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Merge pull request #1337 from broadinstitute/db_issue_1121 

Fixed bug in which PrintReads left out @PG header record
This commit is contained in:
David Benjamin 2016-04-22 10:47:31 -04:00
parent a43d2a7ed1 f639564599
commit 34a1b7d0b0
2 changed files with 2 additions and 1 deletions
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2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java
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@ -195,7 +195,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> 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);

1
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
View File

@ -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";
// --------------------------------------------------------------------------------------------------------------