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r670: added PE support to mappy

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and minor code cleanup
This commit is contained in:
Heng Li
2018-01-31 11:33:08 -05:00
parent 12a5a5fa3c
commit 46d6349af4
9 changed files with 71 additions and 23 deletions
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python/mappy.pyx
+10 -4
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@@ -10,9 +10,10 @@ cdef class Alignment:
cdef int _NM, _mlen, _blen
cdef int8_t _strand, _trans_strand
cdef uint8_t _mapq, _is_primary
cdef int _seg_id
cdef _ctg, _cigar # these are python objects
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand):
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand, seg_id):
self._ctg = ctg if isinstance(ctg, str) else ctg.decode()
self._ctg_len, self._r_st, self._r_en = cl, cs, ce
self._strand, self._q_st, self._q_en = strand, qs, qe
@@ -21,6 +22,7 @@ cdef class Alignment:
self._cigar = cigar
self._is_primary = is_primary
self._trans_strand = trans_strand
self._seg_id = seg_id
@property
def ctg(self): return self._ctg
@@ -64,6 +66,9 @@ cdef class Alignment:
@property
def cigar(self): return self._cigar
@property
def read_num(self): return self._seg_id + 1
@property
def cigar_str(self):
return "".join(map(lambda x: str(x[0]) + 'MIDNSH'[x[1]], self._cigar))
@@ -125,7 +130,7 @@ cdef class Aligner:
def __bool__(self):
return (self._idx != NULL)
def map(self, seq, buf=None):
def map(self, seq, seq2=None, buf=None):
cdef cmappy.mm_reg1_t *regs
cdef cmappy.mm_hitpy_t h
cdef ThreadBuffer b
@@ -134,7 +139,8 @@ cdef class Aligner:
if self._idx is NULL: return None
if buf is None: b = ThreadBuffer()
else: b = buf
regs = cmappy.mm_map(self._idx, len(seq), str.encode(seq), &n_regs, b._b, &self.map_opt, NULL)
if seq2 is None: regs = cmappy.mm_map_aux(self._idx, str.encode(seq), NULL, &n_regs, b._b, &self.map_opt)
else: regs = cmappy.mm_map_aux(self._idx, str.encode(seq), str.encode(seq2), &n_regs, b._b, &self.map_opt)
for i in range(n_regs):
cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)
@@ -142,7 +148,7 @@ 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.mlen, 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, h.seg_id)
cmappy.mm_free_reg1(&regs[i])
free(regs)