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Merge remote-tracking branch 'unstable/master'

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2 parents ba531bd + 38b80a5 commit 4b00c81181138068f5f7641877787f67ee0c825d @eitanbanks eitanbanks committed Aug 21, 2013
Showing with 6,560 additions and 2,378 deletions.
  1. +47 −26 build.xml
  2. +0 −22 licensing/GATK1_LICENSE
  3. BIN licensing/GATK2_beta_license.doc
  4. +30 −12 protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
  5. +4 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
  6. +3 −6 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
  7. +17 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
  8. +79 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
  9. +9 −2 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
  10. +4 −1 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
  11. +19 −2 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
  12. +5 −3 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
  13. +88 −44 protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
  14. +2 −3 protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
  15. +118 −305 protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
  16. +1 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
  17. +14 −38 ...d/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
  18. +2 −1 ...ected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
  19. +2 −7 ...a/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
  20. +5 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
  21. +31 −4 protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
  22. +1 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
  23. +25 −86 ...oadinstitute/sting/gatk/walkers/haplotypecaller/{DeBruijnGraphBuilder.java → AssemblyResult.java}
  24. +0 −269 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java
  25. +7 −4 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
  26. +281 −125 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
  27. +145 −22 ...d/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
  28. +27 −24 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
  29. +72 −0 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
  30. +476 −0 ...cted/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
  31. +4 −21 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
  32. +1 −1 ...d/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
  33. +7 −21 ...rg/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/{DeBruijnGraph.java → TestGraph.java}
  34. +28 −20 ...c/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
  35. +45 −18 ...a/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
  36. +5 −3 protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
  37. +6 −2 protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
  38. +7 −2 protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
  39. +11 −6 ...ected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
  40. +17 −3 ...ted/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
  41. +1 −1 ...ted/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
  42. +97 −29 ...ected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
  43. +15 −24 ...cted/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
  44. +10 −6 ...broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
  45. +2 −2 ...ava/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
  46. +298 −0 protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
  47. +169 −0 protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
  48. +5 −6 protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
  49. +6 −8 protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
  50. +39 −40 protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
  51. +135 −0 protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java
  52. +182 −66 .../DeBruijnAssemblyGraphUnitTest.java → src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java}
  53. +4 −1 protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
  54. +6 −1 protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java
  55. +8 −0 ...ed/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
  56. +10 −10 ...ava/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java
  57. +61 −19 ...est/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
  58. +162 −31 ...ava/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
  59. +56 −193 .../java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
  60. +1 −1 ...oadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
  61. +1 −1 ...oadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
  62. +10 −10 .../org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
  63. +78 −14 ...ed/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
  64. +10 −10 ...org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
  65. +3 −3 .../org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java
  66. +6 −6 .../sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
  67. +33 −135 ...alkers/haplotypecaller/{DeBruijnAssemblerUnitTest.java → HaplotypeCallerGVCFIntegrationTest.java}
  68. +68 −21 ...va/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
  69. +2 −2 ...org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
  70. +48 −0 ...st/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
  71. +20 −39 .../java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
  72. +408 −0 .../test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
  73. +2 −68 ...ted/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
  74. +1 −1 ...cted/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
  75. +1 −1 ...oadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
  76. +9 −3 ...g/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
  77. +27 −1 .../java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
  78. +48 −0 ...d/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
  79. +71 −0 ...a/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java
  80. +45 −17 ...institute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
  81. +10 −5 protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
  82. +27 −33 ...cted/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
  83. +333 −0 protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
  84. +161 −0 protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
  85. +82 −0 ...ed/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java
  86. +8 −12 ...ected/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
  87. +1 −1 protected/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
  88. +92 −0 protected/java/test/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java
  89. +19 −6 protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
  90. +1 −1 public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
  91. +16 −0 public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
