Bugfix lofreq-merge sorting of TSV

bbimber · bbimber · commit d6fa2055d004 · 2020-09-11T11:25:44.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -710,7 +710,7 @@ private int getReadDepth(File vcf, Map<String, Integer> contigToOffset, String c
 
         private void sortTsvFile(JobContext ctx, File input) throws PipelineJobException
         {
-            File output = new File(input.getPath() + ".tmp");
+            File output = new File(input.getParentFile(), "tmpTable.txt.gz");
             File script = new File(input.getParentFile(), "script.sh");
             try (PrintWriter writer = PrintWriters.getPrintWriter(script))
             {

Original file line number	Diff line number	Diff line change
`@@ -710,7 +710,7 @@ private int getReadDepth(File vcf, Map<String, Integer> contigToOffset, String c`
`710`	`710`
`711`	`711`	`private void sortTsvFile(JobContext ctx, File input) throws PipelineJobException`
`712`	`712`	`{`
`713`		`- File output = new File(input.getPath() + ".tmp");`
	`713`	`+ File output = new File(input.getParentFile(), "tmpTable.txt.gz");`
`714`	`714`	`File script = new File(input.getParentFile(), "script.sh");`
`715`	`715`	`try (PrintWriter writer = PrintWriters.getPrintWriter(script))`
`716`	`716`	`{`