From b8d8856ccddcea08771e1c63cf2f7466b76ad0d6 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Tue, 29 Oct 2013 16:32:37 -0400
Subject: [PATCH] Fixed test for Bam vs Bgzip to allow for empty references.
---
src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
index 2044120b..32132ea9 100644
--- a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
@@ -175,9 +175,8 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar, bool &mustApp
_bamReader = new BamTools::BamReader();
_bamReader->OpenStream(_finalInputStream);
QuickString bamHeader(_bamReader->GetHeaderText());
- BamTools::RefVector bamRefs(_bamReader->GetReferenceData());
- if (bamHeader.empty() || bamRefs.empty()) {
+ if (bamHeader.empty()) {
//This is NOT a bam file.
_pushBackStreamBuf->clear();
_compressedSaveData.clear();
--
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