Respect minInsertSize in all cases

bbimber · bbimber · commit f1e44c2ea454 · 2020-09-14T07:44:14.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java
@@ -166,9 +166,9 @@ private static String inferInsertSize(PipelineContext ctx, File bam, int minInse
             throw new PipelineJobException(e);
         }
 
-        ctx.getLogger().error("unable to infer insert size, defaulting to 250");
+        ctx.getLogger().error("unable to infer insert size, defaulting to " + minInsertSize);
 
-        return "100";
+        return String.valueOf(minInsertSize);
     }
 
     public static File runPindel(AnalysisOutputImpl output, PipelineContext ctx, Readset rs, File outDir, File inputBam, File fasta, double minFraction, int minDepth, boolean removeDuplicates, File gatkDepth, int minInsertSize) throws PipelineJobException

Original file line number	Diff line number	Diff line change
`@@ -166,9 +166,9 @@ private static String inferInsertSize(PipelineContext ctx, File bam, int minInse`
`166`	`166`	`throw new PipelineJobException(e);`
`167`	`167`	`}`
`168`	`168`
`169`		`- ctx.getLogger().error("unable to infer insert size, defaulting to 250");`
	`169`	`+ ctx.getLogger().error("unable to infer insert size, defaulting to " + minInsertSize);`
`170`	`170`
`171`		`- return "100";`
	`171`	`+ return String.valueOf(minInsertSize);`
`172`	`172`	`}`
`173`	`173`
`174`	`174`	`public static File runPindel(AnalysisOutputImpl output, PipelineContext ctx, Readset rs, File outDir, File inputBam, File fasta, double minFraction, int minDepth, boolean removeDuplicates, File gatkDepth, int minInsertSize) throws PipelineJobException`