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more functional minimap2.py; added categories

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Heng Li
2017-09-17 17:06:39 -04:00
parent 0b660c70e2
commit cf93e5c0a1
5 changed files with 43 additions and 7 deletions
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5
python/mappy.pyx
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@@ -67,8 +67,11 @@ cdef class Alignment:
else: strand = '?'
if self._is_primary != 0: tp = 'tp:A:P'
else: tp = 'tp:A:S'
if self._trans_strand > 0: ts = 'ts:A:+'
elif self._trans_strand < 0: ts = 'ts:A:-'
else: ts = 'ts:A:.'
return "\t".join([str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
str(self._blen - self._NM), str(self._blen), str(self._mapq), "NM:i:" + str(self._NM), tp, "cg:Z:" + self.cigar_str])
str(self._blen - self._NM), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
cdef class ThreadBuffer:
cdef cmappy.mm_tbuf_t *_b