Ensure bismark ends with sorted BAM

bbimber · bbimber · commit 86605c95ed72 · 2026-06-05T13:39:49.000-07:00
diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamSorter.java
@@ -40,7 +40,7 @@ public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder s
         boolean replaceOriginal = output == null;
         if (output == null)
         {
-            output = new File(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input));
+            output = FileUtil.appendName(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input));
         }
 
         List<String> params = new ArrayList<>();

Original file line number	Diff line number	Diff line change
`@@ -40,7 +40,7 @@ public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder s`
`40`	`40`	`boolean replaceOriginal = output == null;`
`41`	`41`	`if (output == null)`
`42`	`42`	`{`
`43`		`- output = new File(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input));`
	`43`	`+ output = FileUtil.appendName(getOutputDir(input), FileUtil.getBaseName(input) + ".sorted" + "." + FileUtil.getExtension(input));`
`44`	`44`	`}`
`45`	`45`
`46`	`46`	`List<String> params = new ArrayList<>();`