Fix syntax

bbimber · bbimber · commit bcb26d015380 · 2022-11-21T17:40:29.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java
@@ -248,7 +248,7 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno
 
                 for (File s : inputs)
                 {
-                    String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' | awk ' { $1 == \"" + contig + "\" } ' | wc -l")));
+                    String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' | awk ' $1 == \"" + contig + "\" ' | wc -l")));
                     if ("0".equals(ret))
                     {
                         ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());

Original file line number	Diff line number	Diff line change
`@@ -248,7 +248,7 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno`
`248`	`248`
`249`	`249`	`for (File s : inputs)`
`250`	`250`	`{`
`251`		`- String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk ' { $1 == \"" + contig + "\" } ' \| wc -l")));`
	`251`	`+ String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk ' $1 == \"" + contig + "\" ' \| wc -l")));`
`252`	`252`	`if ("0".equals(ret))`
`253`	`253`	`{`
`254`	`254`	`ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());`