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Refactored maven directories and java packages replacing "sting" with "gatk". 

To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
This commit is contained in:
Khalid Shakir 2014-03-04 23:10:36 +07:00
parent 4e6d43d003
commit 2c854e554a
1457 changed files with 8211 additions and 8123 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
ant-bridge.sh
View File

@ -100,44 +100,44 @@ for arg in "${@}" ; do
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true"
mvn_args="${mvn_args} -Dgatk.packagecommittests.skipped=false"
# TODO: This runs only the queue tests (full, non-dry run), but not the commit tests for Queue.
elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
local_repo="sitetemprepo"
mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
mvn_args="${mvn_args} -Dsting.packagequeuetests.skipped=false"
mvn_args="${mvn_args} -Dsting.queuetests.run=true"
mvn_args="${mvn_args} -Dgatk.packagetests.enabled=true"
mvn_args="${mvn_args} -Dgatk.packagequeuetests.skipped=false"
mvn_args="${mvn_args} -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "committests" ]] ; then
mvn_args="verify -Dsting.committests.skipped=false"
mvn_args="verify -Dgatk.committests.skipped=false"
elif [[ "${arg}" == "test" ]] ; then
mvn_args="test -Dsting.unittests.skipped=false"
mvn_args="test -Dgatk.unittests.skipped=false"
elif [[ "${arg}" == "unittest" ]] ; then
mvn_args="test -Dsting.unittests.skipped=false"
mvn_args="test -Dgatk.unittests.skipped=false"
elif [[ "${arg}" == "integrationtest" ]] ; then
mvn_args="verify -Dsting.integrationtests.skipped=false"
mvn_args="verify -Dgatk.integrationtests.skipped=false"
elif [[ "${arg}" == "largescaletest" ]] ; then
mvn_args="verify -Dsting.largescaletests.skipped=false"
mvn_args="verify -Dgatk.largescaletests.skipped=false"
elif [[ "${arg}" == "knowledgebasetest" ]] ; then
mvn_args="verify -Dsting.knowledgebasetests.skipped=false"
mvn_args="verify -Dgatk.knowledgebasetests.skipped=false"
elif [[ "${arg}" == "queuetest" ]] ; then
mvn_args="verify -Dsting.queuetests.skipped=false"
mvn_args="verify -Dgatk.queuetests.skipped=false"
elif [[ "${arg}" == "queuetestrun" ]] ; then
mvn_args="verify -Dsting.queuetests.skipped=false -Dsting.queuetests.run=true"
mvn_args="verify -Dgatk.queuetests.skipped=false -Dgatk.queuetests.run=true"
elif [[ "${arg}" == "fasttest" ]] ; then
mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true"
mvn_args="verify -Dgatk.committests.skipped=false -pl private/gatk-tools-private -am -Dresource.bundle.skip=true"
else
unknown_args="${unknown_args} \"${arg}\""

