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Use bam_set_qname in query_name setter #1389

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Use bam_set_qname in query_name setter #1389

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30 changes: 2 additions & 28 deletions pysam/libcalignedsegment.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ from libc.stdint cimport INT8_MIN, INT16_MIN, INT32_MIN, \
INT8_MAX, INT16_MAX, INT32_MAX, \
UINT8_MAX, UINT16_MAX, UINT32_MAX

from pysam.libchtslib cimport HTS_IDX_NOCOOR
from pysam.libchtslib cimport HTS_IDX_NOCOOR, bam_set_qname
from pysam.libcutils cimport force_bytes, force_str, \
charptr_to_str, charptr_to_bytes

Expand Down Expand Up @@ -1190,36 +1190,10 @@ cdef class AlignedSegment:

qname = force_bytes(qname)
cdef bam1_t * src = self._delegate
# the qname is \0 terminated
cdef uint8_t l = len(qname) + 1

cdef char * p = pysam_bam_get_qname(src)
cdef uint8_t l_extranul = 0

if l % 4 != 0:
l_extranul = 4 - l % 4

cdef bam1_t * retval = pysam_bam_update(src,
src.core.l_qname,
l + l_extranul,
<uint8_t*>p)
if retval == NULL:
if bam_set_qname(src, qname) < 0:
raise MemoryError("could not allocate memory")

src.core.l_extranul = l_extranul
src.core.l_qname = l + l_extranul

# re-acquire pointer to location in memory
# as it might have moved
p = pysam_bam_get_qname(src)

strncpy(p, qname, l)
# x might be > 255
cdef uint16_t x = 0

for x from l <= x < l + l_extranul:
p[x] = b'\0'

property flag:
"""properties flag"""
def __get__(self):
Expand Down
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