Change quotes in awk expression

bbimber · bbimber · commit ed83b68326d1 · 2022-10-20T20:43:50.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java
@@ -232,7 +232,7 @@ 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
`@@ -232,7 +232,7 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno`
`232`	`232`
`233`	`233`	`for (File s : inputs)`
`234`	`234`	`{`
`235`		`- String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk \" { $1 == '" + contig + "' } \" \| wc -l")));`
	`235`	`+ String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk ' { $1 == \"" + contig + "\" } ' \| wc -l")));`
`236`	`236`	`if ("0".equals(ret))`
`237`	`237`	`{`
`238`	`238`	`ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());`