Dont delete SnpEff sites from lofreq merge

bbimber · bbimber · commit d3dd083b070e · 2020-09-14T11:01:22.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -900,8 +900,8 @@ private void runSnpEff(JobContext ctx, Map<String, SiteAndAlleles> siteToAllele,
                 snpEffSites.forEach(writer::add);
             }
 
-            ctx.getFileManager().addIntermediateFile(vcfOut);
-            ctx.getFileManager().addIntermediateFile(new File(vcfOut.getPath() + ".tbi"));
+            //ctx.getFileManager().addIntermediateFile(vcfOut);
+            //ctx.getFileManager().addIntermediateFile(new File(vcfOut.getPath() + ".tbi"));
 
             SnpEffWrapper snpEffWrapper = new SnpEffWrapper(ctx.getLogger());
             Integer geneFileId = ctx.getParams().optInt(SNPEffStep.GENE_PARAM, -1);

Original file line number	Diff line number	Diff line change
`@@ -900,8 +900,8 @@ private void runSnpEff(JobContext ctx, Map<String, SiteAndAlleles> siteToAllele,`
`900`	`900`	`snpEffSites.forEach(writer::add);`
`901`	`901`	`}`
`902`	`902`
`903`		`- ctx.getFileManager().addIntermediateFile(vcfOut);`
`904`		`- ctx.getFileManager().addIntermediateFile(new File(vcfOut.getPath() + ".tbi"));`
	`903`	`+ //ctx.getFileManager().addIntermediateFile(vcfOut);`
	`904`	`+ //ctx.getFileManager().addIntermediateFile(new File(vcfOut.getPath() + ".tbi"));`
`905`	`905`
`906`	`906`	`SnpEffWrapper snpEffWrapper = new SnpEffWrapper(ctx.getLogger());`
`907`	`907`	`Integer geneFileId = ctx.getParams().optInt(SNPEffStep.GENE_PARAM, -1);`