From 29ed675ee5c4a8fb484cb53df97011b6d7be6d76 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 20 Feb 2018 11:05:54 -0500
Subject: [PATCH] bugfix: in-place revcomp() not working

---
 python/cmappy.h   | 15 +++++++--------
 python/cmappy.pxd |  2 +-
 python/mappy.pyx  | 10 +++++++---
 3 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/python/cmappy.h b/python/cmappy.h
index 4044aeb..313a9dd 100644
--- a/python/cmappy.h
+++ b/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) {
-		uint8_t t = seq_comp_table[seq[i]];
-		seq[i] = seq_comp_table[seq[len - 1 - i]];
-		seq[len - 1 - i] = t;
-	}
-	if (len&1) seq[len>>1] = seq_comp_table[seq[len>>1]];
-	return seq;
+	char *rev;
+	rev = (char*)malloc(len + 1);
+	for (i = 0; i < len; ++i)
+		rev[len - i - 1] = seq_comp_table[seq[i]];
+	rev[len] = 0;
+	return rev;
 }
 
 #endif
diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index 7570103..a40adf0 100644
--- a/python/cmappy.pxd
+++ b/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()
diff --git a/python/mappy.pyx b/python/mappy.pyx
index 1318e16..aeeab5e 100644
--- a/python/mappy.pyx
+++ b/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
-	s = cmappy.mappy_revcomp(len(seq), str.encode(seq))
-	return s if isinstance(s, str) else s.decode()
+	l = len(seq)
+	bseq = seq if isinstance(seq, bytes) else seq.encode()
+	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