bugfix: in-place revcomp() not working

python/cmappy.h

@@ -101,16 +101,15 @@ static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const
 	}
 }
 
-static inline uint8_t *mappy_revcomp(int len, uint8_t *seq)
+static inline char *mappy_revcomp(int len, const uint8_t *seq)
 {
 	int i;
-	for (i = 0; i < len>>1; ++i) {
+	char *rev;
-		uint8_t t = seq_comp_table[seq[i]];
+	rev = (char*)malloc(len + 1);
-		seq[i] = seq_comp_table[seq[len - 1 - i]];
+	for (i = 0; i < len; ++i)
-		seq[len - 1 - i] = t;
+		rev[len - i - 1] = seq_comp_table[seq[i]];
-	}
+	rev[len] = 0;
-	if (len&1) seq[len>>1] = seq_comp_table[seq[len>>1]];
+	return rev;
-	return seq;
 }
 
 #endif

python/cmappy.pxd

@@ -116,6 +116,6 @@ cdef extern from "cmappy.h":
 	void mm_fastx_close(kseq_t *ks)
 	int kseq_read(kseq_t *seq)
 
-	uint8_t *mappy_revcomp(int l, uint8_t *seq)
+	char *mappy_revcomp(int l, const uint8_t *seq)
 	int mm_verbose_level(int v)
 	void mm_reset_timer()

python/mappy.pyx

@@ -1,6 +1,7 @@
 from libc.stdint cimport uint8_t, int8_t
 from libc.stdlib cimport free
 cimport cmappy
+import sys
 
 cmappy.mm_reset_timer()
 
@@ -165,9 +166,12 @@ def fastx_read(fn):
 	cmappy.mm_fastx_close(ks)
 
 def revcomp(seq):
-	cdef uint8_t *s
+	l = len(seq)
-	s = cmappy.mappy_revcomp(len(seq), str.encode(seq))
+	bseq = seq if isinstance(seq, bytes) else seq.encode()
-	return s if isinstance(s, str) else s.decode()
+	cdef char *s = cmappy.mappy_revcomp(l, bseq)
+	r = s[:l] if isinstance(s, str) else s[:l].decode()
+	free(s)
+	return r
 
 def verbose(v=None):
 	if v is None: v = -1