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gatk-3.8
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Actually writes out a good header now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@744 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-05-18 13:34:52 +00:00
parent c10741e9f5
commit 9dec783a82
1 changed files with 3 additions and 2 deletions
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5
python/SimulateReads.py
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@ -651,7 +651,8 @@ def main():
raise Exception('Does not support mutation density > 1 for mutations of class', OPTIONS.mutationType)
readLen = OPTIONS.readLen
header = SAMHeader( "MarkD", readLen )
fastaRecords = [seq for seq in readRef(OPTIONS.reference)]
header = SAMHeader( fastaRecords[0].id, len(fastaRecords[0].seq) )
SAMout = SAMIO( outputSAM, header, debugging=OPTIONS.debug )
mutationsout = open(root + '.mutations.txt', 'w')
@ -665,7 +666,7 @@ def main():
counter = 0
refLen = 0
for ref in readRef(OPTIONS.reference):
for ref in fastaRecords:
refLen = len(ref.seq)
# write the crazy ref file info needed by samtools