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Merge remote-tracking branch 'unstable/master'

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2 parents 2cc9ef8 + 2941c08 commit 28e02c2adb0f5fac9cc3f0ced1ca2943d97d8f21 @eitanbanks eitanbanks committed Dec 17, 2012
Showing with 5,324 additions and 3,150 deletions.
  1. +86 −47 build.xml
  2. +4 −7 ivy.xml
  3. +11 −7 public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
  4. +17 −17 public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
  5. +21 −6 public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
  6. +7 −7 public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
  7. +5 −4 public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
  8. +3 −4 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
  9. +0 −228 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ExperimentalReadShardBalancer.java
  10. +5 −1 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
  11. +129 −0 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LegacyReadShardBalancer.java
  12. +143 −44 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
  13. +55 −22 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
  14. +26 −22 public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java
  15. +106 −0 public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java
  16. +0 −4 public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
  17. +7 −6 public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
  18. +415 −102 ...te/sting/gatk/iterators/{LocusIteratorByStateExperimental.java → LegacyLocusIteratorByState.java}
  19. +111 −412 public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
  20. +2 −2 public/java/src/org/broadinstitute/sting/gatk/iterators/ReadTransformer.java
  21. +13 −2 public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
  22. +3 −0 public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
  23. +111 −99 public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
  24. +18 −4 public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
  25. +6 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
  26. +2 −3 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
  27. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
  28. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
  29. +10 −18 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
  30. +5 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
  31. +16 −5 public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
  32. +73 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java
  33. +2 −2 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
  34. +96 −18 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
  35. +5 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
  36. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
  37. +6 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
  38. +2 −2 ...java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
  39. +44 −34 public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
  40. +26 −15 public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
  41. +5 −5 public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
  42. +5 −5 .../org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
  43. +3 −3 ...c/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
  44. +4 −4 public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
  45. +6 −4 public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
  46. +5 −3 public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
  47. +19 −7 public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
  48. +8 −4 public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
  49. +0 −149 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
  50. +0 −173 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
  51. +12 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
  52. +0 −249 ...ic/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
  53. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
  54. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
  55. +13 −13 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
  56. +0 −8 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
  57. +14 −4 public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java
  58. +12 −203 public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
  59. +24 −0 public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
  60. +40 −9 public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
  61. +28 −30 public/java/src/org/broadinstitute/sting/utils/Haplotype.java
  62. +4 −2 .../src/org/broadinstitute/sting/utils/{ReservoirDownsampler.java → LegacyReservoirDownsampler.java}
  63. +1 −1 public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
  64. +61 −8 public/java/src/org/broadinstitute/sting/utils/Utils.java
  65. +12 −8 public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
  66. +16 −0 public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java
  67. +47 −7 public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
  68. +46 −6 public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java
  69. +1 −1 public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
  70. +6 −5 public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
  71. +1 −1 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
  72. +34 −0 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
  73. +12 −2 public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
  74. +96 −18 public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
  75. +4 −4 public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
  76. +3 −2 public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
  77. +8 −13 public/java/src/org/broadinstitute/sting/utils/nanoScheduler/InputProducer.java
  78. +0 −67 public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NSRuntimeProfile.java
  79. +29 −53 public/java/src/org/broadinstitute/sting/utils/nanoScheduler/NanoScheduler.java
  80. +0 −9 public/java/src/org/broadinstitute/sting/utils/nanoScheduler/Reducer.java
  81. +72 −15 public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
  82. +17 −0 public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java
  83. +25 −0 public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
  84. +45 −20 public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
  85. +60 −0 public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemon.java
  86. +6 −1 public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
  87. +64 −0 public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
  88. +70 −0 public/java/src/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java
  89. +67 −0 public/java/src/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityReadTransformer.java
  90. +177 −186 public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
  91. +0 −7 public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
  92. +74 −4 public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
  93. +0 −1 public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
  94. +8 −5 ...c/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
  95. +90 −42 public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
  96. +37 −0 public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java
  97. +2 −3 public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
  98. +4 −4 ...k/datasources/reads/{ExperimentalReadShardBalancerUnitTest.java → ReadShardBalancerUnitTest.java}
  99. +119 −287 ...erators/{LocusIteratorByStateExperimentalUnitTest.java → LegacyLocusIteratorByStateUnitTest.java}
  100. +283 −115 public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
  101. +572 −0 public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
  102. +2 −2 public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
  103. +20 −0 public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java
  104. +7 −1 ...ic/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
  105. +4 −4 ...c/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
  106. +3 −3 public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
  107. +2 −2 public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java
  108. +1 −1 .../java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
  109. +6 −6 ...c/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
  110. +1 −1 .../java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
  111. +36 −0 public/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java
  112. +1 −1 public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
  113. +8 −8 public/java/test/org/broadinstitute/sting/utils/LegacyReservoirDownsamplerUnitTest.java
  114. +1 −1 public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java
  115. +1 −5 public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
  116. +54 −11 public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
  117. +2 −3 public/java/test/org/broadinstitute/sting/utils/nanoScheduler/InputProducerUnitTest.java
  118. +18 −19 public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerUnitTest.java
  119. +2 −3 public/java/test/org/broadinstitute/sting/utils/nanoScheduler/ReducerUnitTest.java
  120. +25 −2 public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
  121. +66 −0 public/java/test/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java
  122. +1 −1 public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
  123. +115 −4 public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
  124. +3 −0 public/packages/GATKEngine.xml
  125. +507 −0 public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala
  126. +2 −2 public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
  127. +98 −65 public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
  128. +11 −0 public/scala/src/org/broadinstitute/sting/queue/QCommandPlugin.scala
  129. +30 −3 public/scala/src/org/broadinstitute/sting/queue/QScript.scala
  130. +4 −0 public/scala/src/org/broadinstitute/sting/queue/QSettings.scala
  131. +28 −6 public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
  132. +5 −2 public/scala/src/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala
  133. +3 −0 public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
