From f6395645995f075f609848e69c52b129e2df99bf Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Sat, 2 Apr 2016 22:36:54 -0400 Subject: [PATCH] Fixed bug in which PrintReads left out @PG header record --- .../broadinstitute/gatk/tools/walkers/readutils/PrintReads.java | 2 +- .../broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java index 49426a5ad..eb1cf18c0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java @@ -195,7 +195,7 @@ public class PrintReads extends ReadWalker impleme //Add the program record (if appropriate) and set up the writer final boolean preSorted = true; - if (toolkit.getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) { + if (!NO_PG_TAG ) { NWaySAMFileWriter.setupWriter(out, toolkit, outputHeader, preSorted, this, PROGRAM_RECORD_NAME); } else { out.writeHeader(outputHeader); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java index 422bb8c33..540f350ab 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java @@ -34,6 +34,7 @@ public class BAQIntegrationTest extends WalkerTest { private final static String baseCommand = "-T PrintReads -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + " -o %s" + + " --no_pg_tag " + " -L 1:10,000,000-10,100,000"; // --------------------------------------------------------------------------------------------------------------