Fix typo in CRAM conversion/resume logic

BimberLab · Jan 30, 2024 · 9b6e109 · 9b6e109
1 parent 961ab8c
commit 9b6e109
Showing 1 changed file with 1 addition and 1 deletion.
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);
             }