phase = None

for read_pos, ref_pos in read.get_aligned_pairs(matches_only=True):

if ref_pos + 1 in snps and read.query_qualities[read_pos] >= 30:

if phase == None:

try:

# 1 if alternate, -1 if reference

phase = -1 + 2*snps[ref_pos + 1].index(read.seq[read_pos])

except ValueError:

return 0 # This SNP isn't in the dataset

else:

try:

new_phase = -1 + 2*snps[ref_pos + 1].index(read.seq[read_pos])

except ValueError:

return 0

if new_phase != phase:

return 0 # read seems misphased

snps = defaultdict(dict)

if path.exists(path.join(path.dirname(snpfile), 'true_hets.tsv')):

print("using true hets")

true_hets = {tuple(line.strip().split()):True

for line in open(path.join(path.dirname(snpfile), 'true_hets.tsv'))

}

else:

true_hets = defaultdict(lambda x: True)

if snpfile.endswith('.bed'):

for line in open(snpfile):

chrom, _, start, refalt = line.strip().split()

if true_hets.get((chrom, start), True):

snps[chrom][int(start)] = refalt.split('|')

read_results = Counter()

ref_bam = Samfile(ref_reads, 'wb', template=reads)

alt_bam = Samfile(alt_reads, 'wb', template=reads)

prev_phase = None

prev_read = None

prev_qname = None

test = 0

for read in reads.fetch(until_eof=True):

test += 1

chrom = read.reference_name

snps_on_chrom = snp_dict[chrom]

phase = get_phase(read, snps_on_chrom)

read_qname = read.qname

if read_qname == prev_qname:

read_results["tot_read"]+=1

phase_set = set([phase, prev_phase])

phase_set.discard(None)

if len(phase_set) == 1:

read_phase = phase_set.pop()

if read_phase == -1:

ref_bam.write(read)

ref_bam.write(prev_read)

read_results["ref_read"]+=1

elif read_phase == 1:

alt_bam.write(read)

alt_bam.write(prev_read)

read_results["alt_read"]+=1

elif read_phase == 0:

read_results['misphased_read']+=1

elif len(phase_set)==0:

read_results["no_snps_read"]+=1

else:

read_results['misphased_read']+=1

prev_read = read

prev_phase = phase

prev_qname = read_qname

parser = ArgumentParser()

parser.add_argument('snp_file', help="Tab delimited text file of known SNPs with 4 columns: chrom, 0-position, 1-position, ref_allele|alt_allele")

parser.add_argument('reads', type=Samfile, help="BAM file that needs splitting")

parser.add_argument('ref_reads', help="Output BAM file of reference reads.")

parser.add_argument('alt_reads', help="Output BAM file of alternate reads.")

args = parser.parse_args()