fixed a bug on rev strand; added example

python/mm2-lite.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+import sys, getopt
+import minimap2 as mm
+
+def readfq(fp): # multi-line fasta/fastq parser
+	last = None
+	while True:
+		if not last:
+			for l in fp:
+				if l[0] in '>@':
+					last = l[:-1]
+					break
+		if not last: break
+		name, seqs, last = last[1:].split()[0], [], None
+		for l in fp:
+			if l[0] in '@+>':
+				last = l[:-1]
+				break
+			seqs.append(l[:-1])
+		if not last or last[0] != '+':
+			yield name, ''.join(seqs), None
+			if not last: break
+		else:
+			seq, leng, seqs = ''.join(seqs), 0, []
+			for l in fp:
+				seqs.append(l[:-1])
+				leng += len(l) - 1
+				if leng >= len(seq):
+					last = None
+					yield name, seq, ''.join(seqs);
+					break
+			if last:
+				yield name, seq, None
+				break
+
+def main(argv):
+	opts, args = getopt.getopt(argv[1:], "")
+	if len(args) < 2:
+		print("Usage: mm2-lite.py <ref.fa>|<ref.mmi> <query.fq>")
+		sys.exit(1)
+	a = mm.Aligner(args[0]) # load/build index
+	for name, seq, qual in readfq(open(args[1])): # read one sequence
+		for h in a.map(seq): # traverse hits
+			print('{}\t{}\t{}'.format(name, len(seq), h))
+
+if __name__ == "__main__":
+	main(sys.argv)