Ensure merge.done file is unique for the input VCF

bbimber · bbimber · commit 7746b2b1c61c · 2024-11-06T07:34:12.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java
@@ -515,7 +515,7 @@ else if (!samples.equals(header.getGenotypeSamples()))
                 writer.write("} | bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > '" + outputGzip.getPath() + "'\n");
             }
 
-            File mergeDone = new File(outputGzip.getParentFile(), "merge.done");
+            File mergeDone = new File(outputGzip.getPath() + ".merge.done");
             if (mergeDone.exists())
             {
                 log.debug("Merge done file exists, will not repeat merge");

Original file line number	Diff line number	Diff line change
`@@ -515,7 +515,7 @@ else if (!samples.equals(header.getGenotypeSamples()))`
`515`	`515`	`writer.write("} \| bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > '" + outputGzip.getPath() + "'\n");`
`516`	`516`	`}`
`517`	`517`
`518`		`- File mergeDone = new File(outputGzip.getParentFile(), "merge.done");`
	`518`	`+ File mergeDone = new File(outputGzip.getPath() + ".merge.done");`
`519`	`519`	`if (mergeDone.exists())`
`520`	`520`	`{`
`521`	`521`	`log.debug("Merge done file exists, will not repeat merge");`