174
pom.xml
View File

@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<!--
This pom is the aggregator for all sting/gatk poms
This pom is the aggregator for all gatk poms
See also:
http://maven.apache.org/pom.html#Inheritance_v
http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
@ -11,15 +11,15 @@
-->
<parent>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>sting-root</artifactId>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-root</artifactId>
<version>3.2-SNAPSHOT</version>
<relativePath>public/sting-root</relativePath>
<relativePath>public/gatk-root</relativePath>
</parent>
<artifactId>sting-aggregator</artifactId>
<artifactId>gatk-aggregator</artifactId>
<packaging>pom</packaging>
<name>Sting Aggregator</name>
<name>GATK Aggregator</name>
<modules>
<module>public</module>
@ -27,8 +27,8 @@
</modules>
<properties>
<sting.basedir>${project.basedir}</sting.basedir>
<resource.bundle.path>StingText.properties</resource.bundle.path>
<gatk.basedir>${project.basedir}</gatk.basedir>
<resource.bundle.path>GATKText.properties</resource.bundle.path>
<resource.bundle.skip>false</resource.bundle.skip>
<!-- TODO: Need a better a way to say "don't include hidden" by default -->
<gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
@ -36,21 +36,21 @@
<!--
Phases of the build that may be disabled to speed up compilation.
-->
<sting.jar.phase>package</sting.jar.phase>
<sting.generate-resources.phase>generate-resources</sting.generate-resources.phase>
<sting.process-resources.phase>process-resources</sting.process-resources.phase>
<sting.process-test-resources.phase>process-test-resources</sting.process-test-resources.phase>
<gatk.jar.phase>package</gatk.jar.phase>
<gatk.generate-resources.phase>generate-resources</gatk.generate-resources.phase>
<gatk.process-resources.phase>process-resources</gatk.process-resources.phase>
<gatk.process-test-resources.phase>process-test-resources</gatk.process-test-resources.phase>
<!--
Package tests ensure the consistency of the packaged / shaded jars.
It runs the tests where the monolithic jar is the only dependency on the classpath.
-->
<sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
<sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
<sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
<sting.packagequeuetests.skipped>${sting.packagecommittests.skipped}</sting.packagequeuetests.skipped>
<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
<sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
<gatk.packagecommittests.skipped>true</gatk.packagecommittests.skipped>
<gatk.packageunittests.skipped>${gatk.packagecommittests.skipped}</gatk.packageunittests.skipped>
<gatk.packageintegrationtests.skipped>${gatk.packagecommittests.skipped}</gatk.packageintegrationtests.skipped>
<gatk.packagequeuetests.skipped>${gatk.packagecommittests.skipped}</gatk.packagequeuetests.skipped>
<gatk.packagelargescaletests.skipped>true</gatk.packagelargescaletests.skipped>
<gatk.packageknowledgebasetests.skipped>true</gatk.packageknowledgebasetests.skipped>
<!--
Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
@ -59,12 +59,12 @@
TODO: Should there be another level up of tests, possibly running "all tests" via this aggregator level?
TODO: If that require the aggregator to be dependent on the child dependencies, perhaps a better approach might be another monolithic test project.
-->
<sting.serialcommittests.skipped>true</sting.serialcommittests.skipped>
<sting.serialunittests.skipped>${sting.serialcommittests.skipped}</sting.serialunittests.skipped>
<sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
<sting.serialqueuetests.skipped>${sting.serialcommittests.skipped}</sting.serialqueuetests.skipped>
<sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
<sting.serialknowledgebasetests.skipped>true</sting.serialknowledgebasetests.skipped>
<gatk.serialcommittests.skipped>true</gatk.serialcommittests.skipped>
<gatk.serialunittests.skipped>${gatk.serialcommittests.skipped}</gatk.serialunittests.skipped>
<gatk.serialintegrationtests.skipped>${gatk.serialcommittests.skipped}</gatk.serialintegrationtests.skipped>
<gatk.serialqueuetests.skipped>${gatk.serialcommittests.skipped}</gatk.serialqueuetests.skipped>
<gatk.seriallargescaletests.skipped>true</gatk.seriallargescaletests.skipped>
<gatk.serialknowledgebasetests.skipped>true</gatk.serialknowledgebasetests.skipped>
</properties>
<dependencies>
@ -121,11 +121,21 @@
<goal>unpack-dependencies</goal>
</goals>
<phase>none</phase>
<!--
NOTE: Shade include filters do NOT include transient dependencies, only the class directly listed.
Thus to fully include all the classes in packages, we must:
1) List the artifacts we want shaded as direct dependencies
2) Run the unpack direct dependencies into the classes directory
3) Shade the classes directory as we normally would.
-->
<configuration>
<excludeTransitive>true</excludeTransitive>
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
<includeTypes>jar</includeTypes>
<excludeScope>system</excludeScope>
<includeScope>runtime</includeScope>
<!-- Don't unjar the resource bundle, so that shade's AppendingTransformer can merge -->
<excludes>${resource.bundle.path}</excludes>
</configuration>
</execution>
</executions>
@ -140,14 +150,14 @@
<goals>
<goal>resources</goal>
</goals>
<phase>${sting.process-resources.phase}</phase>
<phase>${gatk.process-resources.phase}</phase>
</execution>
<execution>
<id>default-testResources</id>
<goals>
<goal>testResources</goal>
</goals>
<phase>${sting.process-test-resources.phase}</phase>
<phase>${gatk.process-test-resources.phase}</phase>
</execution>
<execution>
<id>copy-resource-bundle-log4j</id>
@ -156,10 +166,14 @@
</goals>
<phase>none</phase>
<configuration>
<!--
Just before running the resource bundle generation, copy a simple log4j
config file to the apidocs execution directory, so that logging prints out.
-->
<outputDirectory>${project.reporting.outputDirectory}/apidocs</outputDirectory>
<resources>
<resource>
<directory>${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help</directory>
<directory>${gatk.basedir}/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help</directory>
</resource>
</resources>
</configuration>
@ -179,13 +193,13 @@
<configuration>
<!-- Allow skipping for "fasttest" -->
<skip>${resource.bundle.skip}</skip>
<doclet>org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet</doclet>
<doclet>org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet</doclet>
<!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
<docletPath>${project.build.outputDirectory}</docletPath>
<docletArtifact>
<groupId>${project.groupId}</groupId>
<!-- TODO: THIS IS SUPPOSED TO BE STING-UTILS! -->
<artifactId>gatk-framework</artifactId>
<!-- TODO: THIS IS SUPPOSED TO BE GATK-UTILS! -->
<artifactId>gatk-tools-public</artifactId>
<version>${project.version}</version>
</docletArtifact>
<maxmemory>2g</maxmemory>
@ -307,14 +321,14 @@
<executions>
<execution>
<id>default-jar</id>
<phase>${sting.jar.phase}</phase>
<phase>${gatk.jar.phase}</phase>
</execution>
<execution>
<id>test-jar</id>
<goals>
<goal>test-jar</goal>
</goals>
<phase>${sting.jar.phase}</phase>
<phase>${gatk.jar.phase}</phase>
<configuration>
<skipIfEmpty>true</skipIfEmpty>
</configuration>
@ -327,7 +341,7 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>sting-executable</id>
<id>gatk-executable</id>
<goals>
<goal>shade</goal>
</goals>
@ -336,8 +350,8 @@
<minimizeJar>true</minimizeJar>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.sting:gsalib:tar.gz:*</exclude>
<exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
<exclude>org.broadinstitute.gatk:gsalib:tar.gz:*</exclude>
<exclude>org.broadinstitute.gatk:*:tar.bz2:example-resources</exclude>
</excludes>
</artifactSet>
<filters>
@ -413,7 +427,7 @@
<links>
<link>
<dst>${basedir}/public/testdata</dst>
<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
<src>${gatk.basedir}/public/gatk-engine/src/test/resources</src>
</link>
</links>
</configuration>
@ -428,7 +442,7 @@
<links>
<link>
<dst>${basedir}/public/testdata</dst>
<src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
<src>${gatk.basedir}/public/gatk-engine/src/test/resources</src>
</link>
</links>
</configuration>
@ -443,7 +457,7 @@
<links>
<link>
<dst>${basedir}/private/testdata</dst>
<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
