Cannot index and use -n

bbimber · bbimber · commit ee6a2e3e67e6 · 2025-02-24T06:12:06.000-08:00
diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BcftoolsRunner.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BcftoolsRunner.java
@@ -39,7 +39,6 @@ public void doIndex(File vcf) throws PipelineJobException
         args.add("index");
         args.add("-t");
         args.add("-f");
-        args.add("-n");
 
         if (!PipelineJobService.get().isWebServer())
         {

Original file line number	Diff line number	Diff line change
`@@ -39,7 +39,6 @@ public void doIndex(File vcf) throws PipelineJobException`
`39`	`39`	`args.add("index");`
`40`	`40`	`args.add("-t");`
`41`	`41`	`args.add("-f");`
`42`		`- args.add("-n");`
`43`	`42`
`44`	`43`	`if (!PipelineJobService.get().isWebServer())`
`45`	`44`	`{`