  92. +19 −11 public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
  93. +63 −3 public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
  94. +17 −6 public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
  95. +79 −4 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
  96. +2 −2 public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
  97. +2 −2 public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
  98. +49 −0 public/java/src/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java
  99. +18 −5 public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java
  100. +3 −4 public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java
  101. +8 −8 public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
  102. +5 −5 public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
  103. BIN public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
  104. BIN public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
  105. +14 −4 public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
  106. +1 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
  107. +6 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
  108. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
  109. +154 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java
  110. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java
  111. +2 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
  112. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
  113. +11 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
  114. +1 −1 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
  115. +0 −105 public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/DownsampleReadsQC.java
  116. +6 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
  117. +86 −0 ...src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java
  118. +7 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
  119. +10 −0 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
  120. +8 −3 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
  121. +1 −5 public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
  122. +1 −1 public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
  123. +4 −7 public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
  124. +30 −0 public/java/src/org/broadinstitute/sting/utils/MathUtils.java
  125. +7 −0 public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
  126. +6 −7 public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
  127. +8 −12 public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
  128. +9 −1 public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
  129. +7 −1 public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
  130. +7 −1 public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
  131. +21 −22 public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
  132. +70 −0 public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
  133. +47 −0 public/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparator.java
  134. +62 −12 public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
  135. +0 −2 public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java
  136. +23 −10 public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java
  137. +41 −0 public/java/src/org/broadinstitute/sting/utils/pairhmm/BatchPairHMM.java
  138. +6 −1 public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
  139. +4 −0 public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
  140. +1 −1 public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
  141. +1 −1 public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
  142. +4 −4 public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
  143. +40 −25 public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
  144. +27 −13 public/java/src/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java
  145. +26 −35 public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
  146. +9 −2 public/java/test/org/broadinstitute/sting/BaseTest.java
  147. +242 −7 public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
  148. +77 −6 public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
  149. +4 −4 public/java/test/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java
  150. +4 −2 public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java
  151. +49 −0 public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java
  152. +1 −1 public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java
  153. +1 −1 public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java
  154. +111 −0 public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtilUnitTest.java
  155. +8 −3 public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java
  156. +8 −3 public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java
  157. +8 −3 public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java
  158. +75 −3 public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
  159. +6 −2 public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java
  160. +19 −20 public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
  161. +47 −4 public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java
  162. +8 −24 public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java
  163. +1 −1 public/java/test/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
  164. +20 −1 public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
  165. +95 −0 public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
  166. +2 −2 public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
  167. +1 −1 public/scala/src/org/broadinstitute/sting/queue/QScript.scala
  168. +33 −0 public/scala/src/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala
  169. +100 −0 public/scala/src/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobRunner.scala
  170. +6 −1 public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
  171. +1 −1 public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
  172. +2 −4 public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
  173. +9 −8 public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
  174. +3 −1 ...a/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
  175. +3 −0 public/testdata/exampleINTERVAL.intervals
  176. +19 −5 settings/helpTemplates/generic.template.html
  177. +0 −3 settings/repository/net.sf/picard-1.91.1453.xml
  178. BIN settings/repository/net.sf/{picard-1.91.1453.jar → picard-1.96.1534.jar}
  179. +3 −0 settings/repository/net.sf/picard-1.96.1534.xml
  180. +0 −3 settings/repository/net.sf/sam-1.91.1453.xml
  181. BIN settings/repository/net.sf/{sam-1.91.1453.jar → sam-1.96.1534.jar}
  182. +3 −0 settings/repository/net.sf/sam-1.96.1534.xml
  183. BIN settings/repository/org.broad/{tribble-1.91.1453.jar → tribble-1.96.1534.jar}
  184. +1 −1 settings/repository/org.broad/{tribble-1.91.1453.xml → tribble-1.96.1534.xml}
  185. BIN settings/repository/org.broadinstitute/{variant-1.91.1453.jar → variant-1.96.1534.jar}
