Bugfix to nimble regex

bbimber · bbimber · commit b52c0ac7f56f · 2022-12-04T12:42:43.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -364,7 +364,7 @@ else if (!resultsGz.exists())
         if (alignmentOutputFile.exists())
         {
             SimpleScriptWrapper runner = new SimpleScriptWrapper(getPipelineCtx().getLogger());
-            File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replaceAll(".txt.gz$", ".subset.txt.gz$"));
+            File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replace(".txt.gz", ".subset.txt.gz"));
             runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' | awk -F '\t' ' $10!=\"\" ' > " + alignmentOutputFile2.getPath()));
         }
         else

Original file line number	Diff line number	Diff line change
`@@ -364,7 +364,7 @@ else if (!resultsGz.exists())`
`364`	`364`	`if (alignmentOutputFile.exists())`
`365`	`365`	`{`
`366`	`366`	`SimpleScriptWrapper runner = new SimpleScriptWrapper(getPipelineCtx().getLogger());`
`367`		`- File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replaceAll(".txt.gz$", ".subset.txt.gz$"));`
	`367`	`+ File alignmentOutputFile2 = new File(alignmentOutputFile.getParentFile(), alignmentOutputFile.getName().replace(".txt.gz", ".subset.txt.gz"));`
`368`	`368`	`runner.execute(Arrays.asList("/bin/bash", "-c", "zcat '" + alignmentOutputFile.getPath() + "' \| awk -F '\t' ' $10!=\"\" ' > " + alignmentOutputFile2.getPath()));`
`369`	`369`	`}`
`370`	`370`	`else`