fixed a bug on rev strand; added example

Makefile

@@ -56,7 +56,7 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
 		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 clean:
-		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist minimap2.so minimap2.c
+		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist minimap2.so minimap2.c python/minimap2.c minimap2.egg*
 
 depend:
 		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)

python/cminimap2.pxd

@@ -1,4 +1,4 @@
-from libc.stdint cimport uint8_t, int32_t, int64_t, uint32_t, uint64_t
+from libc.stdint cimport int8_t, uint8_t, int32_t, int64_t, uint32_t, uint64_t
 
 cdef extern from "minimap.h":
 	#
@@ -79,13 +79,14 @@ cdef extern from "minimap.h":
 #
 cdef extern from "cminimap2.h":
 	ctypedef struct mm_hitpy_t:
-		const char *ctg;
-		int32_t ctg_start, ctg_end;
-		int32_t qry_start, qry_end;
-		int32_t blen, NM, ctg_len;
-		uint8_t strand, mapq, is_primary, trans_strand;
-		int32_t n_cigar32;
-		uint32_t *cigar32;
+		const char *ctg
+		int32_t ctg_start, ctg_end
+		int32_t qry_start, qry_end
+		int32_t blen, NM, ctg_len
+		uint8_t mapq, is_primary
+		int8_t strand, trans_strand
+		int32_t n_cigar32
+		uint32_t *cigar32
 	
 	void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
 	void mm_free_reg1(mm_reg1_t *r)

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)