Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java

@@ -195,8 +195,8 @@ public class ErrorModel  {
         if (eventLength < 0 && pileupElement.isBeforeDeletionStart() && pileupElement.getEventLength() == -eventLength)
             return true;
 
-        if (eventLength > 0 && pileupElement.isBeforeInsertion() &&
+                if (eventLength > 0 && pileupElement.isBeforeInsertion() &&
-                Arrays.equals(pileupElement.getEventBases().getBytes(),alleleBases))
+                Arrays.equals(pileupElement.getEventBases().getBytes(),Arrays.copyOfRange(alleleBases,1,alleleBases.length))) // allele contains ref byte, but pileupElement's event bases doesn't
             return true;
 
         return false;

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java

@@ -199,6 +199,8 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
                     numAlleles, log10AlleleFrequencyPriors, result);
             combinedPloidy = ploidyPerPool + combinedPloidy; // total number of chromosomes in combinedLikelihoods
         }
+
+        int k=0;
     }
 
     public static CombinedPoolLikelihoods fastCombineMultiallelicPool(final CombinedPoolLikelihoods originalPool, double[] newGL, int originalPloidy, int newGLPloidy, int numAlleles,
@@ -408,6 +410,7 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
 
             result.setLog10LikelihoodOfAFzero(log10Lof0);
             result.setLog10PosteriorOfAFzero(log10Lof0 + log10AlleleFrequencyPriors[0]);
+            return log10Lof0;
 
         }   else {
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java

@@ -34,7 +34,6 @@ public class BQSRIntegrationTest extends WalkerTest {
                     " -I " + bam +
                     " -L " + interval +
                     args +
-                    " --no_plots" +
                     " -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : hg18dbSNP132) +
                     " -o %s";
         }
@@ -50,21 +49,21 @@ public class BQSRIntegrationTest extends WalkerTest {
         String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
         String HiSeqInterval = "chr1:10,000,000-10,100,000";
         return new Object[][]{
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "1cfc73371abb933ca26496745d105ff0")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "be6c7bc0b79a2d0395d21cd0154540d5")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "ee5142776008741b1b2453b1258c6d99")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "65781095beb41d8feca26e93e04dcc0b")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "fbc520794f0f98d52159de956f7217f1")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "8ee1fed1713daca1f36e8b30bee2cd23")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "ab5b93794049c514bf8e407019d76b67")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "9449d8a8baac742f46673e9b8314220b")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "81df636e3d0ed6f16113517e0169bc96")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "39313c6e3b85142548fee9b6c130e7b6")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "ad3c47355448f8c45e172c6e1129c65d")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "15eae9e834ed80b24660393c6df87f85")},
-                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "fef7240140a9b6d6335ce009fa4edec5")},
+                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "8485d8fd5e780e98d720dfbf79f26528")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "600652ee49b9ce1ca2d8ee2d8b7c8211")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "c423d1d443822dae404239bb9a746b96")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "769f95b9dcc78a405d3e6b191e5a19f5")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "fb0a6aef430f562ed5e0002d03e0c619")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "43fcba51264cc98bd8466d21e1b96766")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "efee7bcb89abe36da1cfd8a635d37cd2")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "48aaf9ac54b97eac3663882a59354ab2")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "0e8a3238902a1ff0f0c657fb09b4c022")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "dac04b9e1e1c52af8d3a50c2e550fda9")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "5e58d3dcf5ca38f008a64d1c0743ed83")},
-                {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "90d70542076715a8605a8d4002614b34")},
+                {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "1a8e5c85c7935eb1bd2203f5c86ce1db")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "600652ee49b9ce1ca2d8ee2d8b7c8211")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "c423d1d443822dae404239bb9a746b96")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "26a04f5a28c40750c603cbe8a926d7bd")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "6762b39dc027056365280a9d582a6713")},
         };
     }
 
@@ -88,7 +87,6 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + b36KGReference +
                         " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
                         " -L 1:10,000,000-10,200,000" +
-                        " --no_plots" +
                         " -o %s",
                 1, // just one output file
                 UserException.CommandLineException.class);
@@ -102,7 +100,6 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + b36KGReference +
                         " -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" +
                         " -L 1:50,000-80,000" +
-                        " --no_plots" +
                         " -o %s",
                 1, // just one output file
                 UserException.class);