  134. +5 −2 public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
  135. +0 −1 public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
  136. +5 −23 public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
  137. +4 −4 public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
  138. +3 −4 public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
  139. +53 −0 public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
  140. +10 −0 public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
  141. +1 −0 public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
  142. +1 −0 ...c/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
  143. +11 −0 public/scala/src/org/broadinstitute/sting/queue/util/ClassFieldCache.scala
  144. +131 −0 public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala
  145. +21 −0 public/scala/src/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
  146. +11 −16 public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
  147. +2 −2 public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
  148. +1 −1 public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
  149. +1 −1 public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
  150. +1 −1 ...ic/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
  151. +1 −1 ...c/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
  152. +1 −1 ...c/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
  153. +1 −1 ...a/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
  154. +4 −4 ...a/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
  155. +21 −10 public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
  156. BIN settings/repository/org.broad/{tribble-110.jar → tribble-119.jar}
  157. +1 −1 settings/repository/org.broad/{tribble-110.xml → tribble-119.xml}
View
133 build.xml
@@ -185,10 +185,7 @@
<include name="**/*.class"/>
</fileset>
- <patternset id="dependency.mask" includes="*.jar">
- <exclude name="testng*.jar" />
- <exclude name="bcel*.jar" />
- </patternset>
+ <patternset id="dependency.mask" includes="*.jar" />
<path id="external.dependencies">
<fileset dir="${lib.dir}" erroronmissingdir="false">
@@ -205,6 +202,16 @@
<pathelement location="${scala.classes}" />
</path>
+ <path id="build.results">
+ <!-- Ensure that GenomeAnalysisTK.jar comes first in the path, as it contains overrides for certain classes in our dependencies -->
+ <pathelement location="${dist.dir}/GenomeAnalysisTK.jar" />
+ <!-- After GenomeAnalysisTK.jar we include all of the other jars in the dist directory -->
+ <fileset dir="${dist.dir}" erroronmissingdir="false">
+ <patternset refid="dependency.mask" />
+ <exclude name="GenomeAnalysisTK.jar" />
+ </fileset>
+ </path>
+
<fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
<include name="**/*.java" />
</fileset>
@@ -226,20 +233,20 @@
<!-- the path for resources that need to go into the GATK jar;
any additional resources should go into this set. -->
<path id="gatk.resources">
- <fileset dir="${basedir}">
- <include name="${java.public.source.dir}/**/templates/*" />
- <include name="${java.private.source.dir}/**/templates/*" if="include.private" />
- <include name="${java.protected.source.dir}/**/templates/*" if="include.protected" />
+ <fileset dir="${java.public.source.dir}">
+ <include name="**/resources/*" />
+ <include name="**/templates/*" />
+ </fileset>
+ <fileset dir="${java.private.source.dir}" erroronmissingdir="false">
+ <include name="**/resources/*" if="include.private" />
+ <include name="**/templates/*" if="include.private" />
+ </fileset>
+ <fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
+ <include name="**/resources/*" if="include.protected" />
+ <include name="**/templates/*" if="include.protected" />
</fileset>
</path>
- <path id="build.results">
- <fileset dir="${dist.dir}">
- <patternset refid="dependency.mask" />
- </fileset>
- </path>
-
-
<!-- ******************************************************************************** -->
<!-- Ivy Retrieve -->
<!-- ******************************************************************************** -->
@@ -327,14 +334,18 @@
<!-- INIT OVERRIDES: call these targets BEFORE init to override build defaults -->
- <target name="init.publiconly">
+ <target name="init.build.publiconly">
<property name="build.target" value="public" />
</target>
- <target name="init.publicprotectedonly">
+ <target name="init.build.publicprotectedonly">
<property name="build.target" value="protected" />
</target>
+ <target name="init.build.all">
+ <property name="build.target" value="all" />
+ </target>
+
<target name="init.javaonly">
<property name="compile.scala" value="false" />
</target>
@@ -668,6 +679,24 @@
</jar>
</target>
+ <target name="na12878kb.jar" depends="gatk.compile,init.jar">
+ <jar jarfile="${dist.dir}/na12878kb.jar">
+ <fileset dir="${java.classes}">
+ <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
+ <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
+ <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
+ <include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
+ <include name="org/broadinstitute/sting/utils/Utils.class"/>
+ <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
