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uniqify PG IDs in FilterAlignmentArtifacts #6304

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Merged
merged 2 commits into from
Dec 6, 2019
Merged

uniqify PG IDs in FilterAlignmentArtifacts #6304

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b431eef
uniqify PG IDs in FilterAlignmentArtifacts
davidbenjamin Dec 6, 2019
9e097d6
test files
davidbenjamin Dec 6, 2019
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2 changes: 1 addition & 1 deletion ...g/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
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Expand Up @@ -191,7 +191,7 @@ public void onTraversalStart() {
assemblyEngine = MTAC.createReadThreadingAssembler();
likelihoodCalculationEngine = AssemblyBasedCallerUtils.createLikelihoodCalculationEngine(MTAC.likelihoodArgs);
haplotypeBAMWriter = bamOutputPath == null ? Optional.empty() :
Optional.of(new HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType.ALL_POSSIBLE_HAPLOTYPES, IOUtils.getPath(bamOutputPath), true, false, bamHeader));
Optional.of(new HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType.ALL_POSSIBLE_HAPLOTYPES, IOUtils.getPath(bamOutputPath), true, false, getHeaderForSAMWriter()));
}

@Override
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMDestination.java
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Expand Up @@ -44,7 +44,7 @@ protected HaplotypeBAMDestination(SAMFileHeader sourceHeader, final String haplo
readGroups.add(rgRec);
bamOutputHeader.setReadGroups(readGroups);
final List<SAMProgramRecord> programRecords = new ArrayList<>(sourceHeader.getProgramRecords());
programRecords.add(new SAMProgramRecord("HalpotypeBAMWriter"));
programRecords.add(new SAMProgramRecord("HaplotypeBAMWriter"));
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This is an amazing typo catch

bamOutputHeader.setProgramRecords(programRecords);
}

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2 changes: 1 addition & 1 deletion ...g/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriter/expected/fromHeaderSAM.sam
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Expand Up @@ -23,7 +23,7 @@
@PG ID:0 CL:run 0 VN:1.0 PN:Program0
@PG ID:1 CL:run 1 VN:1.0 PP:0 PN:Program1
@PG ID:2 CL:run 2 VN:1.0 PP:1 PN:Program2
@PG ID:HalpotypeBAMWriter
@PG ID:HaplotypeBAMWriter
READ_0_0 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
READ_0_1 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
READ_1_0 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
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2 changes: 1 addition & 1 deletion ...ces/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriter/expected/testSAM.sam
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Expand Up @@ -23,7 +23,7 @@
@PG ID:0 CL:run 0 VN:1.0 PN:Program0
@PG ID:1 CL:run 1 VN:1.0 PP:0 PN:Program1
@PG ID:2 CL:run 2 VN:1.0 PP:1 PN:Program2
@PG ID:HalpotypeBAMWriter
@PG ID:HaplotypeBAMWriter
READ_0_0 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
READ_0_1 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
READ_1_0 0 2 1 0 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
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