_lod", required = false, doc = "Initial LOD threshold for calling tumor variant")
     public double INITIAL_TUMOR_LOD_THRESHOLD = 4.0;
 
-
+    /**
+     * This is the LOD threshold corresponding to the minimum amount of reference evidence in the normal for a variant to be considered somatic and emitted in the VCF
+     */
     @Argument(fullName = "initial_normal_lod", required = false, doc = "Initial LOD threshold for calling normal variant")
     public double INITIAL_NORMAL_LOD_THRESHOLD = 0.5;
 
     /**
-     * Only variants with tumor LODs exceeding this thresholds can pass filtration
+     * Only variants with tumor LODs exceeding this threshold can pass filtering.
      */
     @Argument(fullName = "tumor_lod", required = false, doc = "LOD threshold for calling tumor variant")
     public double TUMOR_LOD_THRESHOLD = 6.3;
 
     /**
-     * This is a measure of the minimum evidence to show that a variant observed in the tumor is not also present in its normal
+     * This is a measure of the minimum evidence to support that a variant observed in the tumor is not also present in the normal.
      */
     @Argument(fullName = "normal_lod", required = false, doc = "LOD threshold for calling normal non-germline")
     public double NORMAL_LOD_THRESHOLD = 2.2;
@@ -98,19 +100,22 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
     public double NORMAL_DBSNP_LOD_THRESHOLD = 5.5;
 
     /**
-     * This argument is used for the M2 internal "alt_allele_in_normal" filter
+     * This argument is used for the internal "alt_allele_in_normal" filter.
+     * A variant will PASS the filter if the value tested is lower or equal to the threshold value. It will FAIL the filter if the value tested is greater than the max threshold value.
      **/
     @Argument(fullName = "max_alt_alleles_in_normal_count", required = false, doc="Threshold for maximum alternate allele counts in normal")
-    public int MAX_ALT_ALLELES_IN_NORMAL_COUNT = 2;
+    public int MAX_ALT_ALLELES_IN_NORMAL_COUNT = 1;
 
     /**
-     * This argument is used for the M2 internal "alt_allele_in_normal" filter
+     * This argument is used for the internal "alt_allele_in_normal" filter.
+     * A variant will PASS the filter if the value tested is lower or equal to the threshold value. It will FAIL the filter if the value tested is greater than the max threshold value.
      */
     @Argument(fullName = "max_alt_alleles_in_normal_qscore_sum", required = false, doc="Threshold for maximum alternate allele quality score sum in normal")
     public int MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM = 20;
 
     /**
-     * This argument is used for the M2 internal "alt_allele_in_normal" filter
+     * This argument is used for the internal "alt_allele_in_normal" filter.
+     * A variant will PASS the filter if the value tested is lower or equal to the threshold value. It will FAIL the filter if the value tested is greater than the max threshold value.
      */
     @Argument(fullName = "max_alt_allele_in_normal_fraction", required = false, doc="Threshold for maximum alternate allele fraction in normal")
     public double MAX_ALT_ALLELE_IN_NORMAL_FRACTION = 0.03;

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -88,6 +88,7 @@ import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
 import org.broadinstitute.gatk.utils.fragments.FragmentUtils;
 import org.broadinstitute.gatk.utils.genotyper.*;
 import org.broadinstitute.gatk.utils.haplotype.Haplotype;
+import org.broadinstitute.gatk.utils.haplotypeBAMWriter.DroppedReadsTracker;
 import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter;
 import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.gatk.utils.help.HelpConstants;
@@ -141,7 +142,7 @@ import static java.lang.Math.pow;
  * <pre>
  *   java
  *     -jar GenomeAnalysisTK.jar
- *     -T HaplotypeCaller
+ *     -T MuTect2
  *     -R reference.fasta
  *     -I:tumor normal1.bam \
  *     [--dbsnp dbSNP.vcf] \
@@ -561,6 +562,10 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
         final ActiveRegion regionForGenotyping = assemblyResult.getRegionForGenotyping();
         logReadInfo(DEBUG_READ_NAME, regionForGenotyping.getReads(), "Present in region for genotyping");
 
+        if ( MTAC.bamWriter != null && MTAC.emitDroppedReads ) {
+            haplotypeBAMWriter.addDroppedReadsFromDelta(DroppedReadsTracker.Reason.TRIMMMED, originalActiveRegion.getReads(), regionForGenotyping.getReads());
+        }
+
 //
 //        final ActiveRegion regionForGenotyping = trimmingResult.getCallableRegion();
 
