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don't sort output #8053

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merged 1 commit into from
Oct 13, 2022
Merged

don't sort output #8053

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13 changes: 10 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -187,10 +187,17 @@ public void onTraversalStart() {
reference = new Reference(ReferenceDataSource.of(referenceArguments.getReferencePath()));
codonTracker = new CodonTracker(orfCoords, reference.getRefSeq(), logger);
if ( writeRejectedReads ) {
rejectedReadsBAMWriter = createSAMWriter(new GATKPath(outputFilePrefix + ".rejected.bam"), false);
rejectedReadsBAMWriter = createSAMWriter(new GATKPath(outputFilePrefix + ".rejected.bam"), true);
}
}

@Override
protected SAMFileHeader getHeaderForSAMWriter() {
final SAMFileHeader header = super.getHeaderForSAMWriter();
header.setSortOrder(SortOrder.unsorted);
return header;
}

@Override
public void traverse() {
// ignore non-primary alignments
Expand Down Expand Up @@ -1324,11 +1331,11 @@ public void reportWildCodonCounts( final Interval refCoverage ) {
throw new UserException("Can't interpret ORF as list of pairs of coords: " + orfCoords);
}
try {
final int start = Integer.valueOf(coords[0]);
final int start = Integer.parseInt(coords[0]);
if ( start < 1 ) {
throw new UserException("Coordinates of ORF are 1-based.");
}
final int end = Integer.valueOf(coords[1]);
final int end = Integer.parseInt(coords[1]);
if ( end < start ) {
throw new UserException("Found ORF end coordinate less than start: " + orfCoords);
}
Expand Down