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add cs_long flag to mappy.Aligner.map, and a "-C" option to minimap2.py #1194

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add cs_long flag to mappy.Aligner.map, and a "-C" option to minimap2.py #1194

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15 changes: 7 additions & 8 deletions python/mappy.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ cdef class Aligner:
def __bool__(self):
return (self._idx != NULL)

def map(self, seq, seq2=None, buf=None, cs=False, MD=False, max_frag_len=None, extra_flags=None):
def map(self, seq, seq2=None, buf=None, cs=False, cs_long=False, MD=False, max_frag_len=None, extra_flags=None):
cdef cmappy.mm_reg1_t *regs
cdef cmappy.mm_hitpy_t h
cdef ThreadBuffer b
Expand Down Expand Up @@ -199,13 +199,12 @@ cdef class Aligner:
for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array
c = h.cigar32[k]
cigar.append([c>>4, c&0xf])
if cs or MD: # generate the cs and/or the MD tag, if requested
if cs:
l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 1)
_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
if MD:
l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq)
_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
if cs or cs_long:
l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 0 if cs_long else 1)
_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
if MD:
l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq)
_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
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.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _MD)
cmappy.mm_free_reg1(&regs[i])
i += 1
Expand Down
7 changes: 5 additions & 2 deletions python/minimap2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import mappy as mp

def main(argv):
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cM")
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cCM")
if len(args) < 2:
print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
print("Options:")
Expand All @@ -16,11 +16,13 @@ def main(argv):
print(" -w INT minimizer window length")
print(" -r INT band width")
print(" -c output the cs tag")
print(" -C output the cs tag (long version)")
print(" -M output the MD tag")
sys.exit(1)

preset = min_cnt = min_sc = k = w = bw = None
out_cs = out_MD = False
out_cs_long = False
for opt, arg in opts:
if opt == '-x': preset = arg
elif opt == '-n': min_cnt = int(arg)
Expand All @@ -29,12 +31,13 @@ def main(argv):
elif opt == '-k': k = int(arg)
elif opt == '-w': w = int(arg)
elif opt == '-c': out_cs = True
elif opt == '-C': out_cs_long = True
elif opt == '-M': out_MD = True

a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
for h in a.map(seq, cs=out_cs, MD=out_MD): # traverse hits
for h in a.map(seq, cs=out_cs, cs_long=out_cs_long, MD=out_MD): # traverse hits
print('{}\t{}\t{}'.format(name, len(seq), h))

if __name__ == "__main__":
Expand Down