<src>${gatk.basedir}/private/gatk-tools-private/src/test/resources</src>
</link>
</links>
</configuration>
@ -458,7 +472,7 @@
<links>
<link>
<dst>${basedir}/private/testdata</dst>
<src>${sting.basedir}/private/gatk-private/src/test/resources</src>
<src>${gatk.basedir}/private/gatk-tools-private/src/test/resources</src>
</link>
</links>
</configuration>
@ -473,7 +487,7 @@
<links>
<link>
<dst>${basedir}/public/scala/qscript</dst>
<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
<src>${gatk.basedir}/public/gatk-queue-extensions-public/src/main/qscripts</src>
</link>
</links>
</configuration>
@ -488,7 +502,7 @@
<links>
<link>
<dst>${basedir}/public/scala/qscript</dst>
<src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
<src>${gatk.basedir}/public/gatk-queue-extensions-public/src/main/qscripts</src>
</link>
</links>
</configuration>
@ -503,7 +517,7 @@
<links>
<link>
<dst>${basedir}/private/scala/qscript</dst>
<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
<src>${gatk.basedir}/private/gatk-queue-extensions-internal/src/main/qscripts</src>
</link>
</links>
</configuration>
@ -518,7 +532,27 @@
<links>
<link>
<dst>${basedir}/private/scala/qscript</dst>
<src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
<src>${gatk.basedir}/private/gatk-queue-extensions-internal/src/main/qscripts</src>
</link>
</links>
</configuration>
</execution>
<!--
HACK: Adding the source directory via build-helper-maven-plugin doesn't work with IntelliJ.
Add compatibility link from public's extensions source code to target/generated-sources.
see: http://wiki.jetbrains.net/intellij/Maven_FAQ
-->
<execution>
<id>link-extensions-sources</id>
<goals>
<goal>link</goal>
</goals>
<phase>none</phase>
<configuration>
<links>
<link>
<dst>${project.build.directory}/generated-sources/gatk-queue-extensions-public-src-main-scala</dst>
<src>${gatk.basedir}/public/gatk-queue-extensions-public/src/main/scala</src>
</link>
</links>
</configuration>
@ -532,7 +566,7 @@
<configuration>
<links>
<link>
<dst>${sting.basedir}/target/${sting.binary-dist.name}.${project.packaging}</dst>
<dst>${gatk.basedir}/target/${gatk.binary-dist.name}.${project.packaging}</dst>
<src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
</link>
</links>
@ -547,7 +581,7 @@
<configuration>
<links>
<link>
<dst>${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2</dst>
<dst>${project.build.directory}/${gatk.binary-dist.name}-${build.version}.tar.bz2</dst>
<src>${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2</src>
</link>
</links>
@ -561,19 +595,19 @@
<configuration>
<skipInvocation>true</skipInvocation>
<debug>false</debug>
<pom>${sting.basedir}/public/package-tests/pom.xml</pom>
<pom>${gatk.basedir}/public/package-tests/pom.xml</pom>
<noLog>true</noLog>
<streamLogs>true</streamLogs>
<localRepositoryPath>${sting.basedir}/${maven.repo.local}</localRepositoryPath>
<localRepositoryPath>${gatk.basedir}/${maven.repo.local}</localRepositoryPath>
<properties>
<test>${test}</test>
<it.test>${it.test}</it.test>
<skip>false</skip>
<maven.test.skip>false</maven.test.skip>
<sting.packagetests.artifactId>${sting.packagetests.artifactId}</sting.packagetests.artifactId>
<sting.packagetests.testClasses>${project.build.testOutputDirectory}</sting.packagetests.testClasses>
<sting.packagetests.basedir>${project.basedir}</sting.packagetests.basedir>
<sting.queuetests.run>${sting.queuetests.run}</sting.queuetests.run>
<gatk.packagetests.artifactId>${gatk.packagetests.artifactId}</gatk.packagetests.artifactId>
<gatk.packagetests.testClasses>${project.build.testOutputDirectory}</gatk.packagetests.testClasses>
<gatk.packagetests.basedir>${project.basedir}</gatk.packagetests.basedir>
<gatk.queuetests.run>${gatk.queuetests.run}</gatk.queuetests.run>
<maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
<maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
</properties>
@ -599,10 +633,10 @@
<goal>test</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/unit/${test}</reportsDirectory>
<skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
<skipInvocation>${gatk.packageunittests.skipped}</skipInvocation>
<properties>
<unittests.profile.enabled>true</unittests.profile.enabled>
<sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
<gatk.packageunittests.skipped>${gatk.packageunittests.skipped}</gatk.packageunittests.skipped>
</properties>
</configuration>
</execution>
@ -617,10 +651,10 @@
<goal>verify</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/integration/${it.test}</reportsDirectory>
<skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
<skipInvocation>${gatk.packageintegrationtests.skipped}</skipInvocation>
<properties>
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
<sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
<gatk.packageintegrationtests.skipped>${gatk.packageintegrationtests.skipped}</gatk.packageintegrationtests.skipped>
</properties>
</configuration>
</execution>
@ -635,10 +669,10 @@
<goal>verify</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/queuetest/${it.test}</reportsDirectory>
<skipInvocation>${sting.packagequeuetests.skipped}</skipInvocation>
<skipInvocation>${gatk.packagequeuetests.skipped}</skipInvocation>
<properties>
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
<sting.packagequeuetests.skipped>${sting.packagequeuetests.skipped}</sting.packagequeuetests.skipped>
<gatk.packagequeuetests.skipped>${gatk.packagequeuetests.skipped}</gatk.packagequeuetests.skipped>
</properties>
</configuration>
</execution>
@ -653,10 +687,10 @@
<goal>verify</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/largescale/${it.test}</reportsDirectory>
<skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
<skipInvocation>${gatk.packagelargescaletests.skipped}</skipInvocation>
<properties>
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
<sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
<gatk.packagelargescaletests.skipped>${gatk.packagelargescaletests.skipped}</gatk.packagelargescaletests.skipped>
</properties>
</configuration>
</execution>
@ -671,10 +705,10 @@
<goal>verify</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/knowledgebase/${it.test}</reportsDirectory>
<skipInvocation>${sting.packageknowledgebasetests.skipped}</skipInvocation>
<skipInvocation>${gatk.packageknowledgebasetests.skipped}</skipInvocation>
<properties>
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
<sting.packageknowledgebasetests.skipped>${sting.packageknowledgebasetests.skipped}</sting.packageknowledgebasetests.skipped>
<gatk.packageknowledgebasetests.skipped>${gatk.packageknowledgebasetests.skipped}</gatk.packageknowledgebasetests.skipped>
</properties>
</configuration>
</execution>
@ -776,7 +810,7 @@
<!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
<inherited>false</inherited>
<configuration>
<doclet>org.broadinstitute.sting.utils.help.GATKDoclet</doclet>
<doclet>org.broadinstitute.gatk.utils.help.GATKDoclet</doclet>
<docletArtifact>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-package</artifactId>
@ -785,7 +819,7 @@
<useStandardDocletOptions>false</useStandardDocletOptions>
<quiet>true</quiet>
<show>private</show>
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${sting.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs</additionalparam>
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs</additionalparam>
</configuration>
</reportSet>
</reportSets>
@ -852,17 +886,17 @@
<id>packagetests-enabled</id>
<activation>
<property>
<name>sting.packagetests.enabled</name>
<name>gatk.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<maven.javadoc.skip>true</maven.javadoc.skip>
<sting.generate-gatk-extensions.skipped>true</sting.generate-gatk-extensions.skipped>
<sting.jar.phase>none</sting.jar.phase>
<sting.generate-resources.phase>none</sting.generate-resources.phase>
<sting.process-resources.phase>none</sting.process-resources.phase>
<sting.process-test-resources.phase>none</sting.process-test-resources.phase>
<gatk.generate-gatk-extensions.skipped>true</gatk.generate-gatk-extensions.skipped>
<gatk.jar.phase>none</gatk.jar.phase>
<gatk.generate-resources.phase>none</gatk.generate-resources.phase>
<gatk.process-resources.phase>none</gatk.process-resources.phase>
<gatk.process-test-resources.phase>none</gatk.process-test-resources.phase>
</properties>
</profile>
</profiles>

