fixed a bug in computing qe

diff --git a/ksw.c b/ksw.c
index 92c376636d531e346c90825b3d5e7fbe9ecadf13..d91ad71e3d154e8d308536ecfffe3c90fbb27d26 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -195,10 +195,11 @@ end_loop:
        }
        a->score = gmax + sum; a->te = te;
        { // get a->qe, the end of query match; find the 2nd best score
-               int max = -1, low, high;
+               int max = -1, low, high, qlen = slen * 16;
                uint8_t *t = (uint8_t*)Hmax;
-               for (i = 0, a->qe = -1; i < q->qlen; ++i, ++t)
+               for (i = 0, a->qe = -1; i < qlen; ++i, ++t)
                        if ((int)*t > max) max = *t, a->qe = i / 16 + i % 16 * slen;
+               //printf("%d,%d\n", max, gmax);
                i = (a->score + q->max - 1) / q->max;
                low = te - i; high = te + i;
                for (i = 0, a->score2 = 0; i < n_b; ++i) {
@@ -291,9 +292,9 @@ end_loop8:
        }
        a->score = gmax; a->te = te;
        {
-               int max = -1, low, high;
+               int max = -1, low, high, qlen = slen * 8;
                uint16_t *t = (uint16_t*)Hmax;
-               for (i = 0, a->qe = -1; i < q->qlen; ++i, ++t)
+               for (i = 0, a->qe = -1; i < qlen; ++i, ++t)
                        if ((int)*t > max) max = *t, a->qe = i / 8 + i % 8 * slen;
                i = (a->score + q->max - 1) / q->max;
                low = te - i; high = te + i;