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#!/usr/bin/env python
import sys
import getopt
import mappy as mp
def main(argv):
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:")
print(" -x STR preset: sr, map-pb, map-ont, asm5, asm10 or splice")
print(" -n INT mininum number of minimizers")
print(" -m INT mininum chaining score")
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
out_cs = False
for opt, arg in opts:
if opt == '-x': preset = arg
elif opt == '-n': min_cnt = int(arg)
elif opt == '-m': min_chain_score = int(arg)
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, cs=out_cs): # traverse hits
print('{}\t{}\t{}'.format(name, len(seq), h))
if __name__ == "__main__":
main(sys.argv)
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