Commit 333b85c0 authored by Aaron Quinlan's avatar Aaron Quinlan
Browse files

Merge pull request #14 from nkindlon/master

Added fix for Bam files with empty headers. Added test for this to unit ...
parents 6d5a7587 a16562f4
......@@ -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
......
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,
......@@ -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
......
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