comparison BSseeker2/bs_align/output.py @ 1:8b26adf64adc draft default tip

V2.0.5

0:e6df770c0e58

                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome))

            self.f.write(a)

1:8b26adf64adc

                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome))

            self.f.write(a)


    def store2(self, qname, flag, N_mismatch, FR, refname, strand, pos, cigar, original_BS, methy, STEVE, rnext = -1, pnext = -1, qual = None, output_genome = None,
              rrbs = False, my_region_serial = -1, my_region_start = 0, my_region_end = 0):

        if self.format == BS_SEEKER1:

            # remove the soft clipped bases from the read
            # this is done for backwards compatibility with the old format
            r_start, r_end, _ = get_read_start_end_and_genome_length(cigar)
            original_BS = original_BS[r_start : r_end]

            if rrbs:
                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, STEVE))
            else:
                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, my_region_serial, my_region_start, my_region_end, STEVE))


        elif self.format == BAM or self.format == SAM:

            a = pysam.AlignedRead()
            a.qname = qname
            a.seq = original_BS if strand == '+' else reverse_compl_seq(original_BS)
            a.flag = flag
            a.tid = self.chrom_ids[refname]
            a.pos = pos
            a.mapq = 255
            a.cigar = cigar if strand == '+' else list(reversed(cigar))
            a.rnext = rnext if rnext == -1 else self.chrom_ids[rnext]
            a.pnext = pnext
            a.qual= qual
            if rrbs:
                a.tags = (('XO', FR),
                          ('XS', STEVE),
                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome),
                          ('YR', my_region_serial),
                          ('YS', my_region_start),
                          ('YE', my_region_end)
                          )

            else:
                a.tags = (('XO', FR),
                          ('XS', STEVE),
                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome))

            self.f.write(a)