bug in some cases

diff --git a/ksw.c b/ksw.c
index 15301c00216ac44d0e2ab47103e92e072676c22f..dd8c8032fac927b041cd105ac8e0854253fcd72e 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -333,8 +333,7 @@ kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con
        kswr_t r, rr;
        kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int);
 
-       if (qry == 0 || *qry == 0)
-               q = ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
+       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;
        r = func(q, tlen, target, gapo, gape, xtra);