  186. +1 −1 settings/repository/org.broadinstitute/{variant-1.91.1453.xml → variant-1.96.1534.xml}
View
@@ -22,6 +22,7 @@
~ OTHER DEALINGS IN THE SOFTWARE.
-->
+<!-- To get a list of the major build targets, run "ant -p" -->
<project name="Sting" default="dist" basedir="."
xmlns:artifact="antlib:org.apache.maven.artifact.ant"
xmlns:ivy="antlib:org.apache.ivy.ant">
@@ -291,7 +292,7 @@
<property name="init.resolve.done" value="true"/>
</target>
- <target name="resolve" depends="init.resolve,init" description="locate and download library dependencies">
+ <target name="resolve" depends="init.resolve,init" description="Locate and download library dependencies">
<property name="ivy.conf" value="default"/>
<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
<!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
@@ -465,7 +466,7 @@
</subant>
</target>
- <target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" description="Compile the GATK source" />
+ <target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" />
<target name="gatk.contracts" depends="gatk.compile.source" if="include.contracts">
<javac fork="true" memoryMaximumSize="512m" destdir="${java.contracts.dir}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
@@ -502,7 +503,7 @@
</target>
<!-- NOTE: Extracting help first to avoid "Unable to load help text. Help output will be sparse." warning message. -->
- <target name="queue-extensions.generate" depends="gatk.compile,extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate" description="generate GATK modules for Queue">
+ <target name="queue-extensions.generate" depends="gatk.compile,extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate">
<mkdir dir="${queue-extensions.source.dir}"/>
<echo>Generating Queue GATK extensions...</echo>
<java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" >
@@ -520,7 +521,7 @@
</touch>
</target>
- <target name="init.scala.compile" depends="resolve" description="Initializes the scala ant tasks from scala-compiler.jar">
+ <target name="init.scala.compile" depends="resolve">
<path id="scala.classpath">
<fileset dir="${lib.dir}">
<include name="scala-compiler-*.jar"/>
@@ -595,8 +596,7 @@
</condition>
</target>
- <target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp"
- description="Extract help key/value pair file from the JavaDoc tags.">
+ <target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp">
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
@@ -687,7 +687,7 @@
</jar>
</target>
- <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
+ <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
<path refid="gatk.resources"/>
<fileset dir="${java.contracts.dir}" />
@@ -786,20 +786,20 @@
<!-- Top-Level Build Targets -->
<!-- ******************************************************************************** -->
- <target name="dist" depends="sting.manifests" />
+ <target name="dist" depends="sting.manifests" description="Build the GATK and Queue" />
- <target name="gatk" depends="init.javaonly, sting.manifests" />
+ <target name="gatk" depends="init.javaonly, sting.manifests" description="Build the GATK only" />
<target name="queue" depends="dist" /> <!-- Obsolete target. Now just an alias for dist -->
- <target name="scala" depends="scala.jar" description="build the scala directory" />
+ <target name="scala" depends="scala.jar" />
<!-- ******************************************************************************** -->
<!-- GATKDocs -->
<!-- ******************************************************************************** -->
- <target name="gatkdocs" depends="gatk.compile" description="Extract help key/value pair file from the JavaDoc tags.">
+ <target name="gatkdocs" depends="gatk.compile" description="Generate GATK HTML documentation">
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
@@ -831,7 +831,7 @@
<mkdir dir="${javadoc.dir}" />
</target>
- <target name="javadoc" depends="init.javadoc,resolve">
+ <target name="javadoc" depends="init.javadoc,resolve" description="Generate Javadoc">
<javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
<fileset refid="java.source.files" />
<sourcepath path="${external.dir}" />
@@ -849,7 +849,7 @@
<!-- NOTE: the scaladoc target requires that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
- <target name="scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc">
+ <target name="scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc" description="Generate Scaladoc">
<scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<patternset refid="scala.source.files.pattern" />
<include name="${queue-extensions.source.dir}/**/*.scala" />
@@ -887,8 +887,29 @@
<fail message="No executable defined. Call a more specific packaging/release target, or define an executable manually" if="no.executable.defined" />
</target>
+ <target name="require.bcel">
+ <fileset id="bcel.jar" dir="${user.home}/.ant/lib">
+ <include name="bcel-*.jar" />
+ </fileset>
+ <pathconvert refid="bcel.jar" property="bcel.jar.installed" setonempty="false" />
+
+ <fileset id="ant.bcel.jar" dir="${user.home}/.ant/lib">
+ <include name="ant-apache-bcel-*.jar" />
+ </fileset>
+ <pathconvert refid="ant.bcel.jar" property="ant.bcel.jar.installed" setonempty="false" />
+
+ <condition property="bcel.installed">
+ <and>
+ <isset property="bcel.jar.installed" />
+ <isset property="ant.bcel.jar.installed" />
+ </and>
+ </condition>
+ <fail unless="bcel.installed"
+ message="Required bcel libraries for GATK packaging not installed in ${user.home}/.ant/lib/${line.separator}The bcel jar can be found in the lib directory of a GATK clone after compiling, and the ant-apache-bcel jar can be downloaded from here: http://repo1.maven.org/maven2/ant/ant-apache-bcel/1.6.5/ant-apache-bcel-1.6.5.jar${line.separator}Please copy these two jar files to ${user.home}/.ant/lib/" />
+ </target>
+
<!-- Unzip all classes from their current locations and assemble them in a staging directory -->
- <target name="stage" description="stage files for distribution">
+ <target name="stage">
<mkdir dir="${staging.dir}"/>
<!--
HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
@@ -910,7 +931,7 @@
<!-- Build a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
- <target name="package" depends="require.clean,dist,stage,require.executable" description="bundle up an executable for distribution">
+ <target name="package" depends="require.clean,require.bcel,dist,stage,require.executable">
<mkdir dir="${package.output.dir}" />
<xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/>
@@ -927,17 +948,17 @@
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<!-- GATK "full" == public + protected, ie., the standard binary release of the GATK -->
- <target name="package.gatk.full" depends="init.executable.gatkfull,package" />
+ <target name="package.gatk.full" depends="init.executable.gatkfull,package" description="Create a standalone GATK jar with public and protected code" />
<!-- GATK "all" == public + protected + private. Should never be publicly released -->
