bam_md.c

   1 #include <unistd.h>
   2 #include <assert.h>
   3 #include <string.h>
   4 #include <ctype.h>
   5 #include "faidx.h"
   6 #include "sam.h"
   7 #include "kstring.h"
   8
   9 void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
  10 {
  11         uint8_t *seq = bam1_seq(b);
  12         uint32_t *cigar = bam1_cigar(b);
  13         bam1_core_t *c = &b->core;
  14         int i, x, y, u = 0;
  15         kstring_t *str;
  16         uint8_t *old_md, *old_nm;
  17         int32_t old_nm_i = -1, nm = 0;
  18
  19         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  20         for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
  21                 int j, l = cigar[i]>>4, op = cigar[i]&0xf;
  22                 if (op == BAM_CMATCH) {
  23                         for (j = 0; j < l; ++j) {
  24                                 int z = y + j;
  25                                 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
  26                                 if (ref[x+j] == 0) break; // out of boundary
  27                                 if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
  28                                         if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
  29                                         ++u;
  30                                 } else {
  31                                         ksprintf(str, "%d", u);
  32                                         kputc(ref[x+j], str);
  33                                         u = 0; ++nm;
  34                                 }
  35                         }
  36                         if (j < l) break;
  37                         x += l; y += l;
  38                 } else if (op == BAM_CDEL) {
  39                         ksprintf(str, "%d", u);
  40                         kputc('^', str);
  41                         for (j = 0; j < l; ++j) {
  42                                 if (ref[x+j] == 0) break;
  43                                 kputc(ref[x+j], str);
  44                         }
  45                         u = 0;
  46                         if (j < l) break;
  47                         x += l; nm += l;
  48                 } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
  49                         y += l;
  50                         if (op == BAM_CINS) nm += l;
  51                 } else if (op == BAM_CREF_SKIP) {
  52                         x += l;
  53                 }
  54         }
  55         ksprintf(str, "%d", u);
  56         // apply max_nm
  57         if (max_nm > 0 && nm >= max_nm) {
  58                 for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
  59                         int j, l = cigar[i]>>4, op = cigar[i]&0xf;
  60                         if (op == BAM_CMATCH) {
  61                                 for (j = 0; j < l; ++j) {
  62                                         int z = y + j;
  63                                         int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
  64                                         if (ref[x+j] == 0) break; // out of boundary
  65                                         if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
  66                                                 seq[z/2] |= (z&1)? 0x0f : 0xf0;
  67                                                 bam1_qual(b)[z] = 0;
  68                                         }
  69                                 }
  70                                 if (j < l) break;
  71                                 x += l; y += l;
  72                         } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
  73                         else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
  74                 }
  75         }
  76         // update NM
  77         old_nm = bam_aux_get(b, "NM");
  78         if (c->flag & BAM_FUNMAP) return;
  79         if (old_nm) old_nm_i = bam_aux2i(old_nm);
  80         if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
  81         else if (nm != old_nm_i) {
  82                 fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
  83                 bam_aux_del(b, old_nm);
  84                 bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
  85         }
  86         // update MD
  87         old_md = bam_aux_get(b, "MD");
  88         if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
  89         else {
  90                 int is_diff = 0;
  91                 if (strlen((char*)old_md+1) == str->l) {
  92                         for (i = 0; i < str->l; ++i)
  93                                 if (toupper(old_md[i+1]) != toupper(str->s[i]))
  94                                         break;
  95                         if (i < str->l) is_diff = 1;
  96                 } else is_diff = 1;
  97                 if (is_diff) {
  98                         fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
  99                         bam_aux_del(b, old_md);
 100                         bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
 101                 }
 102         }
 103         free(str->s); free(str);
 104 }
 105
 106 void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 107 {
 108         bam_fillmd1_core(b, ref, is_equal, 0);
 109 }
 110
 111 int bam_fillmd(int argc, char *argv[])
 112 {
 113         int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0;
 114         samfile_t *fp, *fpout = 0;
 115         faidx_t *fai;
 116         char *ref = 0, mode_w[8], mode_r[8];
 117         bam1_t *b;
 118
 119         is_bam_out = is_sam_in = is_uncompressed = 0;
 120         mode_w[0] = mode_r[0] = 0;
 121         strcpy(mode_r, "r"); strcpy(mode_w, "w");
 122         while ((c = getopt(argc, argv, "eubSn:")) >= 0) {
 123                 switch (c) {
 124                 case 'e': is_equal = 1; break;
 125                 case 'b': is_bam_out = 1; break;
 126                 case 'u': is_uncompressed = is_bam_out = 1; break;
 127                 case 'S': is_sam_in = 1; break;
 128                 case 'n': max_nm = atoi(optarg); break;
 129                 default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
 130                 }
 131         }
 132         if (!is_sam_in) strcat(mode_r, "b");
 133         if (is_bam_out) strcat(mode_w, "b");
 134         else strcat(mode_w, "h");
 135         if (is_uncompressed) strcat(mode_w, "u");
 136         if (optind + 1 >= argc) {
 137                 fprintf(stderr, "\n");
 138                 fprintf(stderr, "Usage:   samtools fillmd [-eubS] <aln.bam> <ref.fasta>\n\n");
 139                 fprintf(stderr, "Options: -e       change identical bases to '='\n");
 140                 fprintf(stderr, "         -u       uncompressed BAM output (for piping)\n");
 141                 fprintf(stderr, "         -b       compressed BAM output\n");
 142                 fprintf(stderr, "         -S       the input is SAM with header\n\n");
 143                 return 1;
 144         }
 145         fp = samopen(argv[optind], mode_r, 0);
 146         if (fp == 0) return 1;
 147         if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
 148                 fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
 149                 return 1;
 150         }
 151         fpout = samopen("-", mode_w, fp->header);
 152         fai = fai_load(argv[optind+1]);
 153
 154         b = bam_init1();
 155         while ((ret = samread(fp, b)) >= 0) {
 156                 if (b->core.tid >= 0) {
 157                         if (tid != b->core.tid) {
 158                                 free(ref);
 159                                 ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 160                                 tid = b->core.tid;
 161                                 if (ref == 0)
 162                                         fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
 163                                                         fp->header->target_name[tid]);
 164                         }
 165                         if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
 166                 }
 167                 samwrite(fpout, b);
 168         }
 169         bam_destroy1(b);
 170
 171         free(ref);
 172         fai_destroy(fai);
 173         samclose(fp); samclose(fpout);
 174         return 0;
 175 }