From 3b7e0c56bfa96c8b88cc785df3b2f435a614ea39 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Wed, 18 May 2016 00:03:36 -0400 Subject: [PATCH 1/6] Moved post-IR MQ reverter filter to public --- ...OriginalMQAfterIndelRealignmentFilter.java | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOriginalMQAfterIndelRealignmentFilter.java diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOriginalMQAfterIndelRealignmentFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOriginalMQAfterIndelRealignmentFilter.java new file mode 100644 index 000000000..f979f0ad8 --- /dev/null +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOriginalMQAfterIndelRealignmentFilter.java @@ -0,0 +1,68 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.engine.filters; + +import htsjdk.samtools.SAMRecord; +import org.broadinstitute.gatk.utils.commandline.Argument; + +/** + * Revert the MQ of reads that were modified by IndelRealigner + * + *

IndelRealigner systematically adds +10 to the MQ of the reads it realigns. In some cases, that brings the resulting MQ to a value higher than MQ 60, which is the normal cap for MQ values. Since many downstream tools assume that MQ is <= 60, this may potentially cause problems.

+ * + *

This read filter makes it possible to revert the MQ values of all the reads touched by IndelRealigner. It works by subtracting 10 from the MQ of all reads that have an "OC" tag, which stands for "original CIGAR" and is added by IndelRealigner to any read that it realigns.

+ * + *

Usage example

+ * + *

Enable the filter

+ * 
+ *     java -jar GenomeAnalysisTk.jar \
+ *         -T ToolName \
+ *         -R reference.fasta \
+ *         -I input.bam \
+ *         -o output.file \
+ *         -rf ReassignOriginalMQAfterIndelRealignmentFilter
+ *
+ * + * + * + *

Caveat

+ * + *

There is currently no way to tell programmatically that a file has already been processed with this filter, so you should check the header manually before running this tool. Running it multiple times on the same BAM file would levy an unjustified penalty on realigned reads.

+ * + * @author ami + * @since 1/30/15. + */ +public class ReassignOriginalMQAfterIndelRealignmentFilter extends ReadFilter { + + public boolean filterOut(SAMRecord rec) { + final String ORIGINAL_CIGAR_TAG = "OC"; + + if (rec.getAttribute(ORIGINAL_CIGAR_TAG) != null) + rec.setMappingQuality(rec.getMappingQuality() - 10); + return false; + } +} From c4a06ad20a1adf5cd5bdf2211cbae07e41a79ba3 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 11:45:28 -0400 Subject: [PATCH 2/6] Move indel realignment to public --- .../tools/walkers/indels/LeftAlignIndels.java | 142 ------------- .../gatk/tools/walkers/indels/ReadBin.java | 128 ----------- .../ConstrainedMateFixingManagerUnitTest.java | 198 ------------------ .../indels/IndelRealignerIntegrationTest.java | 187 ----------------- .../indels/IndelRealignerLargeScaleTest.java | 108 ---------- .../indels/IndelRealignerUnitTest.java | 87 -------- .../tools/walkers/indels/ReadBinUnitTest.java | 117 ----------- ...RealignerTargetCreatorIntegrationTest.java | 159 -------------- .../RealignerTargetCreatorLargeScaleTest.java | 85 -------- .../indels/ConstrainedMateFixingManager.java | 62 ++---- .../tools/walkers/indels/IndelRealigner.java | 69 ++---- .../tools/walkers/indels/LeftAlignIndels.java | 116 ++++++++++ .../gatk/tools/walkers/indels/ReadBin.java | 102 +++++++++ .../indels/RealignerTargetCreator.java | 67 ++---- .../ConstrainedMateFixingManagerUnitTest.java | 172 +++++++++++++++ .../indels/IndelRealignerIntegrationTest.java | 161 ++++++++++++++ .../indels/IndelRealignerLargeScaleTest.java | 82 ++++++++ .../indels/IndelRealignerUnitTest.java | 61 ++++++ .../tools/walkers/indels/ReadBinUnitTest.java | 91 ++++++++ ...RealignerTargetCreatorIntegrationTest.java | 133 ++++++++++++ .../RealignerTargetCreatorLargeScaleTest.java | 59 ++++++ 21 files changed, 1038 insertions(+), 1348 deletions(-) delete mode 100644 protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java delete mode 100644 protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java delete mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java rename {protected/gatk-tools-protected => public/gatk-tools-public}/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java (65%) rename {protected/gatk-tools-protected => public/gatk-tools-public}/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java (88%) create mode 100644 public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java create mode 100644 public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java rename {protected/gatk-tools-protected => public/gatk-tools-public}/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java (65%) create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java deleted file mode 100644 index 484529373..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java +++ /dev/null @@ -1,142 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import htsjdk.samtools.Cigar; -import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.utils.commandline.Output; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.walkers.ReadWalker; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.sam.AlignmentUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; - - -/** - * Left-align indels within reads in a bam file - * - *

This tool left-aligns any indels within read cigars in order to standardize representation when there are multiple valid - * representations possible (i.e. where the same indel can be placed at multiple positions and still represent the same haplotype). - * The standard convention is to place an indel at the left-most position possible, but this is not always followed, so - * this tool can be used to correct the representation of indels.

- * - *

Note

- *

This is only really needed when calling variants with legacy locus-based tools such as UnifiedGenotyper. With more - * sophisticated tools (like HaplotypeCaller) that involve reconstructing haplotypes (eg through reassembly), the problem - * of multiple valid representations is handled internally and does not need to be corrected explicitly.

