Always trim output from Bcftools

bbimber · bbimber · commit d2b2f33b54b4 · 2023-07-11T11:59:32.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java
@@ -501,7 +501,7 @@ private static String countUsingBcfTools(File vcf, Logger log) throws PipelineJo
     {
         BcftoolsRunner wrapper = new BcftoolsRunner(log);
 
-        return wrapper.executeWithOutput(Arrays.asList(wrapper.getBcfToolsPath().getPath(), "index", "-n", vcf.getPath()));
+        return StringUtils.trimToNull(wrapper.executeWithOutput(Arrays.asList(wrapper.getBcfToolsPath().getPath(), "index", "-n", vcf.getPath())));
     }
 
     public static String getVCFLineCount(File vcf, Logger log, boolean passOnly, boolean useBcfTools) throws PipelineJobException

Original file line number	Diff line number	Diff line change
`@@ -501,7 +501,7 @@ private static String countUsingBcfTools(File vcf, Logger log) throws PipelineJo`
`501`	`501`	`{`
`502`	`502`	`BcftoolsRunner wrapper = new BcftoolsRunner(log);`
`503`	`503`
`504`		`- return wrapper.executeWithOutput(Arrays.asList(wrapper.getBcfToolsPath().getPath(), "index", "-n", vcf.getPath()));`
	`504`	`+ return StringUtils.trimToNull(wrapper.executeWithOutput(Arrays.asList(wrapper.getBcfToolsPath().getPath(), "index", "-n", vcf.getPath())));`
`505`	`505`	`}`
`506`	`506`
`507`	`507`	`public static String getVCFLineCount(File vcf, Logger log, boolean passOnly, boolean useBcfTools) throws PipelineJobException`