Release samtools-0.1.4

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 6b2b5e03260da470801ce70b8ff18f788c8fd880..c6c9af7dee454ed91cd75363470473405d7c97ea 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -142,13 +142,14 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
        }
        for (i = n = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
-               uint32_t q, x = 0;
+               uint32_t q, x = 0, qq;
                if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
                q = (uint32_t)bam1_qual(p->b)[p->qpos];
                x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
                if (p->b->core.qual < q) q = p->b->core.qual;
                x |= q << 24;
-               q = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+               qq = bam1_seqi(bam1_seq(p->b), p->qpos);
+               q = bam_nt16_nt4_table[qq? qq : ref_base];
                if (!p->is_del && q < 4) x |= 1 << 21 | q << 16;
                bm->aux->info[n++] = x;
        }
@@ -396,7 +397,8 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                bam_segreg(pos, c, cigar, &seg);
                                for (ps = s = 0, l = seg.qbeg; c->pos + l < right && l < seg.qend; ++l) {
                                        int cq = bam1_seqi(bam1_seq(p->b), l), ct;
-                                       ct = c->pos + l >= left? ref2[c->pos + l - left] : 15; // "<" will happen if reads are too long
+                                       // in the following line, "<" will happen if reads are too long
+                                       ct = c->pos + l - seg.qbeg >= left? ref2[c->pos + l - seg.qbeg - left] : 15;
                                        if (cq < 15 && ct < 15) {
                                                s += cq == ct? 1 : -mi->mm_penalty;
                                                if (cq != ct) ps += bam1_qual(p->b)[l];
@@ -406,7 +408,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                if (types[i] != 0) { // then try the other way to calculate the score
                                        for (ps = s = 0, l = seg.qbeg; c->pos + l + types[i] < right && l < seg.qend; ++l) {
                                                int cq = bam1_seqi(bam1_seq(p->b), l), ct;
-                                               ct = c->pos + l + types[i] >= left? ref2[c->pos + l + types[i] - left] : 15;
+                                               ct = c->pos + l - seg.qbeg + types[i] >= left? ref2[c->pos + l - seg.qbeg + types[i] - left] : 15;
                                                if (cq < 15 && ct < 15) {
                                                        s += cq == ct? 1 : -mi->mm_penalty;
                                                        if (cq != ct) ps += bam1_qual(p->b)[l];
@@ -416,7 +418,8 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                if (score[i*n+j] < s) score[i*n+j] = s; // choose the higher of the two scores
                                if (pscore[i*n+j] > ps) pscore[i*n+j] = ps;
                                if (types[i] != 0) score[i*n+j] -= mi->indel_err;
-                               //printf("%d, %d, %d, %d\n", i, types[i], j, score[i*n+j]);
+                               //printf("%d, %d, %d, %d, %d, %d, %d\n", p->b->core.pos + 1, seg.qbeg, i, types[i], j,
+                               //         score[i*n+j], pscore[i*n+j]);
                        }
                }
                { // get final result
@@ -460,20 +463,17 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                        ret->s[1][k+1] = ref[pos + k + 1];
                        } else ret->s[1][0] = '*';
                        // write count
-                       for (j = 0; j < n; ++j) {
-                               if (score[max1_i*n+j] < 0 && score[max2_i*n+j] < 0) ++ret->cnt_anti;
-                               else {
-                                       int diff = score[max1_i*n+j] - score[max2_i*n+j];
-                                       if (diff > mi->ambi_thres) ++ret->cnt1;
-                                       else if (diff < -mi->ambi_thres) ++ret->cnt2;
-                                       else ++ret->cnt_ambi;
-                               }
+                       for (i = 0; i < n; ++i) {
+                               const bam_pileup1_t *p = pl + i;
+                               if (p->indel == ret->indel1) ++ret->cnt1;
+                               else if (p->indel == ret->indel2) ++ret->cnt2;
+                               else ++ret->cnt_anti;
                        }
                        // write gl[]
                        ret->gl[0] = ret->gl[1] = 0;
                        for (j = 0; j < n; ++j) {
                                int s1 = pscore[max1_i*n + j], s2 = pscore[max2_i*n + j];
-                               //printf("%d, %d\n", s1, s2);
+                               //printf("%d, %d, %d, %d, %d\n", pl[j].b->core.pos+1, max1_i, max2_i, s1, s2);
                                if (s1 > s2) ret->gl[0] += s1 - s2 < mi->q_indel? s1 - s2 : mi->q_indel;
                                else ret->gl[1] += s2 - s1 < mi->q_indel? s2 - s1 : mi->q_indel;
                        }