Catch more forms of pindel output

bbimber · bbimber · commit f1822098da47 · 2020-09-02T12:03:28.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -302,9 +302,14 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     }
 
                     String pindelBasename = SequenceAnalysisService.get().getUnzippedBaseName(so.getFile().getName());
-                    if (pindelBasename.endsWith("lofreq"))
+                    if (pindelBasename.contains(".all"))
                     {
-                        pindelBasename = FileUtil.getBaseName(pindelBasename);
+                        pindelBasename = pindelBasename.replaceAll("\\.all", "");
+                    }
+
+                    if (pindelBasename.contains(".lofreq"))
+                    {
+                        pindelBasename = pindelBasename.replaceAll("\\.lofreq", "");
                     }
 
                     File pindelFile = new File(so.getFile().getParentFile(), pindelBasename + ".pindel.txt");

Original file line number	Diff line number	Diff line change
`@@ -302,9 +302,14 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`302`	`302`	`}`
`303`	`303`
`304`	`304`	`String pindelBasename = SequenceAnalysisService.get().getUnzippedBaseName(so.getFile().getName());`
`305`		`- if (pindelBasename.endsWith("lofreq"))`
	`305`	`+ if (pindelBasename.contains(".all"))`
`306`	`306`	`{`
`307`		`- pindelBasename = FileUtil.getBaseName(pindelBasename);`
	`307`	`+ pindelBasename = pindelBasename.replaceAll("\\.all", "");`
	`308`	`+ }`
	`309`	`+`
	`310`	`+ if (pindelBasename.contains(".lofreq"))`
	`311`	`+ {`
	`312`	`+ pindelBasename = pindelBasename.replaceAll("\\.lofreq", "");`
`308`	`313`	`}`
`309`	`314`
`310`	`315`	`File pindelFile = new File(so.getFile().getParentFile(), pindelBasename + ".pindel.txt");`