prob_realn() seems working!

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index 746b2c03e6f471593721ce55f69c43ef04845923..7023046b87748de170de994a2565ec0b7a8172a2 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -261,6 +261,63 @@ int bam_realn(bam1_t *b, const char *ref)
        return 0;
 }
 
+int bam_prob_realn(bam1_t *b, const char *ref)
+{
+       int k, i, bw, x, y, yb, ye, xb, xe;
+       uint32_t *cigar = bam1_cigar(b);
+       bam1_core_t *c = &b->core;
+       ka_probpar_t conf = ka_probpar_def;
+       // find the start and end of the alignment
+       if (c->flag & BAM_FUNMAP) return -1;
+       x = c->pos, y = 0, yb = ye = xb = xe = -1;
+       for (k = 0; k < c->n_cigar; ++k) {
+               int op, l;
+               op = cigar[k]&0xf; l = cigar[k]>>4;
+               if (op == BAM_CMATCH) {
+                       if (yb < 0) yb = y;
+                       if (xb < 0) xb = x;
+                       ye = y + l; xe = x + l;
+                       x += l; y += l;
+               } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+               else if (op == BAM_CDEL) x += l;
+               else if (op == BAM_CREF_SKIP) return -1;
+       }
+       // set bandwidth and the start and the end
+       bw = 7;
+       if (abs((xe - xb) - (ye - yb)) > bw)
+               bw = abs((xe - xb) - (ye - yb)) + 3;
+       conf.bw = bw;
+       xb -= yb + bw/2; if (xb < 0) xb = 0;
+       xe += c->l_qseq - ye + bw/2;
+       if (xe - xb - c->l_qseq > bw)
+               xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
+       { // glocal
+               uint8_t *s, *r, *q, *seq = bam1_seq(b), *qual = bam1_qual(b);
+               int *state;
+               s = calloc(c->l_qseq, 1);
+               for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
+               r = calloc(xe - xb, 1);
+               for (i = xb; i < xe; ++i)
+                       r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
+               state = calloc(c->l_qseq, sizeof(int));
+               q = calloc(c->l_qseq, 1);
+               ka_prob_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
+               for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+                       int op = cigar[k]&0xf, l = cigar[k]>>4;
+                       if (op == BAM_CMATCH) {
+                               for (i = y; i < y + l; ++i) {
+                                       if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) qual[i] = 0;
+                                       else qual[i] = qual[i] < q[i]? qual[i] : q[i];
+                               }
+                               x += l; y += l;
+                       } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+                       else if (op == BAM_CDEL) x += l;
+               }
+               free(s); free(r); free(q); free(state);
+       }
+       return 0;
+}
+
 int bam_fillmd(int argc, char *argv[])
 {
        int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
@@ -318,7 +375,8 @@ int bam_fillmd(int argc, char *argv[])
                                        fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
                                                        fp->header->target_name[tid]);
                        }
-                       if (is_realn) bam_realn(b, ref);
+//                     if (is_realn) bam_realn(b, ref);
+                       if (is_realn) bam_prob_realn(b, ref);
                        if (capQ > 10) {
                                int q = bam_cap_mapQ(b, ref, capQ);
                                if (b->core.qual > q) b->core.qual = q;