- * - *

Input

- *

- * A bam file with mapped reads. - *

- * - *

Output

- *

- * A bam file in which indels have been left-aligned where appropriate. - *

- * - *

Usage example

- * 
- * java -jar GenomeAnalysisTK.jar \
- *   -R reference.fasta \
- *   -T LeftAlignIndels \
- *   -I reads.bam \
- *   -o output_with_leftaligned_indels.bam
- *
- * - */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) -public class LeftAlignIndels extends ReadWalker { - - @Output(required=false, doc="Output bam") - protected GATKSAMFileWriter writer = null; - - public void initialize() {} - - private void emit(final SAMRecord read) { - if ( writer != null ) - writer.addAlignment(read); - } - - public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { - // we can not deal with screwy records - if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) { - emit(read); - return 0; - } - - // move existing indels (for 1 indel reads only) to leftmost position within identical sequence - int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); - if ( numBlocks == 2 ) { - Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true); - newCigar = IndelRealigner.reclipCigar(newCigar, read); - read.setCigar(newCigar); - } - - emit(read); - return 1; - } - - public Integer reduceInit() { - return 0; - } - - public Integer reduce(Integer value, Integer sum) { - return sum + value; - } - - public void onTraversalDone(Integer result) {} -} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java deleted file mode 100644 index 532041688..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java +++ /dev/null @@ -1,128 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import com.google.java.contract.Requires; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.HasGenomeLocation; -import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; - -import java.util.ArrayList; -import java.util.List; - -/** -* User: carneiro -* Date: 2/16/13 -* Time: 11:15 PM -*/ -class ReadBin implements HasGenomeLocation { - - private final ArrayList reads = new ArrayList(); - private byte[] reference = null; - private GenomeLoc loc = null; - private final GenomeLocParser parser; - private final int referencePadding; - - public ReadBin(final GenomeLocParser parser, final int referencePadding) { - this.parser = parser; - this.referencePadding = referencePadding; - } - - // Return false if we can't process this read bin because the reads are not correctly overlapping. - // This can happen if e.g. there's a large known indel with no overlapping reads. - public void add(GATKSAMRecord read) { - - final int readStart = read.getSoftStart(); - final int readStop = read.getSoftEnd(); - if ( loc == null ) - loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion - else if ( readStop > loc.getStop() ) - loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop); - - reads.add(read); - } - - public List getReads() { - return reads; - } - - @Requires("referenceReader.isUppercasingBases()") - public byte[] getReference(CachingIndexedFastaSequenceFile referenceReader) { - // set up the reference if we haven't done so yet - if ( reference == null ) { - // first, pad the reference to handle deletions in narrow windows (e.g. those with only 1 read) - int padLeft = Math.max(loc.getStart()- referencePadding, 1); - int padRight = Math.min(loc.getStop()+ referencePadding, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength()); - loc = parser.createGenomeLoc(loc.getContig(), loc.getContigIndex(), padLeft, padRight); - reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); - } - - return reference; - } - - public GenomeLoc getLocation() { - return loc; - } - - public int size() { - return reads.size(); - } - - public void clear() { - reads.clear(); - reference = null; - loc = null; - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java deleted file mode 100644 index 420ccceef..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java +++ /dev/null @@ -1,198 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMFileWriter; -import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.util.ProgressLoggerInterface; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -import java.util.ArrayList; -import java.util.List; - - -public class ConstrainedMateFixingManagerUnitTest extends BaseTest { - - private static SAMFileHeader header; - private static GenomeLocParser genomeLocParser; - - @BeforeClass - public void beforeClass() { - header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000); - genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); - } - - @Test - public void testSecondaryAlignmentsDoNotInterfere() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setAlignmentStart(8); // move the read - read1.setFlags(99); // first in proper pair, mate negative strand - - final GATKSAMRecord read2Primary = properReads.get(1); - read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment - - Assert.assertEquals(read1.getInferredInsertSize(), 21); - - final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); - read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand - - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000); - manager.addRead(read1, true, false); - manager.addRead(read2NonPrimary, false, false); - manager.addRead(read2Primary, false, false); - - Assert.assertEquals(manager.getNReadsInQueue(), 3); - - for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) { - if ( read.getFirstOfPairFlag() ) { - Assert.assertEquals(read.getFlags(), 99); - Assert.assertEquals(read.getInferredInsertSize(), 23); - } else if ( read.getNotPrimaryAlignmentFlag() ) { - Assert.assertEquals(read.getFlags(), 393); - Assert.assertEquals(read.getInferredInsertSize(), -21); - } else { - Assert.assertEquals(read.getFlags(), 147); - Assert.assertEquals(read.getInferredInsertSize(), -23); - } - } - } - - @Test - public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setFlags(99); // first in proper pair, mate negative strand - - final GATKSAMRecord read2Primary = properReads.get(1); - read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment - read2Primary.setAlignmentStart(1596); // move the read - - final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); - read2NonPrimary.setReadName("foo"); - read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand - read2NonPrimary.setAlignmentStart(451); - read2NonPrimary.setMateAlignmentStart(451); - - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000); - manager.addRead(read2NonPrimary, false, false); - manager.addRead(read1, false, false); - - for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ ) - manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false); - - Assert.assertTrue(manager.forMateMatching.containsKey("foo")); - } - - @Test - public void testSupplementaryAlignmentsDoNotCauseBadMateFixing() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setFlags(99); // first in pair, negative strand - - final GATKSAMRecord read2 = properReads.get(1); - read2.setFlags(161); // second in pair, mate negative strand - - final GATKSAMRecord read2Supp = new GATKSAMRecord(read2); - read2Supp.setReadName("foo"); - read2Supp.setFlags(2209); // second in pair, mate negative strand, supplementary - read2Supp.setAlignmentStart(100); - read2Supp.setMateAlignmentStart(1000); - - final DummyWriter writer = new DummyWriter(); - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(writer, genomeLocParser, 10000, 200, 10000); - manager.addRead(read2Supp, false, false); - manager.addRead(read1, false, false); - manager.addRead(read2, false, false); - manager.close(); // "write" the reads to our dummy writer - - // check to make sure that none of the mate locations were changed, which is the problem brought to us by a user - for ( final SAMRecord read : writer.reads ) { - final int start = read.getAlignmentStart(); - switch (start) { - case 100: - Assert.assertEquals(read.getMateAlignmentStart(), 1000); - break; - case 1000: - Assert.assertEquals(read.getMateAlignmentStart(), 2000); - break; - case 2000: - Assert.assertEquals(read.getMateAlignmentStart(), 1000); - break; - default: - Assert.assertTrue(false, "We saw a read located at the wrong position"); - } - } - } - - private class DummyWriter implements SAMFileWriter { - - public List reads; - - public DummyWriter() { reads = new ArrayList<>(10); } - - public void addAlignment(final SAMRecord alignment) { reads.add(alignment);} - - public SAMFileHeader getFileHeader() { return null; } - - public void setProgressLogger(final ProgressLoggerInterface progress) {} - - public void close() {} - } -} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java deleted file mode 100644 index 98afc3bfc..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java +++ /dev/null @@ -1,187 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.testng.annotations.Test; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - -public class IndelRealignerIntegrationTest extends WalkerTest { - - private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam"; - private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; - private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; - private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; - private static final String baseCommand = baseCommandPrefix + "-o %s "; - private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4"; - private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364"; - - @Test - public void testDefaults() { - - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand, - 1, - Arrays.asList(base_md5)); - executeTest("test realigner defaults", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "-known " + knownIndels, - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("test realigner defaults with VCF", spec2); - } - - @Test - public void testKnownsOnly() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, - 1, - Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30")); - executeTest("realigner known indels only from VCF", spec1); - } - - @Test - public void testUseSW() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels, - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("realigner use SW from VCF", spec1); - } - - @Test - public void testLods() { - HashMap e = new HashMap(); - e.put("-LOD 60", base_md5); - e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "0c4597e48b4e194de32ebe494704ea6b" ); - - for ( Map.Entry entry : e.entrySet() ) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + entry.getKey(), - 1, - Arrays.asList(entry.getValue())); - executeTest(String.format("realigner [%s]", entry.getKey()), spec); - } - } - - @Test - public void testLongRun() { - WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", - 1, - Arrays.asList("19e6859b9ef09c7e0a79a19626908b17")); - executeTest("realigner long run", spec); - } - - @Test - public void testNoTags() { - WalkerTestSpec spec = new WalkerTestSpec( - baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", - 1, - Arrays.asList("8f5684359d7b26acaacfa657ef395a0c")); - executeTest("realigner no output tags", spec); - } - - @Test - public void testStats() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommandPrefix + "-stats %s -o /dev/null", - 1, - Arrays.asList("7ed8d4eed635613fd031598a5c9ef5a3")); - executeTest("realigner stats", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null", - 1, - Arrays.asList("e8b02bfc5debec55fe936a38c59463cc")); - executeTest("realigner stats", spec2); - } - - @Test - public void testMaxReadsInMemory() { - HashMap e = new HashMap(); - e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378"); - e.put( "--maxReadsInMemory 40000", base_md5 ); - - for ( Map.Entry entry : e.entrySet() ) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + entry.getKey(), - 1, - Arrays.asList(entry.getValue())); - executeTest(String.format("realigner [%s]", entry.getKey()), spec); - } - } - - @Test - public void testNWayOut() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommandPrefix + " -nWayOut .clean.bam ", - 1, - Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); - executeTest("test realigner nWayOut", spec1); - } - - @Test - public void testBadCigarStringDoesNotFail() { - // Just making sure the test runs without an error, don't care about the MD5 value - WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -targetIntervals 19:5787205-5787300 -o %s", - 1, - Arrays.asList("")); - executeTest("test bad cigar string does not fail", spec); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java deleted file mode 100644 index 217e06631..