don't sort rejected reads output from AnalyzeSaturationMutagenesis (#…

…8053)
broadinstitute · Oct 13, 2022 · 07a8278 · 07a8278
1 parent 8dbb78f
commit 07a8278
Showing 1 changed file with 10 additions and 3 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java b/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java
@@ -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
@@ -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);
                     }