bug caused by the last minute change

diff --git a/ksw.c b/ksw.c
index 75002030d20d6243eb8f686908e067b496b13cd1..400a81f45f0976a1fc695ef09f3c9bb9b81f9044 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -121,7 +121,7 @@ kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
        // initialization
        r = g_defr;
        minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
-       endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0;
+       endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
        m_b = n_b = 0; b = 0;
        zero = _mm_set1_epi32(0);
        gapoe = _mm_set1_epi8(_gapo + _gape);
@@ -194,7 +194,7 @@ end_loop16:
                        gmax = imax; te = i; // te is the end position on the target
                        for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
                                _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
-                       if (gmax + q->shift >= 255 || gmax + q->shift == endsc) break;
+                       if (gmax + q->shift >= 255 || gmax + q->shift >= endsc) break;
                }
                S = H1; H1 = H0; H0 = S; // swap H0 and H1
        }
@@ -237,7 +237,7 @@ kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape,
        // initialization
        r = g_defr;
        minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
-       endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0;
+       endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
        m_b = n_b = 0; b = 0;
        zero = _mm_set1_epi32(0);
        gapoe = _mm_set1_epi16(_gapo + _gape);
@@ -340,8 +340,7 @@ kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con
        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);
-       xtra = KSW_XSTOP | r.score;
-       rr = func(q, tlen, target, gapo, gape, xtra);
+       rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score);
        revseq(r.qe + 1, query); revseq(r.te + 1, target);
        free(q);
        if (r.score == rr.score)