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java +++ /dev/null @@ -1,108 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.testng.annotations.Test; - -import java.util.ArrayList; - -public class IndelRealignerLargeScaleTest extends WalkerTest { - @Test( timeOut = 18000000 ) - public void testHighCoverage() { - WalkerTestSpec spec = new WalkerTestSpec( - - "-R " + b36KGReference + - " -T IndelRealigner" + - " -I " + validationDataLocation + "indelRealignerTest.pilot1.veryHighCoverage.bam" + - " -L 20:49,500-55,500" + - " -o /dev/null" + - " -targetIntervals " + validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerHighCoverage", spec); - } - - @Test( timeOut = 18000000 ) - public void testRealigner() { - WalkerTestSpec spec1 = new WalkerTestSpec( - - "-R " + hg18Reference + - " -T IndelRealigner" + - " -LOD 5" + - " -maxConsensuses 100" + - " -greedy 100" + - " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -o /dev/null" + - " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + - " -L chr1:1-5,650,000" + - " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerWholeGenome", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T IndelRealigner" + - " -LOD 5" + - " -maxConsensuses 100" + - " -greedy 100" + - " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -o /dev/null" + - " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + - " -L chr1:1-150,000,000" + - " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerWholeExome", spec2); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java deleted file mode 100644 index bb3d66c1b..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java +++ /dev/null @@ -1,87 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -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.utils.sam.GATKSAMRecord; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -import java.io.File; -import java.io.FileNotFoundException; - -public class IndelRealignerUnitTest extends BaseTest { - - private SAMFileHeader header; - - @BeforeClass - public void setup() throws FileNotFoundException { - final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); - header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); - } - - @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); - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java deleted file mode 100644 index 492f4e63f..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java +++ /dev/null @@ -1,117 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -/** - * User: carneiro - * Date: 2/16/13 - * Time: 11:48 PM - */ -public class ReadBinUnitTest { - private GenomeLocParser parser; - private ReadBin readBin; - - private final int readLength = 100; // all reads will have the same size - private final int referencePadding = 10; // standard reference padding - - @BeforeClass - public void init() { - parser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader().getSequenceDictionary()); - readBin = new ReadBin(parser, referencePadding); - } - - @DataProvider(name = "reads") - public Object[][] reads() { - - return new Object[][]{ - {"20S80M", 80}, - {"80M20S", 1}, - {"20S60M20S", 50}, - {"50I", 60}, - {"100M", 500} - }; - } - - /** - * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads - * - * @param cigarString the read's cigar string - * @param alignmentStart the read's alignment start - */ - @Test(enabled = true, dataProvider = "reads") - public void testAddingReads(String cigarString, int alignmentStart) { - final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart); - final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd())); - Assert.assertEquals(readBin.getLocation(), readLoc); - readBin.clear(); - } - - public GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) { - final GATKSAMRecord read = ReadUtils.createRandomRead(readLength); - read.setCigarString(cigarString); - read.setAlignmentStart(alignmentStart); - readBin.add(read); - return read; - } -} - - diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java deleted file mode 100644 index be41b6a96..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ /dev/null @@ -1,159 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import htsjdk.samtools.reference.ReferenceSequenceFile; -import htsjdk.samtools.util.Interval; -import htsjdk.samtools.util.IntervalList; -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.interval.IntervalUtils; -import org.testng.Assert; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; - -public class RealignerTargetCreatorIntegrationTest extends WalkerTest { - - @DataProvider(name = "intervals1") - public Object[][] intervals1() { - String arguments = "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000"; - return new Object[][]{ - {"test standard nt=1", arguments}, - {"test standard nt=4", "-nt 4 " + arguments} - }; - } - - @DataProvider(name = "intervals2") - public Object[][] intervals2() { - String arguments = "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000"; - return new Object[][]{ - {"test with dbsnp nt=1", arguments}, - {"test with dbsnp nt=4", "-nt 4 " + arguments} - }; - } - - @Test(dataProvider = "intervals1") - public void testIntervals1(String testName, String arguments) { - String md5 = "3f0b63a393104d0c4158c7d1538153b8"; - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); - executeTest(testName, spec); - } - - @Test(dataProvider = "intervals2") - public void testIntervals2(String testName, String arguments) { - String md5 = "d073237694175c75d37bd4f40b8c64db"; - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); - executeTest(testName, spec); - } - - @Test - public void testKnownsOnly() { - WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + b36KGReference + " --known " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s", - 1, - Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96")); - executeTest("test rods only", spec3); - } - - @Test() - public void testBadCigarStringDoesNotFail() { - // Just making sure the test runs without an error, don't care about the MD5 value - WalkerTestSpec spec = new WalkerTestSpec( - "-T RealignerTargetCreator -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -o %s", - 1, - Arrays.asList("")); - executeTest("test bad cigar string string does not fail", spec); - } - - @Test(dataProvider = "intervals1") - public void testTargetListAgainstIntervalList(String testName, String arguments) throws IOException { - final List md5 = Collections.emptyList(); - final File targetListFile = createTempFile("RTCTest", ".targets"); - final File intervalListFile = createTempFile("RTCTest", ".interval_list"); - - WalkerTest.WalkerTestSpec targetListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); - WalkerTest.WalkerTestSpec intervalListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); - - targetListSpec.setOutputFileLocation(targetListFile); - intervalListSpec.setOutputFileLocation(intervalListFile); - - executeTest(testName + " (compare target-list and interval-list output)", targetListSpec); - executeTest(testName + " (compare target-list and interval-list output)", intervalListSpec); - - final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference)); - final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(seq); - final List targetList = IntervalUtils.intervalFileToList(hg19GenomeLocParser, - targetListFile.getAbsolutePath()); - final List targetListResult = new ArrayList<>(); - for ( GenomeLoc target : targetList ) { - targetListResult.add(new Interval(target.getContig(), target.getStart(), target.getStop())); - } - - final List intervalListResult = IntervalList.fromFile(intervalListFile).getIntervals(); - - Assert.assertFalse(targetListResult.isEmpty()); - Assert.assertFalse(intervalListResult.isEmpty()); - Assert.assertEquals(targetListResult, intervalListResult); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java deleted file mode 100644 index cfe634acf..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java +++ /dev/null @@ -1,85 +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 2012-2016 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. -* -* 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.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.testng.annotations.Test; - -import java.util.ArrayList; - -public class RealignerTargetCreatorLargeScaleTest extends WalkerTest { - @Test( timeOut = 18000000 ) - public void testRealignerTargetCreator() { - - WalkerTestSpec spec1 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T RealignerTargetCreator" + - " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + - " -L chr1:1-50,000,000" + - " -o /dev/null", - 0, - new ArrayList(0)); - executeTest("testRealignerTargetCreatorWholeGenome", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T RealignerTargetCreator" + - " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + - " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + - " -o /dev/null", - 0, - new ArrayList(0)); - executeTest("testRealignerTargetCreatorWholeExome", spec2); - } -} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java similarity index 65% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java index eb45b5b76..766371358 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java @@ -1,52 +1,26 @@ /* -* 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 2012-2016 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. * -* 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. +* 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: * -* 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. +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* 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. +* 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. */ package org.broadinstitute.gatk.tools.walkers.indels; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java similarity index 88% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java index 99c3b5c46..afc710c9d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java @@ -1,52 +1,26 @@ /* -* 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 2012-2016 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. * -* 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. +* 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: * -* 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. +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* 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. +* 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. */ package org.broadinstitute.gatk.tools.walkers.indels; @@ -101,10 +75,11 @@ import java.util.*; * it is impossible to place reads on the reference genome such at mismatches are minimized across all reads. Consequently, even when some reads are * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel, * also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus - * indel suitable for standard variant discovery approaches. Unlike most mappers, this walker uses the full alignment context to determine whether an - * appropriate alternate reference (i.e. indel) exists. Following local realignment, the GATK tool Unified Genotyper can be used to sensitively and - * specifically identify indels. + * indel suitable for standard variant discovery approaches. *

