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exposed timer and verbose-level to mappy

This commit is contained in:
Heng Li 2017-09-17 15:21:36 -04:00
parent c8a019fae8
commit 5715c423ff
3 changed files with 23 additions and 1 deletions
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12
python/cmappy.h
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@ -55,4 +55,16 @@ static inline void mm_fastx_close(kseq_t *ks)
gzclose(fp); gzclose(fp);
} }
static inline int mm_verbose_level(int v)
{
if (v >= 0) mm_verbose = v;
return mm_verbose;
}
static inline void mm_reset_timer(void)
{
extern double realtime(void);
mm_realtime0 = realtime();
}
#endif #endif

4
python/cmappy.pxd
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@ -32,6 +32,7 @@ cdef extern from "minimap.h":
int mini_batch_size int mini_batch_size
int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
int mm_verbose
# #
# Indexing # Indexing
@ -106,3 +107,6 @@ cdef extern from "cmappy.h":
kseq_t *mm_fastx_open(const char *fn) kseq_t *mm_fastx_open(const char *fn)
void mm_fastx_close(kseq_t *ks) void mm_fastx_close(kseq_t *ks)
int kseq_read(kseq_t *seq) int kseq_read(kseq_t *seq)
int mm_verbose_level(int v)
void mm_reset_timer()

8
python/mappy.pyx
View File

@ -2,6 +2,8 @@ from libc.stdint cimport uint8_t, int8_t
from libc.stdlib cimport free from libc.stdlib cimport free
cimport cmappy cimport cmappy
cmappy.mm_reset_timer()
cdef class Alignment: cdef class Alignment:
cdef int _ctg_len, _r_st, _r_en cdef int _ctg_len, _r_st, _r_en
cdef int _q_st, _q_en cdef int _q_st, _q_en
@ -139,7 +141,11 @@ def fastx_read(fn):
ks = cmappy.mm_fastx_open(str.encode(fn)) ks = cmappy.mm_fastx_open(str.encode(fn))
if ks is NULL: return None if ks is NULL: return None
while cmappy.kseq_read(ks) >= 0: while cmappy.kseq_read(ks) >= 0:
qual = None
if ks.qual.l > 0: qual = str(ks.qual.s) if ks.qual.l > 0: qual = str(ks.qual.s)
else qual = None
yield str(ks.name.s), str(ks.seq.s), qual yield str(ks.name.s), str(ks.seq.s), qual
cmappy.mm_fastx_close(ks) cmappy.mm_fastx_close(ks)
def verbose(v=None):
if v is None: v = -1
return cmappy.mm_verbose_level(v)