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updated mappy and example.c

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This commit is contained in:
Heng Li
2017-10-16 11:15:07 -04:00
parent adf6cd7f52
commit b24c9c90c7
6 changed files with 28 additions and 15 deletions
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16
python/mappy.pyx
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@@ -7,15 +7,15 @@ cmappy.mm_reset_timer()
cdef class Alignment:
cdef int _ctg_len, _r_st, _r_en
cdef int _q_st, _q_en
cdef int _NM, _blen
cdef int _NM, _mlen, _blen
cdef int8_t _strand, _trans_strand
cdef uint8_t _mapq, _is_primary
cdef _ctg, _cigar # these are python objects
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, blen, NM, trans_strand):
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand):
self._ctg, self._ctg_len, self._r_st, self._r_en = str(ctg), cl, cs, ce
self._strand, self._q_st, self._q_en = strand, qs, qe
self._NM, self._blen = NM, blen
self._NM, self._mlen, self._blen = NM, mlen, blen
self._mapq = mapq
self._cigar = cigar
self._is_primary = is_primary
@@ -39,6 +39,12 @@ cdef class Alignment:
@property
def trans_strand(self): return self._trans_strand
@property
def blen(self): return self._blen
@property
def mlen(self): return self._mlen
@property
def NM(self): return self._NM
@@ -71,7 +77,7 @@ cdef class Alignment:
elif self._trans_strand < 0: ts = 'ts:A:-'
else: ts = 'ts:A:.'
return "\t".join([str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
str(self._blen - self._NM), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
cdef class ThreadBuffer:
cdef cmappy.mm_tbuf_t *_b
@@ -135,7 +141,7 @@ cdef class Aligner:
for k in range(h.n_cigar32):
c = h.cigar32[k]
cigar.append([c>>4, c&0xf])
yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.blen, h.NM, h.trans_strand)
yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand)
cmappy.mm_free_reg1(&regs[i])
free(regs)