138
protected/gatk-package-distribution/pom.xml
View File

@ -3,29 +3,44 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>sting-aggregator</artifactId>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-aggregator</artifactId>
<version>3.2-SNAPSHOT</version>
<relativePath>../..</relativePath>
</parent>
<artifactId>gatk-package</artifactId>
<artifactId>gatk-package-distribution</artifactId>
<packaging>jar</packaging>
<name>GATK Package</name>
<name>GATK Package Distribution</name>
<properties>
<sting.basedir>${project.basedir}/../..</sting.basedir>
<sting.unpack.phase>prepare-package</sting.unpack.phase>
<sting.shade.phase>package</sting.shade.phase>
<app.main.class>org.broadinstitute.sting.gatk.CommandLineGATK</app.main.class>
<sting.binary-dist.name>GenomeAnalysisTK</sting.binary-dist.name>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
<app.main.class>org.broadinstitute.gatk.engine.CommandLineGATK</app.main.class>
<gatk.binary-dist.name>GenomeAnalysisTK</gatk.binary-dist.name>
</properties>
<dependencies>
<!-- Package everything in org.broadinstitute.sting -->
<!-- Package everything in org.broadinstitute.gatk -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-engine</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-public</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-protected</artifactId>
<version>${project.version}</version>
</dependency>
<!-- Tribble codecs & the variant package (VCF, BCF, and VariantContext) -->
@ -46,26 +61,29 @@
<!-- Required for binary-dist assembly, excluded by shade -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-engine</artifactId>
<version>${project.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>
</dependency>
<!-- Test dependencies to run for for serial tests -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-tools-public</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-protected</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<scope>test</scope>
</dependency>
<!-- Transitive dependencies for the serial test artifacts above -->
<dependency>
<groupId>com.google.caliper</groupId>
<artifactId>caliper</artifactId>
@ -82,9 +100,9 @@
<execution>
<id>unit-tests</id>
<configuration>
<skip>${sting.serialunittests.skipped}</skip>
<skip>${gatk.serialunittests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
@ -98,36 +116,36 @@
<execution>
<id>integration-tests</id>
<configuration>
<skip>${sting.serialintegrationtests.skipped}</skip>
<skip>${gatk.serialintegrationtests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>queue-tests</id>
<configuration>
<skip>${sting.serialqueuetests.skipped}</skip>
<skip>${gatk.serialqueuetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>large-scale-tests</id>
<configuration>
<skip>${sting.seriallargescaletests.skipped}</skip>
<skip>${gatk.seriallargescaletests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>knowledge-base-tests</id>
<configuration>
<skip>${sting.serialknowledgebasetests.skipped}</skip>
<skip>${gatk.serialknowledgebasetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
@ -140,7 +158,7 @@
<executions>
<execution>
<id>unpack-direct-dependencies</id>
<phase>${sting.unpack.phase}</phase>
<phase>${gatk.unpack.phase}</phase>
</execution>
</executions>
</plugin>
@ -150,8 +168,8 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>sting-executable</id>
<phase>${sting.shade.phase}</phase>
<id>gatk-executable</id>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -162,7 +180,7 @@
<executions>
<execution>
<id>binary-dist</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -173,11 +191,11 @@
<executions>
<execution>
<id>link-binary-jar</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
<execution>
<id>link-git-release</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -202,52 +220,12 @@
<profiles>
<profile>
<id>protected</id>
<id>private-testdata</id>
<activation>
<file>
<exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
<exists>${basedir}/../../private/pom.xml</exists>
</file>
</activation>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-protected</artifactId>
<version>${project.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-protected</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
<optional>true</optional>
</dependency>
</dependencies>
</profile>
<profile>
<id>private</id>
<activation>
<file>
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
</file>
</activation>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-private</artifactId>
<version>${project.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-private</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
<optional>true</optional>
</dependency>
</dependencies>
<build>
<plugins>
<!-- TODO: All tests require access to private. For now. -->
@ -272,13 +250,13 @@
<id>packagetests-enabled</id>
<activation>
<property>
<name>sting.packagetests.enabled</name>
<name>gatk.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<sting.unpack.phase>none</sting.unpack.phase>
<sting.shade.phase>none</sting.shade.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
</profiles>

6
protected/gatk-package-distribution/src/main/assembly/binary-dist.xml
View File

@ -7,15 +7,15 @@
<dependencySets>
<dependencySet>
<includes>
<include>org.broadinstitute.sting:gatk-package</include>
<include>org.broadinstitute.gatk:gatk-package-distribution</include>
</includes>
<outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
<outputFileNameMapping>${gatk.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
</dependencySet>
<dependencySet>
<outputDirectory>resources</outputDirectory>
<unpack>true</unpack>
<includes>
<include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
<include>org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources</include>
</includes>
</dependencySet>
</dependencySets>

109
protected/gatk-queue-package-distribution/pom.xml
View File

@ -3,34 +3,39 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>sting-aggregator</artifactId>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-aggregator</artifactId>
<version>3.2-SNAPSHOT</version>
<relativePath>../..</relativePath>
</parent>
<artifactId>queue-package</artifactId>
<artifactId>gatk-queue-package-distribution</artifactId>
<packaging>jar</packaging>
<name>Queue Package</name>
<name>GATK Queue Package Distribution</name>
<properties>
<sting.basedir>${project.basedir}/../..</sting.basedir>
<sting.unpack.phase>prepare-package</sting.unpack.phase>
<sting.shade.phase>package</sting.shade.phase>
<sting.binary-dist.name>Queue</sting.binary-dist.name>
<app.main.class>org.broadinstitute.sting.queue.QCommandLine</app.main.class>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
<gatk.binary-dist.name>Queue</gatk.binary-dist.name>
<app.main.class>org.broadinstitute.gatk.queue.QCommandLine</app.main.class>
</properties>
<dependencies>
<!-- Queue -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>queue-framework</artifactId>
<artifactId>gatk-queue</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-package</artifactId>
<artifactId>gatk-package-distribution</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-queue-extensions-distribution</artifactId>
<version>${project.version}</version>
</dependency>
<!-- Scala -->
@ -75,41 +80,29 @@
<!-- Required for binary-dist assembly, excluded by shade -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-engine</artifactId>
<version>${project.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>queue-framework</artifactId>
<artifactId>gatk-queue-extensions-public</artifactId>
<version>${project.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>
</dependency>
<!-- Test dependencies to run for for serial tests -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>queue-framework</artifactId>
<artifactId>gatk-queue</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<scope>test</scope>
</dependency>
<!-- Transitive dependencies for the serial test artifacts above -->
<dependency>
<groupId>com.google.caliper</groupId>
<artifactId>caliper</artifactId>
@ -126,9 +119,9 @@
<execution>
<id>unit-tests</id>
<configuration>
<skip>${sting.serialunittests.skipped}</skip>
<skip>${gatk.serialunittests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
@ -142,36 +135,36 @@
<execution>
<id>integration-tests</id>
<configuration>
<skip>${sting.serialintegrationtests.skipped}</skip>
<skip>${gatk.serialintegrationtests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>queue-tests</id>
<configuration>
<skip>${sting.serialqueuetests.skipped}</skip>
<skip>${gatk.serialqueuetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>large-scale-tests</id>
<configuration>
<skip>${sting.seriallargescaletests.skipped}</skip>
<skip>${gatk.seriallargescaletests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
<execution>
<id>knowledge-base-tests</id>
<configuration>
<skip>${sting.serialknowledgebasetests.skipped}</skip>
<skip>${gatk.serialknowledgebasetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
<scan>org.broadinstitute.gatk:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
@ -184,7 +177,7 @@
<executions>
<execution>
<id>unpack-direct-dependencies</id>
<phase>${sting.unpack.phase}</phase>
<phase>${gatk.unpack.phase}</phase>
</execution>
</executions>
</plugin>
@ -194,8 +187,8 @@
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<id>sting-executable</id>
<phase>${sting.shade.phase}</phase>
<id>gatk-executable</id>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -206,7 +199,7 @@
<executions>
<execution>
<id>binary-dist</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -217,11 +210,11 @@
<executions>
<execution>
<id>link-binary-jar</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
<execution>
<id>link-git-release</id>
<phase>${sting.shade.phase}</phase>
<phase>${gatk.shade.phase}</phase>
</execution>
</executions>
</plugin>
@ -246,35 +239,19 @@
<profiles>
<profile>
<id>private</id>
<id>private-testdata</id>
<activation>
<file>
<exists>${basedir}/../../private/queue-private/pom.xml</exists>
<exists>${basedir}/../../private/pom.xml</exists>
</file>
</activation>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>queue-private</artifactId>
<version>${project.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>queue-private</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
<optional>true</optional>
</dependency>
</dependencies>
<build>
<plugins>
<!-- TODO: All tests require access to private. For now. -->
<plugin>
<groupId>com.pyx4j</groupId>
<artifactId>maven-junction-plugin</artifactId>
<executions>
<!-- TODO: All tests require access to private. For now. -->
<execution>
<id>link-private-testdata</id>
<phase>process-test-resources</phase>
@ -300,13 +277,13 @@
<id>packagetests-enabled</id>
<activation>
<property>
<name>sting.packagetests.enabled</name>
<name>gatk.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<sting.unpack.phase>none</sting.unpack.phase>
<sting.shade.phase>none</sting.shade.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>
</profiles>