+ <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
+ <include name="net/sf/picard/reference/FastaSequenceFile.class"/>
+ </fileset>
+ <fileset dir="${java.private.source.dir}">
+ <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
+ </fileset>
+ </jar>
+ </target>
+
<target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
<path refid="gatk.resources"/>
@@ -842,19 +871,23 @@
<!-- Release-related tasks -->
<!-- ******************************************************************************** -->
- <target name="init.buildgatkfull" depends="init.publicprotectedonly, init.javaonly">
+ <target name="init.executable.gatkfull" depends="init.build.publicprotectedonly, init.javaonly">
<property name="executable" value="GenomeAnalysisTK" />
</target>
- <target name="init.buildgatklite" depends="init.publiconly, init.javaonly">
+ <target name="init.executable.gatklite" depends="init.build.publiconly, init.javaonly">
<property name="executable" value="GenomeAnalysisTKLite" />
</target>
- <target name="init.buildqueuefull" depends="init.publicprotectedonly, init.javaandscala">
+ <target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
+ <property name="executable" value="Queue" />
+ </target>
+
+ <target name="init.executable.queuefull" depends="init.build.publicprotectedonly, init.javaandscala">
<property name="executable" value="Queue" />
</target>
- <target name="init.buildqueuelite" depends="init.publiconly, init.javaandscala">
+ <target name="init.executable.queuelite" depends="init.build.publiconly, init.javaandscala">
<property name="executable" value="QueueLite" />
</target>
@@ -906,13 +939,15 @@
</target>
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
- <target name="package.gatk.full" depends="init.buildgatkfull,package" />
+ <target name="package.gatk.full" depends="init.executable.gatkfull,package" />
+
+ <target name="package.gatk.lite" depends="init.executable.gatklite,package" />
- <target name="package.gatk.lite" depends="init.buildgatklite,package" />
+ <target name="package.queue.all" depends="init.executable.queueall,package" />
- <target name="package.queue.full" depends="init.buildqueuefull,package" />
+ <target name="package.queue.full" depends="init.executable.queuefull,package" />
- <target name="package.queue.lite" depends="init.buildqueuelite,package" />
+ <target name="package.queue.lite" depends="init.executable.queuelite,package" />
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
@@ -975,6 +1010,8 @@
<target name="mvninstall.gatk.lite" depends="package.gatk.lite,mvninstall" />
+ <target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
+
<target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
<target name="mvninstall.queue.lite" depends="package.queue.lite,mvninstall" />
@@ -1091,36 +1128,26 @@
</path>
<path id="testng.default.classpath">
- <pathelement location="${java.classes}" />
- <pathelement location="${scala.classes}" />
+ <path refid="build.results" />
<pathelement location="${java.contracts.dir}" />
<pathelement location="${java.test.classes}" />
<pathelement location="${scala.test.classes}" />
- <pathelement location="${R.tar.dir}" />
- <path refid="R.script.source.path" />
- <pathelement location="${key.dir}" />
- <path refid="external.dependencies" />
</path>
<!-- Test targets -->
<target name="test.init.compile">
<mkdir dir="${java.test.classes}"/>
<mkdir dir="${scala.test.classes}"/>
- <antcall target="resolve">
- <param name="ivy.conf" value="test"/>
- </antcall>
</target>
<target name="test.java.internal.compile" depends="dist,test.init.compile">
<echo message="Sting: Compiling java test cases!"/>
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
<src refid="java.test.source.path" />
<classpath>
- <path refid="external.dependencies" />
- <pathelement location="${java.classes}"/>
+ <path refid="build.results" />
<pathelement location="${java.contracts.dir}"/>
- <pathelement location="${testng.jar}"/>
</classpath>
<compilerarg value="-proc:none"/>
</javac>
@@ -1131,11 +1158,9 @@
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
<include name="*/test/**/*.java"/>
<classpath>
- <path refid="external.dependencies" />
+ <path refid="build.results" />
<pathelement location="${java.test.classes}"/>
- <pathelement location="${java.classes}"/>
<pathelement location="${java.contracts.dir}"/>
- <pathelement location="${testng.jar}"/>
</classpath>
<compilerarg value="-proc:none"/>
</javac>
@@ -1148,9 +1173,8 @@
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
<src refid="scala.test.source.path" />
<classpath>
- <path refid="scala.dependencies"/>
+ <path refid="build.results"/>
<pathelement location="${java.test.classes}"/>
- <pathelement location="${testng.jar}"/>
</classpath>
</scalac>
</target>
@@ -1192,14 +1216,16 @@
<echo message="" />
<echo message="Sting: Running @{testtype} test cases!"/>
+ <!-- no test is allowed to run for more than 10 hours -->
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
<testng outputDir="@{outputdir}"
classpathref="${testng.classpath}"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
+ timeout="36000000"
workingDir="${basedir}"
