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sam2interval: Add read_name column

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This commit is contained in:
Kanwei Li
2011-08-24 16:43:02 -04:00
parent eb036815cb
commit 1502eed32f
1 changed files with 2 additions and 2 deletions
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tools/samtools/sam2interval.py
+2 -2
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@@ -68,7 +68,7 @@ options (listed below) default to 'None' if omitted
cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' )
print '#chrom\tstart\tend\tstrand' # provide a (partial) header so that strand is automatically set in metadata
print '#chrom\tstart\tend\tstrand\tread_name' # provide a (partial) header so that strand is automatically set in metadata
for line in infile:
line = line.rstrip( '\r\n' )
@@ -90,7 +90,7 @@ options (listed below) default to 'None' if omitted
if options.prt_all:
print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
else:
print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand)
print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, read_name)
if __name__ == "__main__": main()