8
protected/gatk-queue-package-distribution/src/main/assembly/binary-dist.xml
View File

@ -7,16 +7,16 @@
<dependencySets>
<dependencySet>
<includes>
<include>org.broadinstitute.sting:queue-package</include>
<include>org.broadinstitute.gatk:gatk-queue-package-distribution</include>
</includes>
<outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
<outputFileNameMapping>${gatk.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
</dependencySet>
<dependencySet>
<outputDirectory>resources</outputDirectory>
<unpack>true</unpack>
<includes>
<include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
<include>org.broadinstitute.sting:queue-framework:tar.bz2:example-resources</include>
<include>org.broadinstitute.gatk:gatk-engine:tar.bz2:example-resources</include>
<include>org.broadinstitute.gatk:gatk-queue-extensions-public:tar.bz2:example-resources</include>
</includes>
</dependencySet>
</dependencySets>

31
protected/gatk-tools-protected/pom.xml
View File

@ -3,25 +3,31 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>sting-aggregator</artifactId>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-aggregator</artifactId>
<version>3.2-SNAPSHOT</version>
<relativePath>../..</relativePath>
</parent>
<artifactId>gatk-protected</artifactId>
<artifactId>gatk-tools-protected</artifactId>
<packaging>jar</packaging>
<name>GATK Protected</name>
<name>GATK Tools Protected</name>
<properties>
<sting.basedir>${project.basedir}/../..</sting.basedir>
<sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.packagetests.artifactId>gatk-package-distribution</gatk.packagetests.artifactId>
</properties>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-engine</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-public</artifactId>
<version>${project.version}</version>
</dependency>
@ -42,17 +48,12 @@
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
<artifactId>gatk-tools-public</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.caliper</groupId>
<artifactId>caliper</artifactId>
@ -108,10 +109,10 @@
<profiles>
<profile>
<id>private</id>
<id>private-testdata</id>
<activation>
<file>
<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
<exists>${basedir}/../../private/pom.xml</exists>
</file>
</activation>
<build>

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java
View File

@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.arguments;
package org.broadinstitute.gatk.engine.arguments;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingOutputMode;
import org.broadinstitute.sting.gatk.walkers.genotyper.OutputMode;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.collections.DefaultHashMap;
import org.broadinstitute.sting.utils.variant.HomoSapiensConstants;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode;
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.gatk.utils.collections.DefaultHashMap;
import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
import htsjdk.variant.variantcontext.VariantContext;
import java.io.File;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java
View File

@ -44,4 +44,4 @@
* 7.7 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.sting;
package org.broadinstitute.gatk;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java
View File

@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import java.util.*;

22
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java
View File

@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java
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@ -44,13 +44,13 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.util.*;

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java
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@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java
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@ -44,22 +44,22 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFFormatHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeBuilder;

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java
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@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeBuilder;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java
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@ -44,23 +44,23 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import cern.jet.math.Arithmetic;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.QualityUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java
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@ -44,21 +44,21 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays;

20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java
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@ -44,17 +44,17 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeaderLineType;

38
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
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@ -44,27 +44,27 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
@ -261,7 +261,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final byte[] b = haplotypeB.getBases();
if (a.length != b.length) {
throw new ReviewedStingException("Haplotypes a and b must be of same length");
throw new ReviewedGATKException("Haplotypes a and b must be of same length");
}
byte chA, chB;

20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java
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@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import htsjdk.tribble.util.popgen.HardyWeinbergCalculation;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.WorkInProgressAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.QualityUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.Genotype;

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java
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@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.GenomeLoc;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;

22
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
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@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.MathUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.Genotype;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java
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@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;

25
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
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@ -44,22 +44,21 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Trio;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.samples.Trio;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.MendelianViolation;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.*;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java
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@ -44,13 +44,13 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.util.*;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
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@ -44,22 +44,22 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java
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@ -44,19 +44,19 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.Genotype;

26
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java
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@ -44,23 +44,23 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.*;

32
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java
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@ -44,24 +44,24 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MannWhitneyU;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.MannWhitneyU;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypesContext;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java
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@ -44,20 +44,20 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import java.util.*;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java
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@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
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@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java
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@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeBuilder;
import htsjdk.variant.variantcontext.VariantContext;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java
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@ -44,9 +44,9 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypesContext;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java
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@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;

20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
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@ -44,17 +44,17 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.utils.collections.Pair;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -44,22 +44,22 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.samples.Sample;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.MathUtils;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.*;

16
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java
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@ -44,15 +44,15 @@
* 7.7 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.sting.gatk.walkers.annotator;
package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.IndelUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.IndelUtils;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;

32
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java
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@ -43,24 +43,24 @@
* 7.6 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.
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.recalibration.RecalUtils;
import org.broadinstitute.sting.utils.recalibration.RecalibrationReport;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Input;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.RodWalker;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.recalibration.RecalUtils;
import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport;
import org.broadinstitute.gatk.utils.recalibration.BaseRecalibration;
import java.io.File;
import java.io.FileNotFoundException;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java
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@ -44,15 +44,15 @@
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import org.apache.commons.collections.CollectionUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Gatherer;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.RecalibrationReport;
import org.broadinstitute.gatk.utils.commandline.Gatherer;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport;
import java.io.File;
import java.io.FileNotFoundException;
@ -125,7 +125,7 @@ public class BQSRGatherer extends Gatherer {
generalReport.combine(inputReport);
}
if (generalReport == null)
throw new ReviewedStingException(EMPTY_INPUT_LIST);
throw new ReviewedGATKException(EMPTY_INPUT_LIST);
generalReport.calculateQuantizedQualities();