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
 
 import java.util.Arrays;
+import org.testng.annotations.Test;
 
 /**
  * Created by IntelliJ IDEA.
@@ -20,6 +20,7 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
     final String REFSAMPLE_NAME = "NA12878";
     final String MTINTERVALS = "MT:1-1000";
     final String LSVINTERVALS = "20:40,500,000-41,000,000";
+    final String LSVINTERVALS_SHORT = "20:40,500,000-41,501,000";
     final String NA12891_CALLS = comparisonDataLocation + "Unvalidated/mtDNA/NA12891.snp.vcf";
     final String NA12878_WG_CALLS = comparisonDataLocation + "Unvalidated/NA12878/CEUTrio.HiSeq.WGS.b37_decoy.recal.ts_95.snp_indel_combined.vcf";
     final String LSV_ALLELES = validationDataLocation + "ALL.chr20_40m_41m.largeScaleValidationSites.vcf";
@@ -38,6 +39,13 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
     }
 
+    private void PC_LSV_Test_short(String args, String name, String model, String md5) {
+        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm %s -ignoreLane ",
+                REF, LSV_BAM, LSVINTERVALS_SHORT, NA12878_WG_CALLS, REFSAMPLE_NAME, model) + " --no_cmdline_in_header -o %s";
+        final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
+        executeTest("testPoolCaller:"+name+" args=" + args, spec);
+    }
+
     private void PC_LSV_Test_NoRef(String args, String name, String model, String md5) {
         final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s -glm %s -ignoreLane",
                 REF, LSV_BAM, LSVINTERVALS, model) + " --no_cmdline_in_header -o %s";
@@ -47,22 +55,26 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0ff90fa3882a3fb5089a7bba50dd8ae3");
+        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","54241500a8ce7df4bedab6e29099dba5");
     }
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","567ae6b2a7f839b1307d4087c2f59cca");
+        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","5515c6b4249505f78eb54140725e3f72");
+    }
+    @Test(enabled = true)
+    public void testSNP_ACS_Pools() {
+        PC_LSV_Test(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","90af837f372e3d5143af30bf5c8c2b75");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9514ed15c7030b6d47e04e6a3a2b0a3e");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","38599f7650a44c5ed7bdd19865483b99");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","d2a22e12f1969ae199557947e5039b58");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","789a54438553179b9abec1fbe4df754c");
     }
 
     @Test(enabled = true)
@@ -72,6 +84,6 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "4d16d3c9475637bad70e9dc2eafe2da2");
+        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "d1b48f6f3a175fcba9aec6d427005a45");
     }
 }

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -63,6 +63,7 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 
 import java.io.File;
+import java.io.OutputStream;
 import java.util.*;
 
 /**

public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java

@@ -50,7 +50,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     private static Logger logger = Logger.getLogger(SAMFileWriterStorage.class);
 
     public SAMFileWriterStorage( SAMFileWriterStub stub ) {
-        this(stub,stub.getSAMFile());   
+        this(stub,stub.getOutputFile());
     }
 
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
@@ -66,7 +66,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         if(stub.getMaxRecordsInRam() != null)
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
 
-        if(stub.getSAMFile() != null) {
+        if(stub.getOutputFile() != null) {
             try {
                 this.writer = createBAMWriter(factory,stub.getFileHeader(),stub.isPresorted(),file,stub.getCompressionLevel());
             }
@@ -74,8 +74,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
                 throw new UserException.CouldNotCreateOutputFile(file,"file could not be created",ex);
             }
         }
-        else if(stub.getSAMOutputStream() != null){
+        else if(stub.getOutputStream() != null){
-            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getSAMOutputStream());
+            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getOutputStream());
         }
         else
             throw new UserException("Unable to write to SAM file; neither a target file nor a stream has been specified");

public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java

@@ -69,9 +69,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
      * @param stub Stub to use when constructing the output file.
      */
     public VariantContextWriterStorage(VariantContextWriterStub stub)  {
-        if ( stub.getFile() != null ) {
+        if ( stub.getOutputFile() != null ) {
-            this.file = stub.getFile();
+            this.file = stub.getOutputFile();
-            writer = vcfWriterToFile(stub,stub.getFile(),true);
+            writer = vcfWriterToFile(stub,stub.getOutputFile(),true);
         }
         else if ( stub.getOutputStream() != null ) {
             this.file = null;

public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java

@@ -150,7 +150,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * Retrieves the SAM file to (ultimately) be created.
      * @return The SAM file.  Must not be null.
      */
-    public File getSAMFile() {
+    public File getOutputFile() {
         return samFile;
     }
 
