From d61a12b4e9f945b86a1e2b9244c23f81263a0ac6 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Fri, 9 Dec 2016 11:49:31 -0500
Subject: [PATCH] - use SEQUENCE_REFERENCE when opening files in
 CheckFingerprints. This should allow fingerprinting CRAM files directly.

---
 src/main/java/picard/fingerprint/CheckFingerprint.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/picard/fingerprint/CheckFingerprint.java b/src/main/java/picard/fingerprint/CheckFingerprint.java
index 9a8e926fa..8bc4fbbcb 100644
--- a/src/main/java/picard/fingerprint/CheckFingerprint.java
+++ b/src/main/java/picard/fingerprint/CheckFingerprint.java
@@ -155,7 +155,7 @@ protected int doWork() {
             SequenceUtil.assertSequenceDictionariesEqual(SAMSequenceDictionaryExtractor.extractDictionary(INPUT), checker.getHeader().getSequenceDictionary(), true);
 
             // Verify that there's only one sample in the SAM/BAM.
-            final SamReader in = SamReaderFactory.makeDefault().open(INPUT);
+            final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
             for (final SAMReadGroupRecord rec : in.getFileHeader().getReadGroups()) {
                 if (observedSampleAlias == null) {
                     observedSampleAlias = rec.getSample();