54
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java
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@ -44,34 +44,34 @@
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.tribble.Feature;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.recalibration.*;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.utils.commandline.Advanced;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.filters.*;
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.baq.BAQ;
import org.broadinstitute.gatk.utils.clipping.ReadClipper;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.recalibration.*;
import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import java.io.IOException;
import java.io.PrintStream;
@ -357,7 +357,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
case P:
break;
default:
throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator());
}
}
return snp;
@ -400,7 +400,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
case P:
break;
default:
throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator());
throw new ReviewedGATKException("Unsupported cigar operator: " + ce.getOperator());
}
}
return indel;
@ -414,7 +414,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
protected static double[] calculateFractionalErrorArray( final int[] errorArray, final byte[] baqArray ) {
if(errorArray.length != baqArray.length ) {
throw new ReviewedStingException("Array length mismatch detected. Malformed read?");
throw new ReviewedGATKException("Array length mismatch detected. Malformed read?");
}
final int BLOCK_START_UNSET = -1;
@ -442,7 +442,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
calculateAndStoreErrorsInBlock(iii-1, blockStartIndex, errorArray, fractionalErrors);
}
if( fractionalErrors.length != errorArray.length ) {
throw new ReviewedStingException("Output array length mismatch detected. Malformed read?");
throw new ReviewedGATKException("Output array length mismatch detected. Malformed read?");
}
return fractionalErrors;
}

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java
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@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.recalibration.EventType;
import org.broadinstitute.gatk.utils.recalibration.ReadCovariates;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
/**
* Created with IntelliJ IDEA.

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -44,15 +44,15 @@
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import com.google.java.contract.Requires;
import htsjdk.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.recalibration.RecalUtils;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.report.GATKReportTable;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.GATKException;
import org.broadinstitute.gatk.utils.recalibration.RecalUtils;
import java.io.File;
import java.io.PrintStream;
@ -407,7 +407,7 @@ public class RecalibrationArgumentCollection implements Cloneable {
try {
return (RecalibrationArgumentCollection) super.clone();
} catch (CloneNotSupportedException e) {
throw new StingException("Unreachable code clone not supported thrown when the class "
throw new GATKException("Unreachable code clone not supported thrown when the class "
+ this.getClass().getName() + " is cloneable ",e);
}
}

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java
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@ -44,13 +44,13 @@
* 7.7 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.sting.gatk.walkers.bqsr;
package org.broadinstitute.gatk.tools.walkers.bqsr;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.recalibration.*;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.collections.NestedIntegerArray;
import org.broadinstitute.gatk.utils.recalibration.*;
import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.util.LinkedList;

26
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java
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@ -44,20 +44,20 @@
* 7.7 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.sting.gatk.walkers.diagnostics;
package org.broadinstitute.gatk.tools.walkers.diagnostics;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.walkers.LocusWalker;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.ArrayList;

32
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java
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@ -44,22 +44,22 @@
* 7.7 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.sting.gatk.walkers.diagnostics;
package org.broadinstitute.gatk.tools.walkers.diagnostics;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.ActiveRegionTraversalParameters;
import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker;
import org.broadinstitute.gatk.engine.walkers.PartitionBy;
import org.broadinstitute.gatk.engine.walkers.PartitionType;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import java.io.PrintStream;
@ -126,7 +126,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
}
@Override
public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
public GenomeLoc map(final org.broadinstitute.gatk.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
if ((!outputUncovered && activeRegion.isActive()) || (outputUncovered && !activeRegion.isActive()))
return activeRegion.getLocation();

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import java.util.HashMap;
import java.util.LinkedList;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* Short one line description of the walker.

32
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -44,24 +44,24 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import htsjdk.samtools.util.PeekableIterator;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.SampleUtils;
import org.broadinstitute.gatk.utils.classloader.PluginManager;
import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.*;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java
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@ -44,13 +44,13 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import java.util.*;
@ -103,7 +103,7 @@ final class IntervalStratification extends AbstractStratification {
SampleStratification sampleStratification = (SampleStratification) samples.get(sample);
if (sampleStratification == null)
throw new ReviewedStingException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample));
throw new ReviewedGATKException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample));
sampleStratification.addLocus(context.getLocation(), samplePileup);
}

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import java.util.List;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
*

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import java.util.Map;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* Created with IntelliJ IDEA.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
/**
* User: carneiro

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java
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@ -44,12 +44,12 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.util.ArrayList;
import java.util.LinkedList;
@ -92,7 +92,7 @@ final class SampleStratification extends AbstractStratification {
*/
public void addLocus(GenomeLoc locus, ReadBackedPileup pileup) {
if (!interval.containsP(locus))
throw new ReviewedStingException(String.format("Locus %s is not part of the Interval %s", locus, interval));
throw new ReviewedGATKException(String.format("Locus %s is not part of the Interval %s", locus, interval));
// a null pileup means there nothing to add
if (pileup != null) {

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java
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@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.diagnostics.diagnosetargets;
package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Output;
import java.io.PrintStream;
import java.util.LinkedList;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.diagnostics.missing;
package org.broadinstitute.gatk.tools.walkers.diagnostics.missing;
/**
* Metrics class for the QualifyMissingInterval walker

38
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -44,26 +44,26 @@
* 7.7 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.sting.gatk.walkers.diagnostics.missing;
package org.broadinstitute.gatk.tools.walkers.diagnostics.missing;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Gather;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportGatherer;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Gather;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.report.GATKReportGatherer;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.GenomeLocSortedSet;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.interval.IntervalUtils;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;
import java.util.List;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
public enum BaseMismatchModel {
THREE_STATE,

26
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java
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@ -44,21 +44,21 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.clipping.ReadClipper;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import htsjdk.variant.variantcontext.*;
import java.util.*;

20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.samtools.SAMUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fragments.FragmentCollection;
import org.broadinstitute.sting.utils.fragments.FragmentUtils;
import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
import org.broadinstitute.gatk.utils.fragments.FragmentUtils;
import org.broadinstitute.gatk.utils.genotyper.DiploidGenotype;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import java.util.List;

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java
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@ -44,17 +44,17 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;

