Copied from SVN revision 4710 and adapted to Git.

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index 8d074870d336677cee2e606ab05ee81a2b4a6f1e..17b0a4a4fa6943313be1b6d78b18c5255fe44982 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -6,7 +6,7 @@
 #include "sam.h"
 #include "kstring.h"
 
-void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
+void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
 {
        uint8_t *seq = bam1_seq(b);
        uint32_t *cigar = bam1_cigar(b);
@@ -53,6 +53,26 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
                }
        }
        ksprintf(str, "%d", u);
+       // apply max_nm
+       if (max_nm > 0 && nm >= max_nm) {
+               for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
+                       int j, l = cigar[i]>>4, op = cigar[i]&0xf;
+                       if (op == BAM_CMATCH) {
+                               for (j = 0; j < l; ++j) {
+                                       int z = y + j;
+                                       int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
+                                       if (ref[x+j] == 0) break; // out of boundary
+                                       if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+                                               seq[z/2] |= (z&1)? 0x0f : 0xf0;
+                                               bam1_qual(b)[z] = 0;
+                                       }
+                               }
+                               if (j < l) break;
+                               x += l; y += l;
+                       } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+                       else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+               }
+       }
        // update NM
        old_nm = bam_aux_get(b, "NM");
        if (c->flag & BAM_FUNMAP) return;
@@ -83,9 +103,14 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
        free(str->s); free(str);
 }
 
+void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
+{
+       bam_fillmd1_core(b, ref, is_equal, 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;
+       int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0;
        samfile_t *fp, *fpout = 0;
        faidx_t *fai;
        char *ref = 0, mode_w[8], mode_r[8];
@@ -94,12 +119,13 @@ int bam_fillmd(int argc, char *argv[])
        is_bam_out = is_sam_in = is_uncompressed = 0;
        mode_w[0] = mode_r[0] = 0;
        strcpy(mode_r, "r"); strcpy(mode_w, "w");
-       while ((c = getopt(argc, argv, "eubS")) >= 0) {
+       while ((c = getopt(argc, argv, "eubSn:")) >= 0) {
                switch (c) {
                case 'e': is_equal = 1; break;
                case 'b': is_bam_out = 1; break;
                case 'u': is_uncompressed = is_bam_out = 1; break;
                case 'S': is_sam_in = 1; break;
+               case 'n': max_nm = atoi(optarg); break;
                default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
                }
        }
@@ -132,8 +158,11 @@ int bam_fillmd(int argc, char *argv[])
                                free(ref);
                                ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
                                tid = b->core.tid;
+                               if (ref == 0)
+                                       fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+                                                       fp->header->target_name[tid]);
                        }
-                       bam_fillmd1(b, ref, is_equal);
+                       if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
                }
                samwrite(fpout, b);
        }