+ *

Note that indel realignment is no longer necessary for variant discovery if you plan to use a variant caller that performs a haplotype assembly + * step, such as HaplotypeCaller or MuTect2. However it is still required when using legacy callers such as UnifiedGenotyper or the original MuTect.

+ * *

There are 2 steps to the realignment process:

*
    *
  1. Determining (small) suspicious intervals which are likely in need of realignment (see the RealignerTargetCreator tool)
    2. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java new file mode 100644 index 000000000..58202f059 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java @@ -0,0 +1,116 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.Cigar; +import htsjdk.samtools.SAMRecord; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + + +/** + * Left-align indels within reads in a bam file + * + *

    This tool left-aligns any indels within read cigars in order to standardize representation when there are multiple valid + * representations possible (i.e. where the same indel can be placed at multiple positions and still represent the same haplotype). + * The standard convention is to place an indel at the left-most position possible, but this is not always followed, so + * this tool can be used to correct the representation of indels.

    + * + *

    Note

    + *

    This is only really needed when calling variants with legacy locus-based tools such as UnifiedGenotyper. With more + * sophisticated tools (like HaplotypeCaller) that involve reconstructing haplotypes (eg through haplotype assembly), the problem + * of multiple valid representations is handled internally and does not need to be corrected explicitly.

    + * + *

    Input

    + *

    + * A bam file with mapped reads. + *

    + * + *

    Output

    + *

    + * A bam file in which indels have been left-aligned where appropriate. + *

    + * + *

    Usage example

    + * 
    + * java -jar GenomeAnalysisTK.jar \
+ *   -R reference.fasta \
+ *   -T LeftAlignIndels \
+ *   -I reads.bam \
+ *   -o output_with_leftaligned_indels.bam
+ *
    + * + */ +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) +public class LeftAlignIndels extends ReadWalker { + + @Output(required=false, doc="Output bam") + protected GATKSAMFileWriter writer = null; + + public void initialize() {} + + private void emit(final SAMRecord read) { + if ( writer != null ) + writer.addAlignment(read); + } + + public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { + // we can not deal with screwy records + if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) { + emit(read); + return 0; + } + + // move existing indels (for 1 indel reads only) to leftmost position within identical sequence + int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); + if ( numBlocks == 2 ) { + Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true); + newCigar = IndelRealigner.reclipCigar(newCigar, read); + read.setCigar(newCigar); + } + + emit(read); + return 1; + } + + public Integer reduceInit() { + return 0; + } + + public Integer reduce(Integer value, Integer sum) { + return sum + value; + } + + public void onTraversalDone(Integer result) {} +} \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java new file mode 100644 index 000000000..a7eae01e1 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java @@ -0,0 +1,102 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import com.google.java.contract.Requires; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + +import java.util.ArrayList; +import java.util.List; + +/** +* User: carneiro +* Date: 2/16/13 +* Time: 11:15 PM +*/ +class ReadBin implements HasGenomeLocation { + + private final ArrayList reads = new ArrayList(); + private byte[] reference = null; + private GenomeLoc loc = null; + private final GenomeLocParser parser; + private final int referencePadding; + + public ReadBin(final GenomeLocParser parser, final int referencePadding) { + this.parser = parser; + this.referencePadding = referencePadding; + } + + // Return false if we can't process this read bin because the reads are not correctly overlapping. + // This can happen if e.g. there's a large known indel with no overlapping reads. + public void add(GATKSAMRecord read) { + + final int readStart = read.getSoftStart(); + final int readStop = read.getSoftEnd(); + if ( loc == null ) + loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion + else if ( readStop > loc.getStop() ) + loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop); + + reads.add(read); + } + + public List getReads() { + return reads; + } + + @Requires("referenceReader.isUppercasingBases()") + public byte[] getReference(CachingIndexedFastaSequenceFile referenceReader) { + // set up the reference if we haven't done so yet + if ( reference == null ) { + // first, pad the reference to handle deletions in narrow windows (e.g. those with only 1 read) + int padLeft = Math.max(loc.getStart()- referencePadding, 1); + int padRight = Math.min(loc.getStop()+ referencePadding, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength()); + loc = parser.createGenomeLoc(loc.getContig(), loc.getContigIndex(), padLeft, padRight); + reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); + } + + return reference; + } + + public GenomeLoc getLocation() { + return loc; + } + + public int size() { + return reads.size(); + } + + public void clear() { + reads.clear(); + reference = null; + loc = null; + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java similarity index 65% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java index 9475526bc..6d4e86252 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java @@ -1,52 +1,26 @@ /* -* 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. 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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. 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LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. * 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. * -* 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. +* 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: * -* 6. 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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. +* 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. */ package org.broadinstitute.gatk.tools.walkers.indels; @@ -95,9 +69,10 @@ import java.util.TreeSet; * it is impossible to place reads on the reference genome such that mismatches are minimized across all reads. Consequently, even when some reads are * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel, * also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus - * indel suitable for standard variant discovery approaches. Unlike most mappers, this tool uses the full alignment context to determine whether an - * appropriate alternate reference (i.e. indel) exists. + * indel suitable for standard variant discovery approaches. *

