Fix error in GenotypeGVCF intervals for scatter job

bbimber · bbimber · commit a1d5a2c561c6 · 2022-09-01T09:26:21.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
@@ -692,7 +692,7 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                 if (intervals.size() > 5)
                 {
                     ctx.getLogger().debug("Too many intervals, writing to file");
-                    File intervalFile = new File(outputVcf.getParentFile(), "intervals.list");
+                    File intervalFile = new File(outputVcf.getParentFile(), "genotypeIntervals.list");
                     ctx.getFileManager().addIntermediateFile(intervalFile);
                     try (PrintWriter writer = PrintWriters.getPrintWriter(intervalFile))
                     {
@@ -704,6 +704,9 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                     {
                         throw new PipelineJobException(e);
                     }
+
+                    toolParams.add("-L");
+                    toolParams.add(intervalFile.getPath());
                 }
                 else
                 {

Original file line number	Diff line number	Diff line change
`@@ -692,7 +692,7 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge`
`692`	`692`	`if (intervals.size() > 5)`
`693`	`693`	`{`
`694`	`694`	`ctx.getLogger().debug("Too many intervals, writing to file");`
`695`		`- File intervalFile = new File(outputVcf.getParentFile(), "intervals.list");`
	`695`	`+ File intervalFile = new File(outputVcf.getParentFile(), "genotypeIntervals.list");`
`696`	`696`	`ctx.getFileManager().addIntermediateFile(intervalFile);`
`697`	`697`	`try (PrintWriter writer = PrintWriters.getPrintWriter(intervalFile))`
`698`	`698`	`{`
`@@ -704,6 +704,9 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge`
`704`	`704`	`{`
`705`	`705`	`throw new PipelineJobException(e);`
`706`	`706`	`}`
	`707`	`+`
	`708`	`+ toolParams.add("-L");`
	`709`	`+ toolParams.add(intervalFile.getPath());`
`707`	`710`	`}`
`708`	`711`	`else`
`709`	`712`	`{`