useDefaultListeners="false"
- listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
+ listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
<jvmarg value="-Xmx${test.maxmemory}" />
<jvmarg value="-ea" />
<jvmarg value="-Djava.awt.headless=true" />
@@ -1355,14 +1381,13 @@
<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
<!-- Usage: ant fasttest -Dsingle=TestClass -->
- <target name="fasttest" depends="init.javaonly,init,test.init">
+ <target name="fasttest" depends="init.javaonly,init">
<condition property="not.clean">
<and>
<available file="${build.dir}" />
<available file="${lib.dir}" />
<available file="${dist.dir}" />
<available file="${java.test.classes}" />
- <available file="${testng.jar}" />
</and>
</condition>
<fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
@@ -1380,13 +1405,27 @@
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
<src refid="java.test.source.path" />
<classpath>
- <path refid="external.dependencies" />
<pathelement location="${java.classes}"/>
- <pathelement location="${testng.jar}"/>
+ <path refid="external.dependencies" />
</classpath>
<compilerarg value="-proc:none"/>
</javac>
+ <!-- fasttest uses the unpackaged class files in its test classpath to avoid having to rebuild the jars in dist/ -->
+ <path id="testng.fasttest.classpath">
+ <pathelement location="${java.classes}" />
+ <pathelement location="${scala.classes}" />
+ <pathelement location="${java.contracts.dir}" />
+ <pathelement location="${java.test.classes}" />
+ <pathelement location="${scala.test.classes}" />
+ <pathelement location="${R.tar.dir}" />
+ <path refid="R.script.source.path" />
+ <pathelement location="${key.dir}" />
+ <path refid="external.dependencies" />
+ <path refid="java.source.path" /> <!-- Terrible hack to allow fasttest to see resource files stored in the source tree -->
+ </path>
+ <property name="testng.classpath" value="testng.fasttest.classpath" />
+
<run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
</target>
</project>
View
11 ivy.xml
@@ -24,11 +24,8 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="Sting"/>
- <configurations defaultconfmapping="test->default">
+ <configurations>
<conf name="default" description="the core dependencies for the GATK"/>
- <conf name="test" extends="default" description="external dependencies used for testing and metrics"/>
- <conf name="scala" extends="default" description="the dependencies for scala"/>
- <conf name="queue" extends="scala" description="the dependencies for Queue"/>
</configurations>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/>
@@ -83,9 +80,9 @@
<dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
<!-- testing and evaluation dependencies -->
- <dependency org="org.testng" name="testng" rev="5.14.1" conf="test"/>
- <dependency org="org.uncommons" name="reportng" rev="1.1.2" conf="test"/>
- <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test"/>
+ <dependency org="org.testng" name="testng" rev="5.14.1"/>
+ <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
+ <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT"/>
<!-- Contracts for Java and dependencies -->
<dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
@@ -445,13 +445,17 @@ private MicroScheduler createMicroscheduler() {
protected DownsamplingMethod getDownsamplingMethod() {
GATKArgumentCollection argCollection = this.getArguments();
- boolean useExperimentalDownsampling = argCollection.enableExperimentalDownsampling;
+
+ // Legacy downsampler can only be selected via the command line, not via walker annotations
+ boolean useLegacyDownsampler = argCollection.useLegacyDownsampler;
DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod();
- DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useExperimentalDownsampling);
- DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useExperimentalDownsampling);
+ DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useLegacyDownsampler);
+ DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useLegacyDownsampler);
- return commandLineMethod != null ? commandLineMethod : (walkerMethod != null ? walkerMethod : defaultMethod);
+ DownsamplingMethod method = commandLineMethod != null ? commandLineMethod : (walkerMethod != null ? walkerMethod : defaultMethod);
+ method.checkCompatibilityWithWalker(walker);
+ return method;
}
protected void setDownsamplingMethod(DownsamplingMethod method) {
@@ -580,9 +584,9 @@ else if(walker instanceof ReadWalker || walker instanceof ReadPairWalker || walk
throw new UserException.CommandLineException("Pairs traversal cannot be used in conjunction with intervals.");
}
- // Use the experimental ReadShardBalancer if experimental downsampling is enabled
- ShardBalancer readShardBalancer = downsamplingMethod != null && downsamplingMethod.useExperimentalDownsampling ?
- new ExperimentalReadShardBalancer() :
+ // Use the legacy ReadShardBalancer if legacy downsampling is enabled
+ ShardBalancer readShardBalancer = downsamplingMethod != null && downsamplingMethod.useLegacyDownsampler ?
+ new LegacyReadShardBalancer() :
new ReadShardBalancer();
if(intervals == null)
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