    + *

    Note that indel realignment is no longer necessary for variant discovery if you plan to use a variant caller that performs a haplotype assembly + * step, such as HaplotypeCaller or MuTect2. However it is still required when using legacy callers such as UnifiedGenotyper or the original MuTect.

    *

    There are 2 steps to the realignment process:

    *
      *
    1. Determining (small) suspicious intervals which are likely in need of realignment (RealignerTargetCreator)
      2. diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java new file mode 100644 index 000000000..7be6c1ca8 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java @@ -0,0 +1,172 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.ProgressLoggerInterface; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.List; + + +public class ConstrainedMateFixingManagerUnitTest extends BaseTest { + + private static SAMFileHeader header; + private static GenomeLocParser genomeLocParser; + + @BeforeClass + public void beforeClass() { + header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000); + genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + } + + @Test + public void testSecondaryAlignmentsDoNotInterfere() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setAlignmentStart(8); // move the read + read1.setFlags(99); // first in proper pair, mate negative strand + + final GATKSAMRecord read2Primary = properReads.get(1); + read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment + + Assert.assertEquals(read1.getInferredInsertSize(), 21); + + final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); + read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand + + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000); + manager.addRead(read1, true, false); + manager.addRead(read2NonPrimary, false, false); + manager.addRead(read2Primary, false, false); + + Assert.assertEquals(manager.getNReadsInQueue(), 3); + + for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) { + if ( read.getFirstOfPairFlag() ) { + Assert.assertEquals(read.getFlags(), 99); + Assert.assertEquals(read.getInferredInsertSize(), 23); + } else if ( read.getNotPrimaryAlignmentFlag() ) { + Assert.assertEquals(read.getFlags(), 393); + Assert.assertEquals(read.getInferredInsertSize(), -21); + } else { + Assert.assertEquals(read.getFlags(), 147); + Assert.assertEquals(read.getInferredInsertSize(), -23); + } + } + } + + @Test + public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setFlags(99); // first in proper pair, mate negative strand + + final GATKSAMRecord read2Primary = properReads.get(1); + read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment + read2Primary.setAlignmentStart(1596); // move the read + + final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); + read2NonPrimary.setReadName("foo"); + read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand + read2NonPrimary.setAlignmentStart(451); + read2NonPrimary.setMateAlignmentStart(451); + + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000); + manager.addRead(read2NonPrimary, false, false); + manager.addRead(read1, false, false); + + for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ ) + manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false); + + Assert.assertTrue(manager.forMateMatching.containsKey("foo")); + } + + @Test + public void testSupplementaryAlignmentsDoNotCauseBadMateFixing() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setFlags(99); // first in pair, negative strand + + final GATKSAMRecord read2 = properReads.get(1); + read2.setFlags(161); // second in pair, mate negative strand + + final GATKSAMRecord read2Supp = new GATKSAMRecord(read2); + read2Supp.setReadName("foo"); + read2Supp.setFlags(2209); // second in pair, mate negative strand, supplementary + read2Supp.setAlignmentStart(100); + read2Supp.setMateAlignmentStart(1000); + + final DummyWriter writer = new DummyWriter(); + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(writer, genomeLocParser, 10000, 200, 10000); + manager.addRead(read2Supp, false, false); + manager.addRead(read1, false, false); + manager.addRead(read2, false, false); + manager.close(); // "write" the reads to our dummy writer + + // check to make sure that none of the mate locations were changed, which is the problem brought to us by a user + for ( final SAMRecord read : writer.reads ) { + final int start = read.getAlignmentStart(); + switch (start) { + case 100: + Assert.assertEquals(read.getMateAlignmentStart(), 1000); + break; + case 1000: + Assert.assertEquals(read.getMateAlignmentStart(), 2000); + break; + case 2000: + Assert.assertEquals(read.getMateAlignmentStart(), 1000); + break; + default: + Assert.assertTrue(false, "We saw a read located at the wrong position"); + } + } + } + + private class DummyWriter implements SAMFileWriter { + + public List reads; + + public DummyWriter() { reads = new ArrayList<>(10); } + + public void addAlignment(final SAMRecord alignment) { reads.add(alignment);} + + public SAMFileHeader getFileHeader() { return null; } + + public void setProgressLogger(final ProgressLoggerInterface progress) {} + + public void close() {} + } +} \ No newline at end of file diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java new file mode 100644 index 000000000..81b2c457c --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java @@ -0,0 +1,161 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.testng.annotations.Test; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; + +public class IndelRealignerIntegrationTest extends WalkerTest { + + private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam"; + private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; + private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; + private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; + private static final String baseCommand = baseCommandPrefix + "-o %s "; + private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4"; + private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364"; + + @Test + public void testDefaults() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand, + 1, + Arrays.asList(base_md5)); + executeTest("test realigner defaults", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + baseCommand + "-known " + knownIndels, + 1, + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("test realigner defaults with VCF", spec2); + } + + @Test + public void testKnownsOnly() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, + 1, + Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30")); + executeTest("realigner known indels only from VCF", spec1); + } + + @Test + public void testUseSW() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels, + 1, + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("realigner use SW from VCF", spec1); + } + + @Test + public void testLods() { + HashMap e = new HashMap(); + e.put("-LOD 60", base_md5); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "0c4597e48b4e194de32ebe494704ea6b" ); + + for ( Map.Entry entry : e.entrySet() ) { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + entry.getKey(), + 1, + Arrays.asList(entry.getValue())); + executeTest(String.format("realigner [%s]", entry.getKey()), spec); + } + } + + @Test + public void testLongRun() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", + 1, + Arrays.asList("19e6859b9ef09c7e0a79a19626908b17")); + executeTest("realigner long run", spec); + } + + @Test + public void testNoTags() { + WalkerTestSpec spec = new WalkerTestSpec( + baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", + 1, + Arrays.asList("8f5684359d7b26acaacfa657ef395a0c")); + executeTest("realigner no output tags", spec); + } + + @Test + public void testStats() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommandPrefix + "-stats %s -o /dev/null", + 1, + Arrays.asList("7ed8d4eed635613fd031598a5c9ef5a3")); + executeTest("realigner stats", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null", + 1, + Arrays.asList("e8b02bfc5debec55fe936a38c59463cc")); + executeTest("realigner stats", spec2); + } + + @Test + public void testMaxReadsInMemory() { + HashMap e = new HashMap(); + e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378"); + e.put( "--maxReadsInMemory 40000", base_md5 ); + + for ( Map.Entry entry : e.entrySet() ) { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + entry.getKey(), + 1, + Arrays.asList(entry.getValue())); + executeTest(String.format("realigner [%s]", entry.getKey()), spec); + } + } + + @Test + public void testNWayOut() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommandPrefix + " -nWayOut .clean.bam ", + 1, + Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); + executeTest("test realigner nWayOut", spec1); + } + + @Test + public void testBadCigarStringDoesNotFail() { + // Just making sure the test runs without an error, don't care about the MD5 value + WalkerTestSpec spec = new WalkerTestSpec( + "-T IndelRealigner -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -targetIntervals 19:5787205-5787300 -o %s", + 1, + Arrays.asList("")); + executeTest("test bad cigar string does not fail", spec); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java new file mode 100644 index 000000000..649644712 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java @@ -0,0 +1,82 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.testng.annotations.Test; + +import java.util.ArrayList; + +public class IndelRealignerLargeScaleTest extends WalkerTest { + @Test( timeOut = 18000000 ) + public void testHighCoverage() { + WalkerTestSpec spec = new WalkerTestSpec( + + "-R " + b36KGReference + + " -T IndelRealigner" + + " -I " + validationDataLocation + "indelRealignerTest.pilot1.veryHighCoverage.bam" + + " -L 20:49,500-55,500" + + " -o /dev/null" + + " -targetIntervals " + validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerHighCoverage", spec); + } + + @Test( timeOut = 18000000 ) + public void testRealigner() { + WalkerTestSpec spec1 = new WalkerTestSpec( + + "-R " + hg18Reference + + " -T IndelRealigner" + + " -LOD 5" + + " -maxConsensuses 100" + + " -greedy 100" + + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -o /dev/null" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-5,650,000" + + " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerWholeGenome", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T IndelRealigner" + + " -LOD 5" + + " -maxConsensuses 100" + + " -greedy 100" + + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -o /dev/null" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L chr1:1-150,000,000" + + " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerWholeExome", spec2); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java new file mode 100644 index 000000000..801db5269 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java @@ -0,0 +1,61 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +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.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; + +public class IndelRealignerUnitTest extends BaseTest { + + private SAMFileHeader header; + + @BeforeClass + public void setup() throws FileNotFoundException { + final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + } + + @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); + } + +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java new file mode 100644 index 000000000..d843374d2 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java @@ -0,0 +1,91 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +/** + * User: carneiro + * Date: 2/16/13 + * Time: 11:48 PM + */ +public class ReadBinUnitTest { + private GenomeLocParser parser; + private ReadBin readBin; + + private final int readLength = 100; // all reads will have the same size + private final int referencePadding = 10; // standard reference padding + + @BeforeClass + public void init() { + parser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader().getSequenceDictionary()); + readBin = new ReadBin(parser, referencePadding); + } + + @DataProvider(name = "reads") + public Object[][] reads() { + + return new Object[][]{ + {"20S80M", 80}, + {"80M20S", 1}, + {"20S60M20S", 50}, + {"50I", 60}, + {"100M", 500} + }; + } + + /** + * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads + * + * @param cigarString the read's cigar string + * @param alignmentStart the read's alignment start + */ + @Test(enabled = true, dataProvider = "reads") + public void testAddingReads(String cigarString, int alignmentStart) { + final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart); + final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd())); + Assert.assertEquals(readBin.getLocation(), readLoc); + readBin.clear(); + } + + public GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) { + final GATKSAMRecord read = ReadUtils.createRandomRead(readLength); + read.setCigarString(cigarString); + read.setAlignmentStart(alignmentStart); + readBin.add(read); + return read; + } +} + + diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java new file mode 100644 index 000000000..e4b7485d2 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -0,0 +1,133 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +public class RealignerTargetCreatorIntegrationTest extends WalkerTest { + + @DataProvider(name = "intervals1") + public Object[][] intervals1() { + String arguments = "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000"; + return new Object[][]{ + {"test standard nt=1", arguments}, + {"test standard nt=4", "-nt 4 " + arguments} + }; + } + + @DataProvider(name = "intervals2") + public Object[][] intervals2() { + String arguments = "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000"; + return new Object[][]{ + {"test with dbsnp nt=1", arguments}, + {"test with dbsnp nt=4", "-nt 4 " + arguments} + }; + } + + @Test(dataProvider = "intervals1") + public void testIntervals1(String testName, String arguments) { + String md5 = "3f0b63a393104d0c4158c7d1538153b8"; + + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); + executeTest(testName, spec); + } + + @Test(dataProvider = "intervals2") + public void testIntervals2(String testName, String arguments) { + String md5 = "d073237694175c75d37bd4f40b8c64db"; + + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); + executeTest(testName, spec); + } + + @Test + public void testKnownsOnly() { + WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( + "-T RealignerTargetCreator -R " + b36KGReference + " --known " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s", + 1, + Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96")); + executeTest("test rods only", spec3); + } + + @Test() + public void testBadCigarStringDoesNotFail() { + // Just making sure the test runs without an error, don't care about the MD5 value + WalkerTestSpec spec = new WalkerTestSpec( + "-T RealignerTargetCreator -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -o %s", + 1, + Arrays.asList("")); + executeTest("test bad cigar string string does not fail", spec); + } + + @Test(dataProvider = "intervals1") + public void testTargetListAgainstIntervalList(String testName, String arguments) throws IOException { + final List md5 = Collections.emptyList(); + final File targetListFile = createTempFile("RTCTest", ".targets"); + final File intervalListFile = createTempFile("RTCTest", ".interval_list"); + + WalkerTest.WalkerTestSpec targetListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); + WalkerTest.WalkerTestSpec intervalListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); + + targetListSpec.setOutputFileLocation(targetListFile); + intervalListSpec.setOutputFileLocation(intervalListFile); + + executeTest(testName + " (compare target-list and interval-list output)", targetListSpec); + executeTest(testName + " (compare target-list and interval-list output)", intervalListSpec); + + final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference)); + final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(seq); + final List targetList = IntervalUtils.intervalFileToList(hg19GenomeLocParser, + targetListFile.getAbsolutePath()); + final List targetListResult = new ArrayList<>(); + for ( GenomeLoc target : targetList ) { + targetListResult.add(new Interval(target.getContig(), target.getStart(), target.getStop())); + } + + final List intervalListResult = IntervalList.fromFile(intervalListFile).getIntervals(); + + Assert.assertFalse(targetListResult.isEmpty()); + Assert.assertFalse(intervalListResult.isEmpty()); + Assert.assertEquals(targetListResult, intervalListResult); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java new file mode 100644 index 000000000..8b90ef419 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java @@ -0,0 +1,59 @@ +/* +* 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 +* 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. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.testng.annotations.Test; + +import java.util.ArrayList; + +public class RealignerTargetCreatorLargeScaleTest extends WalkerTest { + @Test( timeOut = 18000000 ) + public void testRealignerTargetCreator() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T RealignerTargetCreator" + + " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-50,000,000" + + " -o /dev/null", + 0, + new ArrayList(0)); + executeTest("testRealignerTargetCreatorWholeGenome", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T RealignerTargetCreator" + + " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + + " -o /dev/null", + 0, + new ArrayList(0)); + executeTest("testRealignerTargetCreatorWholeExome", spec2); + } +} From 81d4eaea29beb68710e0a2862c1572fc34a23dac Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 11:49:48 -0400 Subject: [PATCH 3/6] Fixed warnings in LAATV and ValidateVariants --- .../tools/walkers/variantutils/LeftAlignAndTrimVariants.java | 2 +- .../gatk/tools/walkers/variantutils/ValidateVariants.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java index 834c19753..c169a2844 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -249,7 +249,7 @@ public class LeftAlignAndTrimVariants extends RodWalker { // ignore if the reference length is greater than the reference window stop before and after expansion if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength)); return 0; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java index 653bdaf50..6c9912f06 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java @@ -283,7 +283,7 @@ public class ValidateVariants extends RodWalker { // reference length is greater than the reference window stop before and after expansion if ( refLength > 100 && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getContig(), vc.getStart(), refLength)); return; } From 3cc7d7e56daee63338b013e5471a8d052cab4e3c Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 11:59:54 -0400 Subject: [PATCH 4/6] Hide deletion arguments in ASEReadCounter --- .../gatk/tools/walkers/rnaseq/ASEReadCounter.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java index b9f8a5591..634566b25 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java @@ -90,7 +90,7 @@ import java.util.List; * *

