From fa3ff5350800f1449b6e4e5f365cf2b745906932 Mon Sep 17 00:00:00 2001 From: Menachem Fromer Date: Wed, 13 Jul 2011 11:58:16 -0400 Subject: [PATCH 1/5] Filters should only be applied to the new VC if the old VC had filters applied --- .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index e59b29502..af24035c8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -220,6 +220,9 @@ public class ReadBackedPhasingWalker extends RodWalker Date: Wed, 13 Jul 2011 14:40:01 -0400 Subject: [PATCH 3/5] Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools. --- .../walkers/variantutils/VariantsToVCF.java | 4 +-- .../utils/codecs/vcf/VCFIntegrationTest.java | 28 +++++++++++++++++++ 2 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 7eb49da34..79134b553 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker { // setup the header fields Set hInfo = new HashSet(); hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); - hInfo.add(new VCFHeaderLine("source", "VariantsToVCF")); - hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName())); + //hInfo.add(new VCFHeaderLine("source", "VariantsToVCF")); + //hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName())); allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY); for ( VCFHeaderLine field : hInfo ) { diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java new file mode 100644 index 000000000..32ff25c7b --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -0,0 +1,28 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.WalkerTest; +import org.testng.annotations.Test; + +import java.io.File; +import java.util.Arrays; +import java.util.List; + +public class VCFIntegrationTest extends WalkerTest { + + @Test + public void testReadingAndWritingWitHNoChanges() { + + String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447"; + String testVCF = validationDataLocation + "vcf4.1.example.vcf"; + + String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + + String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF)); + List result = executeTest("Test Variant Annotator with no changes", spec1).getFirst(); + + String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath(); + WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF)); + executeTest("Test Variants To VCF from new output", spec2); + } +} From df996a1a738208dac7c42b24645f747304b3de7f Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 13 Jul 2011 14:53:58 -0400 Subject: [PATCH 4/5] more progress report for the Data Processing Pipeline. Bam lists can now have empty lines, comments and whitespaces anywhere. --- .../qscripts/DataProcessingPipeline.scala | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index f9369ee3f..d6caabd23 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -147,13 +147,22 @@ class DataProcessingPipeline extends QScript { } } + println("\n\n*** DEBUG ***\n") // Creating one file for each sample in the dataset val sampleBamFiles = scala.collection.mutable.Map.empty[String, File] for ((sample, flist) <- sampleTable) { + + println(sample + ":") + for (f <- flist) + println (f) + println() + val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam") sampleBamFiles(sample) = sampleFileName add(joinBams(flist, sampleFileName)) } + println("*** DEBUG ***\n\n") + return sampleBamFiles.toMap } @@ -211,8 +220,10 @@ class DataProcessingPipeline extends QScript { if (in.toString.endsWith("bam")) return List(in) var l: List[File] = List() - for (bam <- fromFile(in).getLines) - l :+= new File(bam) + for (bam <- fromFile(in).getLines) { + if (!bam.startsWith("#") && !bam.isEmpty) + l :+= new File(bam.trim) + } return l } @@ -234,9 +245,6 @@ class DataProcessingPipeline extends QScript { // Generate a BAM file per sample joining all per lane files if necessary val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams) - - println("nContigs: " + nContigs) - // Final output list of processed bam files var cohortList: List[File] = List() @@ -244,6 +252,7 @@ class DataProcessingPipeline extends QScript { println("\nFound the following samples: ") for ((sample, file) <- sampleBamFiles) println("\t" + sample + " -> " + file) + println("\n") // If this is a 'knowns only' indel realignment run, do it only once for all samples. val globalIntervals = new File(outputDir + projectName + ".intervals") From bb0e3a26fcf2a0c99ee0e70c46fb6359b3720a40 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 13 Jul 2011 14:57:21 -0400 Subject: [PATCH 5/5] Added integration test for VCF writing. Also, bug fix for writing the GT-free records. --- .../sting/utils/codecs/vcf/StandardVCFWriter.java | 7 ++++--- .../variantutils/VariantsToVCFIntegrationTest.java | 8 ++++---- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java index f7d09f16d..e7ddac185 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java @@ -444,9 +444,10 @@ public class StandardVCFWriter implements VCFWriter { break; } - for (String s : attrs ) { - mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR); - mWriter.write(s); + for (int i = 0; i < attrs.size(); i++) { + if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY) ) + mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR); + mWriter.write(attrs.get(i)); } } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java index 8421076c9..8c96c1e11 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testVariantsToVCFUsingGeliInput() { List md5 = new ArrayList(); - md5.add("815b82fff92aab41c209eedce2d7e7d9"); + md5.add("4accae035d271b35ee2ec58f403c68c6"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + @@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testGenotypesToVCFUsingGeliInput() { List md5 = new ArrayList(); - md5.add("22336ee9c12aa222ce29c3c5babca7d0"); + md5.add("71e8c98d7c3a73b6287ecc339086fe03"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + @@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testGenotypesToVCFUsingHapMapInput() { List md5 = new ArrayList(); - md5.add("9bedaa7670b86a07be5191898c3727cf"); + md5.add("f343085305e80c7a2493422e4eaad983"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + @@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testGenotypesToVCFUsingVCFInput() { List md5 = new ArrayList(); - md5.add("cc215edec9ca28e5c79ab1b67506f9f7"); + md5.add("86f02e2e764ba35854cff2aa05a1fdd8"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference +