Ensure bismark ends with sorted BAM

bbimber · bbimber · commit 9f4255cd23d3 · 2026-06-05T13:37:00.000-07:00
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java b/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java
@@ -242,6 +242,9 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
                     }
 
                     output.addIntermediateFile(bam);
+
+                    dedupBam = new SamSorter(getPipelineCtx().getLogger()).execute(dedupBam, null, SAMFileHeader.SortOrder.coordinate);
+
                     bam = dedupBam;
                 }
                 catch (IOException e)

Original file line number	Diff line number	Diff line change
`@@ -242,6 +242,9 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`242`	`242`	`}`
`243`	`243`
`244`	`244`	`output.addIntermediateFile(bam);`
	`245`	`+`
	`246`	`+ dedupBam = new SamSorter(getPipelineCtx().getLogger()).execute(dedupBam, null, SAMFileHeader.SortOrder.coordinate);`
	`247`	`+`
`245`	`248`	`bam = dedupBam;`
`246`	`249`	`}`
`247`	`250`	`catch (IOException e)`