22
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
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@ -44,17 +44,17 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACcounts;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.gatk.utils.MathUtils;
import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
@ -124,7 +124,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods {
Arrays.fill(log10Likelihoods, MIN_LIKELIHOOD);
} else {
if (logLikelihoods.length != likelihoodDim)
throw new ReviewedStingException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object");
throw new ReviewedGATKException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object");
log10Likelihoods = logLikelihoods; //.clone(); // is clone needed?
}
@ -192,7 +192,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods {
if (restrictSumTo > 0) {
// check that desired vector is valid
if (MathUtils.sum(stateVector) != restrictSumTo)
throw new ReviewedStingException("BUG: initial state vector nor compatible with sum iterator");
throw new ReviewedGATKException("BUG: initial state vector nor compatible with sum iterator");
final int numAlleles = currentState.length;
final int ploidy = restrictSumTo;
@ -200,7 +200,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods {
linearIndex = GeneralPloidyGenotypeLikelihoods.getLinearIndex(stateVector, numAlleles, ploidy);
}
else
throw new ReviewedStingException("BUG: Not supported");
throw new ReviewedGATKException("BUG: Not supported");
}
public void next() {

32
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
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@ -44,21 +44,21 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.*;
import java.util.*;
@ -180,11 +180,11 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
final double topLogGL = mlACPair.second;
if (sampleData.GL.getAlleles().size() != allAlleles.size())
throw new ReviewedStingException("BUG: inconsistent size of alleles!");
throw new ReviewedGATKException("BUG: inconsistent size of alleles!");
// ref allele is always first in array list
if (sampleData.GL.alleles.get(0).isNonReference())
throw new ReviewedStingException("BUG: first allele in list is not reference!");
throw new ReviewedGATKException("BUG: first allele in list is not reference!");
double refGL = sampleData.GL.getLikelihoods()[REFERENCE_IDX];
@ -219,7 +219,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
final List<Allele> allAllelesToUse,
final boolean useBAQedPileup,
final GenomeLocParser locParser,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
HashMap<String, ErrorModel> perLaneErrorModels = getPerLaneErrorModels(tracker, ref, contexts);
if (perLaneErrorModels == null && UAC.referenceSampleName != null)
@ -357,7 +357,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
final boolean useBQAedPileup,
final ReferenceContext ref,
final boolean ignoreLaneInformation,
final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap);
final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap);
protected abstract List<Allele> getInitialAllelesToUse(final RefMetaDataTracker tracker,
final ReferenceContext ref,

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
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@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Allele;
import java.util.*;
@ -73,7 +73,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
double[][] readHaplotypeLikelihoods;
final byte refBase;
final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;
final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;
public GeneralPloidyIndelGenotypeLikelihoods(final List<Allele> alleles,
final double[] logLikelihoods,
@ -83,7 +83,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
final PairHMMIndelErrorModel pairModel,
final LinkedHashMap<Allele, Haplotype> haplotypeMap,
final ReferenceContext referenceContext,
final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) {
final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) {
super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation);
this.pairModel = pairModel;
this.haplotypeMap = haplotypeMap;
@ -204,7 +204,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
}
if (refAllele == null)
throw new ReviewedStingException("BUG: no ref alleles in passed in allele list!");
throw new ReviewedGATKException("BUG: no ref alleles in passed in allele list!");
// count number of elements in pileup
for (PileupElement elt : pileup) {

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
View File

@ -44,16 +44,16 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import htsjdk.variant.variantcontext.*;
import java.util.*;
@ -96,7 +96,7 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener
final boolean useBQAedPileup,
final ReferenceContext ref,
final boolean ignoreLaneInformation,
final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
return new GeneralPloidyIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref, perReadAlleleLikelihoodMap);
}

20
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
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@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
import htsjdk.variant.variantcontext.Allele;
import java.util.ArrayList;
@ -101,7 +101,7 @@ public class GeneralPloidySNPGenotypeLikelihoods extends GeneralPloidyGenotypeLi
Allele refAllele = alleles.get(0);
//sanity check: by construction, first allele should ALWAYS be the reference alleles
if (!refAllele.isReference())
throw new ReviewedStingException("BUG: First allele in list passed to GeneralPloidySNPGenotypeLikelihoods should be reference!");
throw new ReviewedGATKException("BUG: First allele in list passed to GeneralPloidySNPGenotypeLikelihoods should be reference!");
refByte = refAllele.getBases()[0]; // by construction, first allele in list is always ref!

18
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
View File

@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/*
* Copyright (c) 2010.
*
@ -72,13 +72,13 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
import htsjdk.variant.variantcontext.*;
import java.util.*;
@ -98,7 +98,7 @@ public class GeneralPloidySNPGenotypeLikelihoodsCalculationModel extends General
final boolean useBQAedPileup,
final ReferenceContext ref,
final boolean ignoreLaneInformation,
final org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
final org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap){
return new GeneralPloidySNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO);
}

24
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
View File

@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
@ -88,7 +88,7 @@ public abstract class GenotypeLikelihoodsCalculationModel {
* @param UAC unified arg collection
*/
protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
if ( logger == null || UAC == null ) throw new ReviewedStingException("Bad arguments");
if ( logger == null || UAC == null ) throw new ReviewedGATKException("Bad arguments");
this.UAC = UAC;
this.logger = logger;
}
@ -112,7 +112,7 @@ public abstract class GenotypeLikelihoodsCalculationModel {
final List<Allele> allAllelesToUse,
final boolean useBAQedPileup,
final GenomeLocParser locParser,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap);
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap);
protected int getFilteredDepth(ReadBackedPileup pileup) {

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java
View File

@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
public interface GenotypePriors {

42
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
View File

@ -44,29 +44,29 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalc;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFConstants;
@ -228,7 +228,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model,
final boolean inheritAttributesFromInputVC,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;
// if input VC can't be genotyped, exit with either null VCC or, in case where we need to emit all sites, an empty call
@ -653,7 +653,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
protected Map<String,Object> composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc,
final AlignmentContext rawContext, final Map<String, AlignmentContext> stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List<Integer> alleleCountsofMLE, final boolean bestGuessIsRef,
final AFCalcResult AFresult, final List<Allele> allAllelesToUse, final GenotypesContext genotypes,
final GenotypeLikelihoodsCalculationModel.Model model, final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final GenotypeLikelihoodsCalculationModel.Model model, final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final HashMap<String, Object> attributes = new HashMap<>();
final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java
View File

@ -43,7 +43,7 @@
* 7.6 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.
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/**
* Enumeration of possible genotyping modes.

26
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -44,21 +44,21 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.*;
import java.util.*;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java
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@ -43,7 +43,7 @@
* 7.6 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.
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/**
* TODO document this.