@@ -162,7 +162,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
         simplifyBAM = v;
     }
 
-    public OutputStream getSAMOutputStream() {
+    public OutputStream getOutputStream() {
         return samOutputStream;
     }
 
@@ -220,7 +220,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
 
     /**
      * Gets whether to generate an md5 on-the-fly for this BAM.
-     * @return True generates the md5.  False means skip writing the file.
+     * @param generateMD5   True generates the md5.  False means skip writing the file.
      */
     public void setGenerateMD5(boolean generateMD5) {
         if(writeStarted)

public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java

@@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 
+import java.io.File;
+import java.io.OutputStream;
+
 /**
  * A stub used for managing IO. Acts as a proxy for IO streams
  * not yet created or streams that need significant external
@@ -43,4 +46,14 @@ public interface Stub<StreamType> {
      * @param outputTracker The connector used to provide an appropriate stream.
      */
     public void register( OutputTracker outputTracker );
+
+    /**
+     * Returns the OutputStream represented by this stub or null if not available.
+     */
+    public OutputStream getOutputStream();
+
+    /**
+     * Returns the File represented by this stub or null if not available.
+     */
+    public File getOutputFile();
 }

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java

@@ -140,7 +140,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      * Retrieves the file to (ultimately) be created.
      * @return The file.  Can be null if genotypeStream is not.
      */
-    public File getFile() {
+    public File getOutputFile() {
         return genotypeFile;
     }
 
@@ -148,7 +148,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      * Retrieves the output stearm to which to (ultimately) write.
      * @return The file.  Can be null if genotypeFile is not.
      */
-    public PrintStream getOutputStream() {
+    public OutputStream getOutputStream() {
         return genotypeStream;
     }
 
@@ -196,7 +196,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
         if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY);
 
-        if ( forceBCF || (getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile())) )
+        if ( forceBCF || (getOutputFile() != null && VariantContextWriterFactory.isBCFOutput(getOutputFile())) )
             options.add(Options.FORCE_BCF);
 
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);
@@ -271,7 +271,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
     public boolean alsoWriteBCFForTest() {
         return engine.getArguments().numberOfDataThreads == 1 && // only works single threaded
                 ! isCompressed() && // for non-compressed outputs
-                getFile() != null && // that are going to disk
+                getOutputFile() != null && // that are going to disk
                 engine.getArguments().generateShadowBCF; // and we actually want to do it
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -161,6 +161,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
     protected Boolean USE_ALL_ANNOTATIONS = false;
 
+    /**
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
+     */
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
     protected Boolean LIST = false;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java

@@ -49,7 +49,6 @@ public class BQSRGatherer extends Gatherer  {
 
     @Override
     public void gather(List<File> inputs, File output) {
-        RecalibrationReport generalReport = null;
         final PrintStream outputFile;
         try {
             outputFile = new PrintStream(output);
@@ -57,6 +56,7 @@ public class BQSRGatherer extends Gatherer  {
             throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE);
         }
 
+        RecalibrationReport generalReport = null;
         for (File input : inputs) {
             final RecalibrationReport inputReport = new RecalibrationReport(input);
             if (generalReport == null)
@@ -70,14 +70,15 @@ public class BQSRGatherer extends Gatherer  {
         generalReport.calculateQuantizedQualities();
 