      Caveat

      *
        - *
      • This tool will only process biallelic sites. If your callset contains multiallelic sites, they will be ignored. + *
      • This tool will only process biallelic SNP sites. If your callset contains multiallelic sites, they will be ignored. * Optionally, you can subset your callset to just biallelic variants using e.g. * SelectVariants * with the option "-restrictAllelesTo BIALLELIC".
        • @@ -139,19 +139,20 @@ public class ASEReadCounter extends LocusWalker { public CoverageUtils.CountPileupType countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE; /** - * Available options are csv, table, rtable. By default, the format is an r-readable table. + * Available options are csv, table, rtable. By default, the format is rtable (an r-readable table). */ @Argument(fullName = "outputFormat", doc = "Format of the output file, can be CSV, TABLE, RTABLE", required = false) public OUTPUT_FORMAT outputFormat = OUTPUT_FORMAT.RTABLE; + // Hiding these argument pending reevaluation (currently don't seem to work and aren't tested) /** * Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output. */ - @Advanced + @Hidden @Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false) public boolean includeDeletions = false; - @Advanced + @Hidden @Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false) public boolean ignoreDeletionSites = false; From 5b80c92cb701c94b21dc6df17ba5396643750294 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 12:19:59 -0400 Subject: [PATCH 5/6] Improved article linking in error messages --- .../engine/filters/MalformedReadFilter.java | 2 +- .../gatk/utils/exceptions/UserException.java | 32 +++++++++---------- .../gatk/utils/help/HelpConstants.java | 4 +-- .../gatk/utils/sam/ReadUtils.java | 6 ++-- 4 files changed, 22 insertions(+), 22 deletions(-) diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java index bfb7adebd..95a65633f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java @@ -219,7 +219,7 @@ public class MalformedReadFilter extends ReadFilter { if (! filterReadsWithNCigar && !allowNCigars) { throw new UserException.UnsupportedCigarOperatorException( CigarOperator.N,read, - "If you are working with RNA-Seq data, see " + HelpConstants.articlePost("3891") + " for guidance. " + "If you are working with RNA-Seq data, see " + HelpConstants.articlePost(3891) + " for guidance. " + "If you choose to disregard those instructions, or for other uses, you have the option of either " + "filtering out all reads with operator " + CigarOperator.N + " in their CIGAR string" + " (add --" + FILTER_READS_WITH_N_CIGAR_ARGUMENT_FULL_NAME + " to your command line) or overriding this check (add -U " diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java index 859437fb7..b29fb2a41 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java @@ -50,7 +50,7 @@ public class UserException extends ReviewedGATKException { /** * The URL where people can get help messages. Printed when an error occurs */ - public static final String PHONE_HOME_DOCS_URL = "http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest"; + public static final String PHONE_HOME_DOCS_URL = HelpConstants.articlePost(1250); public UserException(String msg) { super(msg); } public UserException(String msg, Throwable e) { super(msg, e); } @@ -136,7 +136,7 @@ public class UserException extends ReviewedGATKException { public static class BadTmpDir extends UserException { public BadTmpDir(String message) { - super(String.format("An error occurred while working with the tmp directory %s. You can specify -Djava.io.tmpdir=X on the command line (before the -jar argument) where X is a directory path, to use a more appropriate temporary directory. The exact error was %s", System.getProperties().get("java.io.tmpdir"), message)); + super(String.format("An error occurred while working with the tmp directory %s. You can specify -Djava.io.tmpdir=X on the command line (before the -jar argument) where X is a directory path, to use a more appropriate temporary directory. Note that this is a JVM argument, not a GATK argument. The exact error was %s", System.getProperties().get("java.io.tmpdir"), message)); } } @@ -160,7 +160,7 @@ public class UserException extends ReviewedGATKException { public static class ErrorWritingBamFile extends UserException { public ErrorWritingBamFile(String message) { - super(String.format("An error occurred when trying to write the BAM file. Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small. Your system administrator can help you resolve these issues. If you know what temporary directory to use, you can specify it by adding -Djava.io.tmpdir=X to the command line (before the -jar argument), where X is the directory path. The exact error was %s", message)); + super(String.format("An error occurred when trying to write the BAM file. Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small. Your system administrator can help you resolve these issues. If you know what temporary directory to use, you can specify it by adding -Djava.io.tmpdir=X to the command line (before the -jar argument), where X is the directory path. Note that this is a JVM argument, not a GATK argument. The exact error was %s", message)); } } @@ -225,20 +225,20 @@ public class UserException extends ReviewedGATKException { public static class MissortedBAM extends UserException { public MissortedBAM(SAMFileHeader.SortOrder order, File file, SAMFileHeader header) { - super(String.format("Missorted input SAM/BAM/CRAM files: %s must be sorted in %s order but order was: %s. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information.", file, order, header.getSortOrder())); + super(String.format("Missorted input SAM/BAM/CRAM files: %s must be sorted in %s order but order was: %s. Please see " + HelpConstants.articlePost(1317) + "for more information.", file, order, header.getSortOrder())); } public MissortedBAM(SAMFileHeader.SortOrder order, String message) { - super(String.format("Missorted input SAM/BAM/CRAM files: files are not sorted in %s order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", order, message)); + super(String.format("Missorted input SAM/BAM/CRAM files: files are not sorted in %s order. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", order, message)); } public MissortedBAM(SAMFileHeader.SortOrder order, SAMRecord read, String message) { - super(String.format("Missorted input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", + super(String.format("Missorted input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", read.getFileSource().getReader(), read.getHeader().getSortOrder(), order, message)); } public MissortedBAM(String message) { - super(String.format("Missorted input SAM/BAM/CRAM files. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", message)); + super(String.format("Missorted input SAM/BAM/CRAM files. