#!/usr/bin/env python

# fix a bug in cufflinks that prevents it to read BAM files in
# which reference sequences (@SQ lines) have more than one colon
# See http://seqanswers.com/forums/showthread.php?t=9304

import sys

i_fn, o_fn = sys.argv[1:3]

i = open(i_fn, 'rU')
o = open(o_fn, 'w')

while True:
	line = i.readline()
	if (line == ''):
		break

	line = line.strip()

	# header section, reference sequence dictionary
	if (line.startswith("@SQ")):
		items = line.split('\t')

		sn_idx = None
		for p, item in enumerate(items):
			if (item.startswith("SN:")):
				sn_idx = p
				break

		if (sn_idx == None):
			print >>sys.stderr, "ERROR: No reference sequence name found (line was '%s')" % line
			sys.exit(1)

		sn = items[sn_idx]

		if (sn.count(':') > 1):
			sn = "SN:" + sn[3:].replace(':', '_')
			line = '\t'.join(items[:sn_idx] + [sn] + items[sn_idx+1:])

	# alignment section
	elif (not line.startswith('@')):
		items = line.split('\t')

		if (len(items) < 11):
			print >>sys.stderr, "ERROR: Invalid alignment (line was '%s')" % line
			sys.exit(1)

		rname = items[2]

		if (rname.count(':') > 0):
			line = '\t'.join(items[:2] + [rname.replace(':', '_')] + items[3:])

	print >>o, line