         RecalibrationArgumentCollection RAC = generalReport.getRAC();
-        if (RAC.recalibrationReport != null && !RAC.NO_PLOTS) {
+        if ( RAC.RECAL_PDF_FILE != null ) {
-            final File recal_out = new File(output.getName() + ".original");
+            RAC.RECAL_TABLE_FILE = output;
-            final RecalibrationReport originalReport = new RecalibrationReport(RAC.recalibrationReport);
+            if ( RAC.existingRecalibrationReport != null ) {
-            RecalUtils.generateRecalibrationPlot(recal_out, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES);
+                final RecalibrationReport originalReport = new RecalibrationReport(RAC.existingRecalibrationReport);
-        }
+                RecalUtils.generateRecalibrationPlot(RAC, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates());
-        else if (!RAC.NO_PLOTS) {
+            }
-            final File recal_out = new File(output.getName() + ".recal");
+            else {
-            RecalUtils.generateRecalibrationPlot(recal_out, generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES);
+                RecalUtils.generateRecalibrationPlot(RAC, generalReport.getRecalibrationTables(), generalReport.getCovariates());
+            }
         }
 
         generalReport.output(outputFile);

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -50,7 +50,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.io.PrintStream;
 import java.lang.reflect.Constructor;
 import java.util.ArrayList;
@@ -110,6 +110,7 @@ import java.util.ArrayList;
 @Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
 public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long>, NanoSchedulable {
+
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates
 
@@ -150,7 +151,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
             RecalUtils.listAvailableCovariates(logger);
             System.exit(0);
         }
-        RAC.recalibrationReport = getToolkit().getArguments().BQSR_RECAL_FILE; // if we have a recalibration file, record it so it goes on the report table
+        RAC.existingRecalibrationReport = getToolkit().getArguments().BQSR_RECAL_FILE; // if we have a recalibration file, record it so it goes on the report table
 
         Pair<ArrayList<Covariate>, ArrayList<Covariate>> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates
         ArrayList<Covariate> requiredCovariates = covariates.getFirst();
@@ -169,6 +170,12 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
             cov.initialize(RAC); // initialize any covariate member variables using the shared argument collection
         }
 
+        try {
+            RAC.RECAL_TABLE = new PrintStream(RAC.RECAL_TABLE_FILE);
+        } catch (IOException e) {
+            throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_TABLE_FILE, e);
+        }
+
         int numReadGroups = 0;
         for ( final SAMFileHeader header : getToolkit().getSAMFileHeaders() )
             numReadGroups += header.getReadGroups().size();
@@ -284,7 +291,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         generateReport();
         logger.info("...done!");
 
-        if (!RAC.NO_PLOTS) {
+        if (RAC.RECAL_PDF_FILE != null) {
             logger.info("Generating recalibration plots...");
             generatePlots();
         }
@@ -296,10 +303,10 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
         File recalFile = getToolkit().getArguments().BQSR_RECAL_FILE;
         if (recalFile != null) {
             RecalibrationReport report = new RecalibrationReport(recalFile);
-            RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, report.getRecalibrationTables(), recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES);
+            RecalUtils.generateRecalibrationPlot(RAC, report.getRecalibrationTables(), recalibrationTables, requestedCovariates);
         }
         else
-            RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES);
+            RecalUtils.generateRecalibrationPlot(RAC, recalibrationTables, requestedCovariates);
     }
 
 
@@ -313,14 +320,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
     }
 
     private void generateReport() {
-        PrintStream output;
+        RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates);
-        try {
-            output = new PrintStream(RAC.RECAL_FILE);
-        } catch (FileNotFoundException e) {
-            throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_FILE, "could not be created");
-        }
-
-        RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, output);
     }
 }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java

@@ -28,10 +28,10 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
 import org.broad.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.recalibration.RecalUtils;
 
 import java.io.File;
+import java.io.PrintStream;
 import java.util.Collections;
 import java.util.List;
 
@@ -59,14 +59,29 @@ public class RecalibrationArgumentCollection {
      * After the header, data records occur one per line until the end of the file. The first several items on a line are the
      * values of the individual covariates and will change depending on which covariates were specified at runtime. The last
      * three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches,
-     * and the raw empirical quality score calculated by phred-scaling the mismatch rate.
+     * and the raw empirical quality score calculated by phred-scaling the mismatch rate.   Use '/dev/stdout' to print to standard out.
      */
     @Gather(BQSRGatherer.class)
-    @Output
+    @Output(doc = "The output recalibration table file to create", required = true)
-    public File RECAL_FILE;
+    public File RECAL_TABLE_FILE = null;
+    public PrintStream RECAL_TABLE;
 