@@ -572,6 +577,11 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
         //TODO - if you move this up you might have to consider to change referenceModelForNoVariation
         //TODO - that does also filter reads.
         final Collection<GATKSAMRecord> filteredReads = filterNonPassingReads(regionForGenotyping);
+
+        if ( MTAC.bamWriter != null && MTAC.emitDroppedReads ) {
+            haplotypeBAMWriter.addDroppedReads(DroppedReadsTracker.Reason.FILTERED, filteredReads);
+        }
+
         final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample(filteredReads);
 
         logReadInfo(DEBUG_READ_NAME, regionForGenotyping.getReads(), "Present in region for genotyping after filtering reads");
@@ -617,6 +627,14 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
         // Realign reads to their best haplotype.
         // KCIBUL: this is new stuff -- review it!
         final Map<GATKSAMRecord,GATKSAMRecord> readRealignments = realignReadsToTheirBestHaplotype(readLikelihoods, assemblyResult.getReferenceHaplotype(), assemblyResult.getPaddedReferenceLoc());
+
+        if ( MTAC.bamWriter != null && MTAC.emitDroppedReads ) {
+            haplotypeBAMWriter.addDroppedReadsFromDelta(
+                    DroppedReadsTracker.Reason.REALIGNMENT_FAILURE,
+                    regionForGenotyping.getReads(),
+                    readRealignments.values());
+        }
+
         readLikelihoods.changeReads(readRealignments);
 
         for (GATKSAMRecord rec : readRealignments.keySet()) {
@@ -657,6 +675,10 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
                     haplotypes,
                     calledHaplotypeSet,
                     readLikelihoods);
+
+            if ( MTAC.emitDroppedReads ) {
+                haplotypeBAMWriter.writeDroppedReads();
+            }
         }
 
         if( MTAC.DEBUG ) { logger.info("----------------------------------------------------------------------------------"); }
@@ -772,7 +794,7 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
             }
         }
 
-        if ( (normalAltCounts >= MTAC.MAX_ALT_ALLELES_IN_NORMAL_COUNT || normalF >= MTAC.MAX_ALT_ALLELE_IN_NORMAL_FRACTION ) && normalAltQualityScoreSum > MTAC.MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM) {
+        if ( (normalAltCounts > MTAC.MAX_ALT_ALLELES_IN_NORMAL_COUNT || normalF > MTAC.MAX_ALT_ALLELE_IN_NORMAL_FRACTION ) && normalAltQualityScoreSum > MTAC.MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM) {
             filters.add(GATKVCFConstants.ALT_ALLELE_IN_NORMAL_FILTER_NAME);
         } else {
 
@@ -1044,7 +1066,7 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
      * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    //protected String[] annotationGroupsToUse = { "Standard" };
+    //protected String[] annotationGroupsToUse = { StandardAnnotation.class.getSimpleName() };
     protected String[] annotationClassesToUse = { };
 
     /**
@@ -1190,6 +1212,10 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
 
         final List<GATKSAMRecord> downsampledReads = DownsamplingUtils.levelCoverageByPosition(ReadUtils.sortReadsByCoordinate(readsToUse), maxReadsInRegionPerSample, minReadsPerAlignmentStart);
 
+        if ( MTAC.bamWriter != null && MTAC.emitDroppedReads ) {
+            haplotypeBAMWriter.addDroppedReadsFromDelta(DroppedReadsTracker.Reason.DOWNSAMPLED, activeRegion.getReads(), downsampledReads);
+        }
+
         // handle overlapping read pairs from the same fragment
         // KC: commented out as we handle overlapping read pairs in a different way...
         //cleanOverlappingReadPairs(downsampledReads, normalSampleNames);

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -261,7 +261,8 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
                     // remove the effect of cosmic from dbSNP
                     boolean germlineAtRisk = (!dbsnpVC.isEmpty() && cosmicVC.isEmpty());
 
-                    NORMAL_LOD_THRESHOLD = (germlineAtRisk)?MTAC.NORMAL_DBSNP_LOD_THRESHOLD:MTAC.NORMAL_LOD_THRESHOLD;
+                    INIT_NORMAL_LOD_THRESHOLD = MTAC.INITIAL_NORMAL_LOD_THRESHOLD; //only set this if this job has a normal
+                            NORMAL_LOD_THRESHOLD = (germlineAtRisk)?MTAC.NORMAL_DBSNP_LOD_THRESHOLD:MTAC.NORMAL_LOD_THRESHOLD;
                     for (int altInd = 0; altInd < numAlts; altInd++)
                         normalLods[altInd] = normalGLs[REF_INDEX] - normalGLs[altInd+1];
                 }
@@ -270,7 +271,7 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
                 int numPassingAlts = 0;
                 int lodInd = 0;
                 for (int altInd = 0; altInd < numAlts; altInd++) {
-                    if (tumorLods[altInd] >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLods[altInd] >= MTAC.INITIAL_NORMAL_LOD_THRESHOLD) {
+                    if (tumorLods[altInd] >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLods[altInd] >= INIT_NORMAL_LOD_THRESHOLD) {
                         numPassingAlts++;
                         lodInd = altInd;
                     }
@@ -280,7 +281,7 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
                 final double normalLod = normalLods[lodInd];
 
                 VariantContext call = null;
-                if (tumorLod >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLod >= MTAC.INITIAL_NORMAL_LOD_THRESHOLD) {
+                if (tumorLod >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLod >= INIT_NORMAL_LOD_THRESHOLD) {
                     VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC);
 
                     if (normalLod < NORMAL_LOD_THRESHOLD) {

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala

@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 *