Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

build.xml

@@ -780,6 +780,50 @@
         </sequential>
     </macrodef>
 
+    <!-- FAILED-TEST -->
+    <macrodef name="run-failed-test">
+        <attribute name="xmlfailedtestfile" />
+        <sequential>
+            <!-- Get the pipeline run type.  Default to dry.  -->
+            <condition property="pipeline.run" value="dry" else="${pipeline.run}">
+                <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
+            </condition>
+
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
+            <mkdir dir="${report}/failed_rerun" />
+            <echo message="Sting: Running @{xmlfailedtestfile} test cases!"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
+            <testng outputDir="${report}/failed_rerun"
+                    haltOnFailure="false" failureProperty="test.failure"
+                    verbose="2"
+                    workingDir="${basedir}"
+                    useDefaultListeners="false"
+                    listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
+                <jvmarg value="-Xmx${test.maxmemory}" />
+                <jvmarg value="-Djava.awt.headless=true" />
+                <jvmarg value="-Dpipeline.run=${pipeline.run}" />
+                <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
+                <jvmarg line="${cofoja.jvm.args}"/>
+<!--                 <jvmarg value="-Xdebug"/> -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+                <classpath>
+                    <path refid="external.dependencies" />
+                    <pathelement location="${java.classes}" />
+                    <pathelement location="${scala.classes}" />
+                    <pathelement location="${java.contracts}" />
+                    <pathelement location="${java.test.classes}" />
+                    <pathelement location="${scala.test.classes}" />
+                </classpath>
+
+                <xmlfileset dir="${basedir}" includes="@{xmlfailedtestfile}" />
+            </testng>
+
+            <fail message="test failed" if="test.failure" />
+        </sequential>
+    </macrodef>
 
     <!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
     <target name="test" depends="test.compile,tribble.test" description="Run unit tests">
@@ -814,6 +858,22 @@
         <run-test testtype="${pipetype}"/>
     </target>
 
+    <target name="failed-test" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*UnitTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-integration" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*IntegrationTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-performance" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PerformanceTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-pipeline" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
+    </target>
+
     <!-- ***************************************************************************** -->
     <!-- ***********                     Tribble                             ********* -->
     <!-- ***************************************************************************** -->

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -242,7 +242,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         return new PhasingStatsAndOutput(phaseStats, completedList);
     }
 
-    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
+    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList(PQ_KEY));
 
     private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala

@@ -3,10 +3,11 @@ package org.broadinstitute.sting.queue.qscripts
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
+import org.broadinstitute.sting.queue.extensions.picard._
+import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
+import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
 
 import collection.JavaConversions._
-import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
-import org.broadinstitute.sting.queue.extensions.picard._
 import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
@@ -29,7 +30,8 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
   var reference: File = _
 
-
+  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
+  var dbSNP: File = _
 
   /****************************************************************************
   * Optional Parameters
@@ -39,14 +41,12 @@ class DataProcessingPipeline extends QScript {
 //  @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
 //  var sortSamJar: File = _
 //
-  @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
-  var bwaPath: File = _
-
-  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
-  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
 
   @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
-  var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
+  var indels: File = _
+
+  @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
+  var bwaPath: File = _
 
   @Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
   var projectName: String = "project"
@@ -288,7 +288,8 @@ class DataProcessingPipeline extends QScript {
     this.out = outIntervals
     this.mismatchFraction = 0.0
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outIntervals + ".target"
     this.jobName = queueLogDir + outIntervals + ".target"
@@ -299,7 +300,8 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs
@@ -322,7 +324,7 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.recal_file = inRecalFile
-    this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
+    this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala

@@ -42,8 +42,8 @@ class RecalibrateBaseQualities extends QScript {
       val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
       val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
       val recalBam: File   = swapExt(bam, ".bam", ".recal.bam")
-      val path1: String    = bam + "before"
+      val path1: String    = bam + ".before"
-      val path2: String    = bam + "after"
+      val path2: String    = bam + ".after"
 
       add(cov(bam, recalFile1),
           recal(bam, recalFile1, recalBam),
@@ -83,7 +83,7 @@ class RecalibrateBaseQualities extends QScript {
   case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
     this.resources = R
     this.recal_file = inRecalFile
-    this.output_dir = outPath.toString
+    this.output_dir = outPath
     this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }