From a16562f4c0840928a91ad42ad77f3c4a20af6d5c Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Fri, 3 Jan 2014 14:57:46 -0500
Subject: [PATCH] Added fix for Bam files with empty headers. Added test for
this to unit test.
---
.../FileReaders/InputStreamMgr.cpp | 5 +----
test/intersect/gdc.bam | Bin 0 -> 204 bytes
test/intersect/gdc_exp | 12 ++++++++++++
test/intersect/new_test-intersect.sh | 9 +++++++++
4 files changed, 22 insertions(+), 4 deletions(-)
create mode 100644 test/intersect/gdc.bam
create mode 100644 test/intersect/gdc_exp
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
index 1f9d0441..5b1d0a9c 100644
--- a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
@@ -204,10 +204,7 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
_bamReader = new BamTools::BamReader();
- _bamReader->OpenStream(_finalInputStream);
- QuickString bamHeader(_bamReader->GetHeaderText());
-
- if (bamHeader.empty()) {
+ if (!_bamReader->OpenStream(_finalInputStream)) {
//This is NOT a bam file, but it is bgzipped.
_pushBackStreamBuf->clear();
//Put all bytes read so far back onto the scan buffer, then reset
diff --git a/test/intersect/gdc.bam b/test/intersect/gdc.bam
new file mode 100644
index 0000000000000000000000000000000000000000..80dcfaa0b3080652c64d10497e4ecfb4e223a389
GIT binary patch
literal 204
zcmb2|=3rp}f&Xj_PR>jW`V7TIUs6*Tm;?^89XToK>So7dF7il{aZRF?s1#6{JevA?
zhRrDr40;M_f8T2!;aJr8!(OD}$)8W3gCv<6ctjN$c?CXvE=~LJxgc#zOIBHPw%CES
zJDr^wS3i?WGSSvb++HbVILmg{hU|SVJ@Z*rIetp^r@6bonN{6!@y?@%4WXZz7Ukr*
XY?WjXkL`Z`f)UexX$EGH>%jm3<v~Hn
literal 0
HcmV?d00001
diff --git a/test/intersect/gdc_exp b/test/intersect/gdc_exp
new file mode 100644
index 00000000..442b7f28
--- /dev/null
+++ b/test/intersect/gdc_exp
@@ -0,0 +1,12 @@
+chr2L 10 15 None 255 + 10 15 0,0,0 1 5, 0,
+chr2L 70 75 None 255 - 70 75 0,0,0 1 5, 0,
+chr2L 70 75 None 255 - 70 75 0,0,0 1 5, 0,
+chr2L 140 145 None 255 - 140 145 0,0,0 1 5, 0,
+chr2L 140 145 None 255 - 140 145 0,0,0 1 5, 0,
+chr2L 150 155 None 255 - 150 155 0,0,0 1 5, 0,
+chr2L 210 215 None 255 + 210 215 0,0,0 1 5, 0,
+chr2L 70 75 None 255 + 70 75 0,0,0 1 5, 0,
+chr2L 70 75 None 255 + 70 75 0,0,0 1 5, 0,
+chr2L 140 145 None 255 + 140 145 0,0,0 1 5, 0,
+chr2L 140 145 None 255 + 140 145 0,0,0 1 5, 0,
+chr2L 160 165 None 255 + 160 165 0,0,0 1 5, 0,
diff --git a/test/intersect/new_test-intersect.sh b/test/intersect/new_test-intersect.sh
index 056278b4..85c6a8bb 100755
--- a/test/intersect/new_test-intersect.sh
+++ b/test/intersect/new_test-intersect.sh
@@ -605,6 +605,15 @@ check obs exp
rm obs exp
+###########################################################
+# Test that we can process a Bam file with no text in
+# it's header.
+############################################################
+echo " intersect.new.t53...\c"
+$BT intersect -a gdc.bam -b gdc.bam -bed > obs
+check obs gdc_exp
+rm obs
+
--
GitLab