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r819: mappy to support cs/MD

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Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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8
python/minimap2.py
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@@ -4,7 +4,7 @@ import sys, getopt
import mappy as mp
def main(argv):
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:")
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:c")
if len(args) < 2:
print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
print("Options:")
@@ -14,9 +14,10 @@ def main(argv):
print(" -k INT k-mer length")
print(" -w INT minimizer window length")
print(" -r INT band width")
print(" -c output the cs tag")
sys.exit(1)
preset, min_cnt, min_sc, k, w, bw = None, None, None, None, None, None
preset, min_cnt, min_sc, k, w, bw, out_cs = None, None, None, None, None, None, False
for opt, arg in opts:
if opt == '-x': preset = arg
elif opt == '-n': min_cnt = int(arg)
@@ -24,11 +25,12 @@ def main(argv):
elif opt == '-r': bw = int(arg)
elif opt == '-k': k = int(arg)
elif opt == '-w': w = int(arg)
elif opt == '-c': out_cs = 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): # traverse hits
for h in a.map(seq, cs=out_cs): # traverse hits
print('{}\t{}\t{}'.format(name, len(seq), h))
if __name__ == "__main__":