From 1d0180482162b744141cd7fb41ba8e6efca93ab1 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 26 Feb 2024 17:26:04 -0800
Subject: [PATCH] Allow PicardAlignmentMetricsHandler to work on CRAMs

---
 .../analysis/PicardAlignmentMetricsHandler.java              | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java
index 70fd46e53..63a49d1ab 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java
@@ -26,6 +26,7 @@
 import org.labkey.sequenceanalysis.run.util.CollectWgsMetricsWithNonZeroCoverageWrapper;
 import org.labkey.sequenceanalysis.run.util.CollectWgsMetricsWrapper;
 import org.labkey.sequenceanalysis.run.util.MarkDuplicatesWrapper;
+import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -39,7 +40,7 @@
  */
 public class PicardAlignmentMetricsHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
 {
-    private final FileType _bamFileType = new FileType("bam", false);
+    private final FileType _bamOrCramFileType = SequenceUtil.FILETYPE.bamOrCram.getFileType();
 
     public PicardAlignmentMetricsHandler()
     {
@@ -68,7 +69,7 @@ public PicardAlignmentMetricsHandler()
     @Override
     public boolean canProcess(SequenceOutputFile o)
     {
-        return o.getFile() != null && _bamFileType.isType(o.getFile());
+        return o.getFile() != null && _bamOrCramFileType.isType(o.getFile());
     }
 
     @Override