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r1290: support ds in Python

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Heng Li
2025-12-12 11:39:01 -05:00
parent bd0cba5012
commit 9bb4d2bed4
7 changed files with 35 additions and 14 deletions
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8
python/minimap2.py
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@@ -5,7 +5,7 @@ import getopt
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:cdM")
if len(args) < 2:
print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
print("Options:")
@@ -16,11 +16,12 @@ def main(argv):
print(" -w INT minimizer window length")
print(" -r INT band width")
print(" -c output the cs tag")
print(" -d output the ds tag")
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 = out_ds = out_MD = False
for opt, arg in opts:
if opt == '-x': preset = arg
elif opt == '-n': min_cnt = int(arg)
@@ -29,12 +30,13 @@ def main(argv):
elif opt == '-k': k = int(arg)
elif opt == '-w': w = int(arg)
elif opt == '-c': out_cs = True
elif opt == '-d': out_ds = 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, ds=out_ds, MD=out_MD): # traverse hits
print('{}\t{}\t{}'.format(name, len(seq), h))
if __name__ == "__main__":