- <target name="package.gatk.all" depends="init.executable.gatkall,package" />
+ <target name="package.gatk.all" depends="init.executable.gatkall,package" description="Create a standalone GATK jar with public, protected, and private code" />
- <target name="package.queue.full" depends="init.executable.queuefull,package" />
+ <target name="package.queue.full" depends="init.executable.queuefull,package" description="Create a standalone Queue jar with public and protected code" />
- <target name="package.queue.all" depends="init.executable.queueall,package" />
+ <target name="package.queue.all" depends="init.executable.queueall,package" description="Create a standalone Queue jar with public, protected, and private code" />
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
- <target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
+ <target name="release" depends="require.executable">
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
</target>
@@ -973,7 +994,7 @@
</target>
<!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
- <target name="mvninstall" depends="package" description="maven install a package into .m2/repository">
+ <target name="mvninstall" depends="package">
<property name="mvn.build.version" value="0.0.2" />
<!--
We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
@@ -1024,7 +1045,7 @@
</exec>
</target>
- <target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs,clean.clover">
+ <target name="clean" description="Clean up old build-related directories" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs,clean.clover">
<delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/>
<delete dir="${contract.dump.dir}"/>
@@ -1059,7 +1080,7 @@
<!-- ******************************************************************************** -->
<!-- Build gsalib R module -->
- <target name="gsalib">
+ <target name="gsalib" description="Build the gsalib R module">
<exec executable="R" failonerror="true">
<arg line="R CMD INSTALL --preclean ${R.public.src.dir}/${R.package.path}/gsalib" />
</exec>
@@ -1346,7 +1367,7 @@
</target>
- <target name="committests" depends="unittest,integrationtest,pipelinetest" />
+ <target name="committests" depends="unittest,integrationtest,pipelinetest" description="Run unit tests, integration tests, and do a dry-run of the pipeline tests" />
<!-- Order of the dependencies is significant in the *.release.tests targets -->
<target name="gatkfull.binary.release.tests" depends="package.gatk.full,init.testgatkjar,unittest,integrationtest" />
@@ -1378,7 +1399,7 @@
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
</target>
- <target name="pipelinetest" depends="test.compile,test.init" description="Run pipeline tests">
+ <target name="pipelinetest" depends="test.compile,test.init" description="Dry-run pipeline tests">
<condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not>
</condition>
@@ -1412,7 +1433,7 @@
<!-- 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">
+ <target name="fasttest" depends="init.javaonly,init" description="Quickly run a single test">
<property name="test.maxmemory" value="${test.default.maxmemory}"/>
<condition property="not.clean">
<and>
View
@@ -1,22 +0,0 @@
-Copyright (c) 2012 The Broad Institute
-
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Binary file not shown.
@@ -54,8 +54,6 @@
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;
-import java.io.PrintStream;
-import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
@@ -70,24 +68,45 @@
public class StandardCallerArgumentCollection {
/**
- * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are:
- * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
+ * The expected heterozygosity value used to compute prior probability that a locus is non-reference.
+ *
+ * The default priors are for provided for humans:
+ *
+ * het = 1e-3
+ *
+ * which means that the probability of N samples being hom-ref at a site is:
+ *
+ * 1 - sum_i_2N (het / i)
+ *
+ * Note that heterozygosity as used here is the population genetics concept:
+ *
+ * http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics
+ *
+ * That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms
+ * would differ from each other (one being A and the other B) at a rate of 1 in 100 bp.
+ *
+ * Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype,
+ * which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there
+ * may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK
+ * only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the
+ * het parameters only increases the chance that a site will be called non-reference across all samples, but
+ * doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all.
+ *
+ * The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy,
+ * which determines how many chromosomes each individual in the species carries.
*/
- @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
+ @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept", required = false)
public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
/**
* This argument informs the prior probability of having an indel at a site.
*/
- @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
+ @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept", required = false)
public double INDEL_HETEROZYGOSITY = 1.0/8000;
@Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false)
public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY;
- @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false)
- public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
-
/**
* The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
* confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
@@ -150,11 +169,11 @@
*/
@Argument(fullName = "contamination_fraction_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION;
- public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05;
+ public static final double DEFAULT_CONTAMINATION_FRACTION = 0.0;
/**
* This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples.
- * Samples that do not appear in this file will be processed with CONTAMINATION_FRACTION
+ * Samples that do not appear in this file will be processed with CONTAMINATION_FRACTION.
**/
@Advanced
@Argument(fullName = "contamination_fraction_per_sample_file", shortName = "contaminationFile", doc = "Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be \"<SampleID><TAB><Contamination>\" (Contamination is double) per line; No header.", required = false)
@@ -199,7 +218,6 @@ public StandardCallerArgumentCollection(final StandardCallerArgumentCollection S
this.heterozygosity = SCAC.heterozygosity;
this.INDEL_HETEROZYGOSITY = SCAC.INDEL_HETEROZYGOSITY;
this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
- this.OutputMode = SCAC.OutputMode;
this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
this.CONTAMINATION_FRACTION = SCAC.CONTAMINATION_FRACTION;
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