prob_realn() seems working!

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index f3f7e228a62c18e5d1beba2686cb2095da385002..7023046b87748de170de994a2565ec0b7a8172a2 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -261,18 +261,75 @@ 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, is_capQ;
+       int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
        samfile_t *fp, *fpout = 0;
        faidx_t *fai;
        char *ref = 0, mode_w[8], mode_r[8];
        bam1_t *b;
 
-       is_bam_out = is_sam_in = is_uncompressed = is_realn = is_capQ = 0;
+       is_bam_out = is_sam_in = is_uncompressed = is_realn = 0;
        mode_w[0] = mode_r[0] = 0;
        strcpy(mode_r, "r"); strcpy(mode_w, "w");
-       while ((c = getopt(argc, argv, "reubSCn:")) >= 0) {
+       while ((c = getopt(argc, argv, "reubSC:n:")) >= 0) {
                switch (c) {
                case 'r': is_realn = 1; break;
                case 'e': is_equal = 1; break;
@@ -280,7 +337,7 @@ int bam_fillmd(int argc, char *argv[])
                case 'u': is_uncompressed = is_bam_out = 1; break;
                case 'S': is_sam_in = 1; break;
                case 'n': max_nm = atoi(optarg); break;
-               case 'C': is_capQ = 1; break;
+               case 'C': capQ = atoi(optarg); break;
                default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
                }
        }
@@ -318,9 +375,10 @@ 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_capQ) {
-                               int q = bam_cap_mapQ(b, ref, 40);
+//                     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;
                        }
                        if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);