     /**
-     * List all implemented covariates.
+     * If not provided, then no plots will be generated (useful for queue scatter/gathering).
+     * However, we *highly* recommend that users generate these plots whenever possible for QC checking.
+     */
+    @Output(fullName = "plot_pdf_file", shortName = "plots", doc = "The output recalibration pdf file to create", required = false)
+    public File RECAL_PDF_FILE = null;
+
+    /**
+     * If not provided, then a temporary file is created and then deleted upon completion.
+     */
+    @Hidden
+    @Argument(fullName = "intermediate_csv_file", shortName = "intermediate", doc = "The intermediate csv file to create", required = false)
+    public File RECAL_CSV_FILE = null;
+
+    /**
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
      */
     @Argument(fullName = "list", shortName = "ls", doc = "List the available covariates and exit", required = false)
     public boolean LIST_ONLY = false;
@@ -166,14 +181,8 @@ public class RecalibrationArgumentCollection {
     @Hidden
     @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
     public String FORCE_PLATFORM = null;
-    @Hidden
-    @Argument(fullName = "keep_intermediate_files", shortName = "k", required = false, doc ="does not remove the temporary csv file created to generate the plots")
-    public boolean KEEP_INTERMEDIATE_FILES = false;
-    @Hidden
-    @Argument(fullName = "no_plots", shortName = "np", required = false, doc = "does not generate any plots -- useful for queue scatter/gathering")
-    public boolean NO_PLOTS = false;
 
-    public File recalibrationReport = null;
+    public File existingRecalibrationReport = null;
 
     public GATKReportTable generateReportTable(final String covariateNames) {
         GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
@@ -205,12 +214,10 @@ public class RecalibrationArgumentCollection {
         argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
         argumentsTable.addRowID("quantizing_levels", true);
         argumentsTable.set("quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
-        argumentsTable.addRowID("keep_intermediate_files", true);
-        argumentsTable.set("keep_intermediate_files", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES);
-        argumentsTable.addRowID("no_plots", true);
-        argumentsTable.set("no_plots", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS);
         argumentsTable.addRowID("recalibration_report", true);
-        argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath());
+        argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, existingRecalibrationReport == null ? "null" : existingRecalibrationReport.getAbsolutePath());
+        argumentsTable.addRowID("plot_pdf_file", true);
+        argumentsTable.set("plot_pdf_file", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RECAL_PDF_FILE == null ? "null" : RECAL_PDF_FILE.getAbsolutePath());
         argumentsTable.addRowID("binary_tag_name", true);
         argumentsTable.set("binary_tag_name", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME);
         return argumentsTable;

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java

@@ -126,7 +126,9 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     @Input(fullName="goldStandard", shortName = "gold", doc="Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison", required=false)
     public RodBinding<VariantContext> goldStandard = null;
 
-    // Help arguments
+    /**
+     * Note that the --list argument requires a fully resolved and correct command-line to work.
+     */
     @Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit", required=false)
     protected Boolean LIST = false;
 

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java

@@ -47,7 +47,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.io.PrintStream;
 import java.util.*;
 
@@ -333,8 +333,8 @@ public class RecalUtils {
         return covariate.getClass().getSimpleName().split("Covariate")[0];
     }
 
-    public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
+    public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) {
-        outputRecalibrationReport(RAC.generateReportTable(covariateNames(requestedCovariates)), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
+        outputRecalibrationReport(RAC.generateReportTable(covariateNames(requestedCovariates)), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), RAC.RECAL_TABLE);
     }
 
     /**
@@ -362,46 +362,36 @@ public class RecalUtils {
         report.print(outputFile);
     }
 