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", message)); } } @@ -252,7 +252,7 @@ public class UserException extends ReviewedGATKException { } public MalformedBAM(String source, String message) { - super(String.format("SAM/BAM/CRAM file %s is malformed. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", source, message)); + super(String.format("SAM/BAM/CRAM file %s is malformed. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", source, message)); } } @@ -262,7 +262,7 @@ public class UserException extends ReviewedGATKException { } public MisencodedBAM(String source, String message) { - super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s. Please see https://www.broadinstitute.org/gatk/guide?id=6470 for more details and options related to this error.", source, message)); + super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s. Please see " + HelpConstants.articlePost(6470) + " for more details and options related to this error.", source, message)); } } @@ -294,13 +294,13 @@ public class UserException extends ReviewedGATKException { public static class ReadMissingReadGroup extends MalformedBAM { public ReadMissingReadGroup(final SAMRecord read) { - super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName())); + super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please see " + HelpConstants.articlePost(59), read.getReadName())); } } public static class ReadHasUndefinedReadGroup extends MalformedBAM { public ReadHasUndefinedReadGroup(final SAMRecord read, final String rgID) { - super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid. Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID)); + super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid. Please see " + HelpConstants.articlePost(59), read.getReadName(), rgID)); } } @@ -312,7 +312,7 @@ public class UserException extends ReviewedGATKException { public static class MissortedFile extends UserException { public MissortedFile(File file, String message, Exception e) { - super(String.format("Missorted input file: %s is must be sorted in coordinate order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s and got error %s", file, message, getMessage(e))); + super(String.format("Missorted input file: %s is must be sorted in coordinate order. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s and got error %s", file, message, getMessage(e))); } } @@ -366,14 +366,14 @@ public class UserException extends ReviewedGATKException { public static class IncompatibleSequenceDictionaries extends UserException { public IncompatibleSequenceDictionaries(String message, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) { - super(String.format("Input files %s and %s have incompatible contigs. Please see " + HelpConstants.forumPost("discussion/63/input-files-have-incompatible-contigs") + "for more information. Error details: %s.\n %s contigs = %s\n %s contigs = %s", + super(String.format("Input files %s and %s have incompatible contigs. Please see " + HelpConstants.articlePost(63) + "for more information. Error details: %s.\n %s contigs = %s\n %s contigs = %s", name1, name2, message, name1, ReadUtils.prettyPrintSequenceRecords(dict1), name2, ReadUtils.prettyPrintSequenceRecords(dict2))); } } public static class LexicographicallySortedSequenceDictionary extends UserException { public LexicographicallySortedSequenceDictionary(String name, SAMSequenceDictionary dict) { - super(String.format("Lexicographically sorted human genome sequence detected in %s. Please see " + HelpConstants.articlePost("1328") + "for more information. Error details: %s contigs = %s", + super(String.format("Lexicographically sorted human genome sequence detected in %s. Please see " + HelpConstants.articlePost(1328) + "for more information. Error details: %s contigs = %s", name, name, ReadUtils.prettyPrintSequenceRecords(dict))); } } @@ -409,7 +409,7 @@ public class UserException extends ReviewedGATKException { public MissingReferenceFaiFile( final File indexFile, final File fastaFile ) { super(String.format("Fasta index file %s for reference %s does not exist. Please see %s for help creating it.", indexFile.getAbsolutePath(), fastaFile.getAbsolutePath(), - HelpConstants.forumPost("discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference"))); + HelpConstants.articlePost(1601))); } } @@ -417,7 +417,7 @@ public class UserException extends ReviewedGATKException { public MissingReferenceDictFile( final File dictFile, final File fastaFile ) { super(String.format("Fasta dict file %s for reference %s does not exist. Please see %s for help creating it.", dictFile.getAbsolutePath(), fastaFile.getAbsolutePath(), - HelpConstants.forumPost("discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference"))); + HelpConstants.articlePost(1601))); } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java index 6c7068b19..279af20ed 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java @@ -62,8 +62,8 @@ public class HelpConstants { return GATK_FORUM_URL + post; } - public static String articlePost(String id) { - return GATK_ARTICLE_URL + "?id=" + id; + public static String articlePost(Integer id) { + return GATK_ARTICLE_URL + "?id=" + id.toString(); } /** diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java index 0cd84f5d9..75617e87d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java @@ -66,7 +66,7 @@ public class ReadUtils { public static Set getSAMFileSamples(final SAMFileHeader header) { if ( header == null ) { throw new IllegalArgumentException("Missing SAM file header. " + - "For more information on read groups, see " + HelpConstants.articlePost("6472")); + "For more information on read groups, see " + HelpConstants.articlePost(6472)); } // get all of the unique sample names @@ -74,13 +74,13 @@ public class ReadUtils { final List readGroups = header.getReadGroups(); if ( readGroups == null ) { throw new UserException("SAM file header is missing the Read Group (@RG). " + - "For more information on read groups, see " + HelpConstants.articlePost("6472")); + "For more information on read groups, see " + HelpConstants.articlePost(6472)); } for ( final SAMReadGroupRecord readGroup : readGroups ) { final String sample = readGroup.getSample(); if ( sample == null ) { throw new UserException("SAM file header is missing the sample field (SM) in the Read Group (@RG). " + - "For more information on read groups, see " + HelpConstants.articlePost("6472")); + "For more information on read groups, see " + HelpConstants.articlePost(6472)); } samples.add(readGroup.getSample()); } From efbbbb1bd94b5b1e181ec7ac305d333402eb9f43 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 13:48:27 -0400 Subject: [PATCH 6/6] Add M2 to the HC annotations check --- .../gatk/tools/walkers/annotator/AnnotationUtils.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java index 70ad7c132..c8f322b08 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java @@ -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; @@ -75,7 +76,7 @@ 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; /** @@ -154,7 +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;