def do_buffer(buffer, msr, spc, psc, args):
outputs = []
for entries in buffer:
l = []
r = []
for sam in entries:
#Print line if its not a pair
if not_a_mate_sam(sam):
if not args.mates_only:
outputs.append(sam.get_line())
continue
if sam.check_flag(64): l.append(sam)
if sam.check_flag(128): r.append(sam)
if not (len(l) == 1 and len(r) == 1):
# more than just a unique pair here
if not args.mates_only:
for sam in l:
outputs.append(sam.get_line())
for sam in r:
outputs.append(sam.get_line())
continue
#Verify pairing by reference and direction
if l[0].value('rname') != r[0].value('rname') or l[0].check_flag(
16) == r[0].check_flag(16):
sys.stderr.write(
"ERROR, these are not actually properly paired as we were led to believe\n"
)
sys.exit()
p1 = PSL(spc.convert_line(l[0].get_line()))
if not re.search('[HP]', l[0].value('cigar')):
p1.set_query(l[0].value('seq'))
p1.set_quality_seq(l[0].value('qual'))
if l[0].check_flag(16):
# set the query to what it actually is
p1.set_query(rc(l[0].value('seq')))
p1.set_quality_seq(l[0].value('qual')[::-1])
p2 = PSL(spc.convert_line(r[0].get_line()))
if not re.search('[HP]', r[0].value('cigar')):
p2.set_query(r[0].value('seq'))
p2.set_quality_seq(r[0].value('qual'))
if r[0].check_flag(16):
# set the query to what it actually is
p2.set_query(rc(r[0].value('seq')))
p2.set_quality_seq(r[0].value('qual')[::-1])
p12 = join_mated(p1, p2)
if not p12:
if not args.mates_only:
outputs.append(l[0].get_line())
outputs.append(r[0].get_line())
continue
#if p1.value('strand') == '-' and p2.value('strand') == '+' \
#and p2.value('tEnd') < p1.value('tStart'):
sline = psc.convert_line(p12.get_line(),
query_sequence=p12.get_query(),
quality_sequence=p12.get_quality_seq())
#print p12.get_line()
outputs.append(sline)
return outputs
def do_buffer(buffer,msr,spc,psc,args):
outputs = []
for entries in buffer:
l = []
r = []
for sam in entries:
#Print line if its not a pair
if not_a_mate_sam(sam):
if not args.mates_only:
outputs.append(sam.get_line())
continue
if sam.check_flag(64): l.append(sam)
if sam.check_flag(128): r.append(sam)
if not (len(l)==1 and len(r)==1):
# more than just a unique pair here
if not args.mates_only:
for sam in l: outputs.append(sam.get_line())
for sam in r: outputs.append(sam.get_line())
continue
#Verify pairing by reference and direction
if l[0].value('rname') != r[0].value('rname') or l[0].check_flag(16) == r[0].check_flag(16):
sys.stderr.write("ERROR, these are not actually properly paired as we were led to believe\n")
sys.exit()
p1 = PSL(spc.convert_line(l[0].get_line()))
if not re.search('[HP]',l[0].value('cigar')):
p1.set_query(l[0].value('seq'))
p1.set_quality_seq(l[0].value('qual'))
if l[0].check_flag(16):
# set the query to what it actually is
p1.set_query(rc(l[0].value('seq')))
p1.set_quality_seq(l[0].value('qual')[::-1])
p2 = PSL(spc.convert_line(r[0].get_line()))
if not re.search('[HP]',r[0].value('cigar')):
p2.set_query(r[0].value('seq'))
p2.set_quality_seq(r[0].value('qual'))
if r[0].check_flag(16):
# set the query to what it actually is
p2.set_query(rc(r[0].value('seq')))
p2.set_quality_seq(r[0].value('qual')[::-1])
p12 = join_mated(p1,p2)
if not p12:
if not args.mates_only:
outputs.append(l[0].get_line())
outputs.append(r[0].get_line())
continue
#if p1.value('strand') == '-' and p2.value('strand') == '+' \
#and p2.value('tEnd') < p1.value('tStart'):
sline = psc.convert_line(p12.get_line(),query_sequence=p12.get_query(),quality_sequence=p12.get_quality_seq())
#print p12.get_line()
outputs.append(sline)
return outputs
