is_next_unmapped = 0x8 #next fragment in the template unmapped
is_revcomp = 0x10 #SEQ being reverse complemented
is_next_reversed = 0x20 #SEQ of the next fragment in the template being reversed
is_read1 = 0x40 #the first fragment in the template
is_read2 = 0x80 #the last fragment in the template
is_secondary = 0x100 #secondary alignment
is_failqc = 0x200 #not passing quality controls
is_dupe = 0x400 #PCR or optical duplicate
for fname in sys.argv[1:]:
data = defaultdict(lambda: [None, None])
infile = pysam.Samfile(fname)
outfile = pysam.Samfile(fname[:-4] + '_fixed_unsorted.bam',
'wb',
template=infile)
maxval, start = get_bam_length(infile)
pbar = ProgressBar(
maxval=maxval - start,
widgets=[fname, ': ',
Percentage(), ' ',
Bar(), ' ',
ETA(), ' '])
pbar.start()
for read in infile:
pbar.update(infile.tell() - start)
qname = read.qname
data[qname][read.is_read2] = read
if None not in data[qname]:
new_header = in_sam.header.copy()
new_SQ = [sub_dict for sub_dict in new_header['SQ']
if keepstr in sub_dict['SN']]
new_header['SQ'] = new_SQ
return new_header
#Operate on each file independently
for fname in sys.argv[1:]:
data = defaultdict(lambda : [None, None])
infile = pysam.Samfile(fname)
outfile = pysam.Samfile(fname[:-4] + '_rescued_unsorted.bam', 'wb',
header=reheader(infile))
irefs = infile.references
orefs = outfile.references
maxval, start = get_bam_length(infile) # For progress bar goodness
pbar = ProgressBar(maxval=maxval - start,
widgets = [fname, ': ', Percentage(), ' ', Bar(), ' ',
ETA(), ' '])
pbar.start()
# Load up all the read pairs that mapped
for read in infile:
pbar.update(infile.tell() - start)
qname = read.qname
read.rname = orefs.index(irefs[read.rname])
data[qname][read.is_read2] = read
# When we have both ends of the read,
is_next_unmapped = 0x8 #next fragment in the template unmapped
is_revcomp = 0x10 #SEQ being reverse complemented
is_next_reversed = 0x20 #SEQ of the next fragment in the template being reversed
is_read1 = 0x40 #the first fragment in the template
is_read2 = 0x80 #the last fragment in the template
is_secondary = 0x100 #secondary alignment
is_failqc = 0x200 #not passing quality controls
is_dupe = 0x400 #PCR or optical duplicate
for fname in sys.argv[1:]:
data = defaultdict(lambda : [None, None])
infile = pysam.Samfile(fname)
outfile = pysam.Samfile(fname[:-4] + '_fixed_unsorted.bam', 'wb',
template=infile)
maxval, start = get_bam_length(infile)
pbar = ProgressBar(maxval=maxval - start,
widgets = [fname, ': ', Percentage(), ' ', Bar(), ' ',
ETA(), ' '])
pbar.start()
for read in infile:
pbar.update(infile.tell() - start)
qname = read.qname
data[qname][read.is_read2] = read
if None not in data[qname]:
read1, read2 = data.pop(qname)
is_same = read1.rname == read2.rname