-    private static Pair<PrintStream, File> initializeRecalibrationPlot(File filename) {
+    private static void outputRecalibrationPlot(final RecalibrationArgumentCollection RAC) {
-        final PrintStream deltaTableStream;
-        final File deltaTableFileName = new File(filename + ".csv");
-        try {
-            deltaTableStream = new PrintStream(deltaTableFileName);
-        } catch (FileNotFoundException e) {
-            throw new UserException.CouldNotCreateOutputFile(deltaTableFileName, "File " + deltaTableFileName + " could not be created");
-        }
-        return new Pair<PrintStream, File>(deltaTableStream, deltaTableFileName);
-    }
-
-    private static void outputRecalibrationPlot(final File gatkReportFilename, Pair<PrintStream, File> files, boolean keepIntermediates) {
-        final File csvFileName = files.getSecond();
-        final File plotFileName = new File(csvFileName + ".pdf");
-        files.getFirst().close();
 
         final RScriptExecutor executor = new RScriptExecutor();
         executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class));
-        executor.addArgs(csvFileName.getAbsolutePath());
+        executor.addArgs(RAC.RECAL_CSV_FILE.getAbsolutePath());
-        executor.addArgs(gatkReportFilename.getAbsolutePath());
+        executor.addArgs(RAC.RECAL_TABLE_FILE.getAbsolutePath());
-        executor.addArgs(plotFileName.getAbsolutePath());
+        executor.addArgs(RAC.RECAL_PDF_FILE.getAbsolutePath());
         executor.exec();
-
-        if (!keepIntermediates)
-            if (!csvFileName.delete())
-                throw new ReviewedStingException("Could not find file " + csvFileName.getAbsolutePath());
-
     }
 
-    public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final Covariate[] requestedCovariates, final boolean keepIntermediates) {
+    public static void generateRecalibrationPlot(final RecalibrationArgumentCollection RAC, final RecalibrationTables original, final Covariate[] requestedCovariates) {
-        final Pair<PrintStream, File> files = initializeRecalibrationPlot(filename);
+        generateRecalibrationPlot(RAC, original, null, requestedCovariates);
-        writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, true);
-        outputRecalibrationPlot(filename, files, keepIntermediates);
     }
 
-    public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final RecalibrationTables recalibrated, final Covariate[] requestedCovariates, final boolean keepIntermediates) {
+    public static void generateRecalibrationPlot(final RecalibrationArgumentCollection RAC, final RecalibrationTables original, final RecalibrationTables recalibrated, final Covariate[] requestedCovariates) {
-        final Pair<PrintStream, File> files = initializeRecalibrationPlot(filename);
+        final PrintStream csvFile;
-        writeCSV(files.getFirst(), recalibrated, "RECALIBRATED", requestedCovariates, true);
+        try {
-        writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, false);
+            if ( RAC.RECAL_CSV_FILE == null ) {
-        outputRecalibrationPlot(filename, files, keepIntermediates);
+                RAC.RECAL_CSV_FILE = File.createTempFile("BQSR", ".csv");
+                RAC.RECAL_CSV_FILE.deleteOnExit();
+            }
+            csvFile = new PrintStream(RAC.RECAL_CSV_FILE);
+        } catch (IOException e) {
+            throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_CSV_FILE, e);
+        }
+
+        if ( recalibrated != null )
+            writeCSV(csvFile, recalibrated, "RECALIBRATED", requestedCovariates, true);
+        writeCSV(csvFile, original, "ORIGINAL", requestedCovariates, recalibrated == null);
+        outputRecalibrationPlot(RAC);
     }
 
     private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) {

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java

@@ -284,14 +284,11 @@ public class RecalibrationReport {
             else if (argument.equals("quantizing_levels"))
                 RAC.QUANTIZING_LEVELS = Integer.parseInt((String) value);
 
-            else if (argument.equals("keep_intermediate_files"))
-                RAC.KEEP_INTERMEDIATE_FILES = Boolean.parseBoolean((String) value);
-
-            else if (argument.equals("no_plots"))
-                RAC.NO_PLOTS = Boolean.parseBoolean((String) value);
-
             else if (argument.equals("recalibration_report"))
-                RAC.recalibrationReport = (value == null) ? null : new File((String) value);
+                RAC.existingRecalibrationReport = (value == null) ? null : new File((String) value);
+
+            else if (argument.equals("plot_pdf_file"))
+                RAC.RECAL_PDF_FILE = (value == null) ? null : new File((String) value);
 
             else if (argument.equals("binary_tag_name"))
                 RAC.BINARY_TAG_NAME = (value == null) ? null : (String) value;