Expand ConvertToCramHandler to support CRAM

bbimber · bbimber · commit 53bfea1a0c51 · 2025-05-19T09:51:11.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java
@@ -55,7 +55,7 @@ public ConvertToCramHandler()
     @Override
     public boolean canProcess(SequenceOutputFile o)
     {
-        return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bam.getFileType().isType(o.getFile());
+        return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().isType(o.getFile());
     }
 
     @Override

Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ public ConvertToCramHandler()`
`55`	`55`	`@Override`
`56`	`56`	`public boolean canProcess(SequenceOutputFile o)`
`57`	`57`	`{`
`58`		`- return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bam.getFileType().isType(o.getFile());`
	`58`	`+ return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().isType(o.getFile());`
`59`	`59`	`}`
`60`	`60`
`61`	`61`	`@Override`