From cd85ff25014059fd4bb71eb5af02e8b294df1a00 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 19 Jan 2024 15:56:19 -0800 Subject: [PATCH] Allow DeepVariant to run on CRAMs --- .../sequenceanalysis/run/analysis/DeepVariantAnalysis.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java index 1e38284fd..2d0a831f5 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java @@ -22,6 +22,7 @@ import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; import org.labkey.api.util.FileUtil; import org.labkey.api.writer.PrintWriters; +import org.labkey.sequenceanalysis.util.SequenceUtil; import java.io.File; import java.io.IOException; @@ -205,7 +206,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu File workDir = outputGvcf.getParentFile(); File inputBamLocal = ensureLocalCopy(inputBam, workDir, tracker); - ensureLocalCopy(new File(inputBam.getPath() + ".bai"), workDir, tracker); + ensureLocalCopy(SequenceUtil.getExpectedIndex(inputBam), workDir, tracker); File refFastaLocal = ensureLocalCopy(refFasta, workDir, tracker); ensureLocalCopy(new File(refFastaLocal.getPath() + ".fai"), workDir, tracker);