def filter(self, bam, read):
if read.is_unmapped:
return False
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_mismatches_gen(self.ref, read, chrom):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True
def filter(self, bam, read):
if read.is_unmapped:
return False
chrom = bam.getrname(read.tid)
mm = 0
snps = 0
for op, pos, seq in read_calc_mismatches_gen(self.ref, read, chrom):
if not self.dbsnp.is_valid_variation(chrom, op, pos, seq):
mm += 1
else:
snps += 1
if mm > self.num:
return False
if snps:
read.tags = read.tags + [('ZS', snps)]
return True