Fix typo in CRAM conversion/resume logic

bbimber · bbimber · commit 9b6e10970ce6 · 2024-01-29T19:43:33.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1113,7 +1113,7 @@ else if (step.expectToCreateNewBam())
             final File cramFile = new File(renamedBam.getParentFile(), FileUtil.getBaseName(renamedBam) + ".cram");
             final File cramFileIdx = new File(cramFile.getPath() + ".crai");
             Integer threads = SequenceTaskHelper.getMaxThreads(getJob());
-            if (cramFileIdx.exists())
+            if (!cramFileIdx.exists())
             {
                 new SamtoolsCramConverter(getJob().getLogger()).convert(renamedBam, cramFile, referenceGenome.getWorkingFastaFileGzipped(), true, threads);
             }

Original file line number	Diff line number	Diff line change
`@@ -1113,7 +1113,7 @@ else if (step.expectToCreateNewBam())`
`1113`	`1113`	`final File cramFile = new File(renamedBam.getParentFile(), FileUtil.getBaseName(renamedBam) + ".cram");`
`1114`	`1114`	`final File cramFileIdx = new File(cramFile.getPath() + ".crai");`
`1115`	`1115`	`Integer threads = SequenceTaskHelper.getMaxThreads(getJob());`
`1116`		`- if (cramFileIdx.exists())`
	`1116`	`+ if (!cramFileIdx.exists())`
`1117`	`1117`	`{`
`1118`	`1118`	`new SamtoolsCramConverter(getJob().getLogger()).convert(renamedBam, cramFile, referenceGenome.getWorkingFastaFileGzipped(), true, threads);`
`1119`	`1119`	`}`