From 1502eed32f88e541cb7e2b2cfc19f66100c7caa0 Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Wed, 24 Aug 2011 16:43:02 -0400 Subject: [PATCH] sam2interval: Add read_name column --- tools/samtools/sam2interval.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/samtools/sam2interval.py b/tools/samtools/sam2interval.py index fd9e4bfddd4..89c6963e765 100644 --- a/tools/samtools/sam2interval.py +++ b/tools/samtools/sam2interval.py @@ -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()