From f9781345fceccdca41cd4d436c64c8f28e3ae72f Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 23 Jan 2024 21:04:46 -0800
Subject: [PATCH] Improve resume behavior for CRAM conversion

---
 .../sequenceanalysis/pipeline/SequenceAlignmentTask.java | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
index f0b4c4aae..bf149d4ff 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1113,7 +1113,14 @@ 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());
-            new SamtoolsCramConverter(getJob().getLogger()).convert(renamedBam, cramFile, referenceGenome.getWorkingFastaFileGzipped(), true, threads);
+            if (cramFileIdx.exists())
+            {
+                new SamtoolsCramConverter(getJob().getLogger()).convert(renamedBam, cramFile, referenceGenome.getWorkingFastaFileGzipped(), true, threads);
+            }
+            else
+            {
+                getJob().getLogger().debug("CRAM index already exists, skipping conversion");
+            }
 
             final File finalBam = renamedBam;
             final File finalBamIdx = new File(renamedBam.getPath() + ".bai");