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exposed fasta/q reader to mappy

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This commit is contained in:
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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18
python/cmappy.pxd
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@@ -75,7 +75,7 @@ cdef extern from "minimap.h":
mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
#
# Helper header (because it is hard to expose mm_reg1_t with Cython
# Helper header (because it is hard to expose mm_reg1_t with Cython)
#
cdef extern from "cmappy.h":
ctypedef struct mm_hitpy_t:
@@ -90,3 +90,19 @@ cdef extern from "cmappy.h":
void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
void mm_free_reg1(mm_reg1_t *r)
ctypedef struct kstring_t:
unsigned l, m
char *s
ctypedef struct kstream_t:
pass
ctypedef struct kseq_t:
kstring_t name, comment, seq, qual
int last_char
kstream_t *f
kseq_t *mm_fastx_open(const char *fn)
void mm_fastx_close(kseq_t *ks)
int kseq_read(kseq_t *seq)