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exposed fasta/q reader to mappy

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Heng Li
2017-09-17 14:41:59 -04:00
parent e9c57f6d8b
commit c8a019fae8
5 changed files with 91 additions and 63 deletions
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12
python/mappy.pyx
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@@ -11,7 +11,7 @@ cdef class Alignment:
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):
self._ctg, self._ctg_len, self._r_st, self._r_en = ctg.decode("ascii"), cl, cs, ce
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._mapq = mapq
@@ -133,3 +133,13 @@ cdef class Aligner:
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)
cmappy.mm_free_reg1(&regs[i])
free(regs)
def fastx_read(fn):
cdef cmappy.kseq_t *ks
ks = cmappy.mm_fastx_open(str.encode(fn))
if ks is NULL: return None
while cmappy.kseq_read(ks) >= 0:
qual = None
if ks.qual.l > 0: qual = str(ks.qual.s)
yield str(ks.name.s), str(ks.seq.s), qual
cmappy.mm_fastx_close(ks)