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java
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@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.gatk.tools.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.gatk.utils.MathUtils;
public class PoolGenotypePriors implements GenotypePriors {
private final double[] flatPriors;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java
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@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.util.Arrays;
@ -75,7 +75,7 @@ public class ProbabilityVector {
int maxValIdx = MathUtils.maxElementIndex(vec);
double maxv = vec[maxValIdx];
if (maxv > 0.0)
throw new ReviewedStingException("BUG: Attempting to create a log-probability vector with positive elements");
throw new ReviewedGATKException("BUG: Attempting to create a log-probability vector with positive elements");
if (compressRange) {
minVal = getMinIdx(vec, maxValIdx);

34
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -44,25 +44,25 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.baq.BAQ;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.genotyper.DiploidGenotype;
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
import htsjdk.variant.variantcontext.*;
import java.util.*;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java
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@ -44,11 +44,11 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.gatk.utils.pairhmm.PairHMM;
import htsjdk.variant.variantcontext.VariantContext;
public class UnifiedArgumentCollection extends StandardCallerArgumentCollection {

44
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
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@ -44,29 +44,29 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
import org.broadinstitute.gatk.engine.filters.BadMateFilter;
import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter;
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.utils.SampleUtils;
import org.broadinstitute.gatk.utils.baq.BAQ;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
@ -179,7 +179,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
/**
* A raw, unfiltered, highly sensitive callset in VCF format.
*/
//@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
//@Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer")
@Output(doc="File to which variants should be written")
protected VariantContextWriter writer = null;

46
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -43,25 +43,25 @@
* 7.6 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.
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.baq.BAQ;
import org.broadinstitute.gatk.utils.classloader.PluginManager;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypesContext;
import htsjdk.variant.variantcontext.VariantContext;
@ -173,7 +173,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, rawContext);
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = new HashMap<>();
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = new HashMap<>();
final VariantCallContext defaultResult = configuration.outputMode == OutputMode.EMIT_ALL_SITES
&& configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
@ -237,7 +237,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
public VariantContext calculateLikelihoods(final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, rawContext);
if ( models.isEmpty() ) {
return null;
@ -303,7 +303,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
final List<Allele> alternateAllelesToUse,
final boolean useBAQedPileup,
final GenotypeLikelihoodsCalculationModel.Model model,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
return glcm.get().get(model.name()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser, perReadAlleleLikelihoodMap);
}
@ -319,7 +319,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final GenotypeLikelihoodsCalculationModel.Model model,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap);
}
@ -333,7 +333,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model,
final boolean inheritAttributesFromInputVC,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;
final VariantCallContext result = super.calculateGenotypes(tracker,refContext,rawContext,stratifiedContexts,vc,model,inheritAttributesFromInputVC,perReadAlleleLikelihoodMap);
if ( verboseWriter != null && !limitedContext )
@ -356,7 +356,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
protected Map<String,Object> composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc,
final AlignmentContext rawContext, final Map<String, AlignmentContext> stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List<Integer> alleleCountsofMLE, final boolean bestGuessIsRef,
final AFCalcResult AFresult, final List<Allele> allAllelesToUse, final GenotypesContext genotypes,
final GenotypeLikelihoodsCalculationModel.Model model, final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final GenotypeLikelihoodsCalculationModel.Model model, final Map<String, org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
final Map<String,Object> result = super.composeCallAttributes(inheritAttributesFromInputVC, vc,rawContext,stratifiedContexts,tracker,refContext,alleleCountsofMLE,bestGuessIsRef,
AFresult,allAllelesToUse,genotypes,model,perReadAlleleLikelihoodMap);

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.genotyper;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.VariantContext;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalc.java
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@ -44,12 +44,12 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.gatk.utils.SimpleTimer;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypesContext;
import htsjdk.variant.variantcontext.VariantContext;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcFactory.java
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@ -44,14 +44,14 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.classloader.PluginManager;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import java.lang.reflect.Constructor;
import java.util.LinkedList;
@ -247,7 +247,7 @@ public class AFCalcFactory {
Constructor c = afClass.getDeclaredConstructor(int.class, int.class, int.class);
return (AFCalc)c.newInstance(args);
} catch (Exception e) {
throw new ReviewedStingException("Could not instantiate AFCalc " + calc, e);
throw new ReviewedGATKException("Could not instantiate AFCalc " + calc, e);
}
}

16
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
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@ -44,18 +44,18 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Logger;
import org.apache.log4j.TTCCLayout;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.report.GATKReportTable;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.SimpleTimer;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcResult.java
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@ -44,12 +44,12 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.Utils;
import htsjdk.variant.variantcontext.Allele;
import java.util.*;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalcTestBuilder.java
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@ -44,12 +44,12 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.Utils;
import htsjdk.variant.variantcontext.*;
import java.util.ArrayList;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalc.java
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@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import htsjdk.variant.variantcontext.GenotypesContext;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java
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@ -44,7 +44,7 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import java.util.Arrays;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java
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@ -44,9 +44,9 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import java.util.Arrays;

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalc.java
View File

@ -44,10 +44,10 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.variantcontext.*;
import java.util.*;
@ -58,7 +58,7 @@ import java.util.*;
abstract class ExactAFCalc extends AFCalc {
protected static final int HOM_REF_INDEX = 0; // AA likelihoods are always first
/**
* Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first.
* Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first.
*/
protected static final Comparator<LikelihoodSum> LIKELIHOOD_SUM_COMPARATOR = new Comparator<LikelihoodSum>() {
@ -68,7 +68,7 @@ abstract class ExactAFCalc extends AFCalc {
}
};
/**
* Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first but make sure that
* Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with higher likelihood are first but make sure that
* NON_REF alleles are place are last.
*/
protected static final Comparator<LikelihoodSum> LIKELIHOOD_NON_REF_THEN_SUM_COMPARATOR = new Comparator<LikelihoodSum>() {
@ -83,7 +83,7 @@ abstract class ExactAFCalc extends AFCalc {
}
};
/**
* Sorts {@link org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with lower alternative allele index are first regardless of
* Sorts {@link org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactAFCalc.LikelihoodSum} instances where those with lower alternative allele index are first regardless of
* the likelihood sum.
*/
protected static final Comparator<LikelihoodSum> LIKELIHOOD_INDEX_COMPARATOR = new Comparator<LikelihoodSum>() {

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java
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@ -44,12 +44,12 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import com.google.java.contract.Requires;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import htsjdk.variant.variantcontext.*;
import java.io.*;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
View File

@ -44,13 +44,13 @@
* 7.7 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.sting.gatk.walkers.genotyper.afcalc;
package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import htsjdk.variant.variantcontext.*;
import java.util.*;
@ -306,7 +306,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
// final int dim2 = GenotypeLikelihoods.numLikelihoods(numAlleles, ploidy2);
//
// if (dim1 != originalPool.getLength() || dim2 != yy.length)
// throw new ReviewedStingException("BUG: Inconsistent vector length");
// throw new ReviewedGATKException("BUG: Inconsistent vector length");
//
// if (ploidy2 == 0)
// return;
@ -367,7 +367,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
// sanity check
int totalAltK = set.getACsum();
if (newPloidy != totalAltK)
throw new ReviewedStingException("BUG: inconsistent sizes of set.getACsum and passed ploidy values");
throw new ReviewedGATKException("BUG: inconsistent sizes of set.getACsum and passed ploidy values");
totalAltK -= set.getACcounts().getCounts()[0];
// totalAltK has sum of alt alleles of conformation now

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