bugfix: segfault in ksw

diff --git a/ksw.c b/ksw.c
index 8f5a534bc3db51e60374d4eb549d3d2376ee854c..9b8c065417e8db91b4561a4ff012b7cfda2a3cfc 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -329,6 +329,7 @@ static void revseq(int l, uint8_t *s)
 
 kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)
 {
+       int size;
        kswq_t *q;
        kswr_t r, rr;
        kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int);
@@ -336,11 +337,12 @@ kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con
        q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
        if (qry && *qry == 0) *qry = q;
        func = q->size == 2? ksw_i16 : ksw_u8;
+       size = q->size;
        r = func(q, tlen, target, gapo, gape, xtra);
        if (qry == 0) free(q);
        if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;
        revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end
-       q = ksw_qinit((*qry)->size, r.qe + 1, query, m, mat);
+       q = ksw_qinit(size, r.qe + 1, query, m, mat);
        rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score);
        revseq(r.qe + 1, query); revseq(r.te + 1, target);
        free(q);