+++ /dev/null
-#include <unistd.h>
-#include <assert.h>
-#include <string.h>
-#include <ctype.h>
-#include "faidx.h"
-#include "sam.h"
-#include "kstring.h"
-
-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);
- bam1_core_t *c = &b->core;
- int i, x, y, u = 0;
- kstring_t *str;
- uint8_t *old_md, *old_nm;
- int32_t old_nm_i = -1, nm = 0;
-
- str = (kstring_t*)calloc(1, sizeof(kstring_t));
- 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
- if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
- ++u;
- } else {
- ksprintf(str, "%d", u);
- kputc(ref[x+j], str);
- u = 0; ++nm;
- }
- }
- if (j < l) break;
- x += l; y += l;
- } else if (op == BAM_CDEL) {
- ksprintf(str, "%d", u);
- kputc('^', str);
- for (j = 0; j < l; ++j) {
- if (ref[x+j] == 0) break;
- kputc(ref[x+j], str);
- }
- u = 0;
- if (j < l) break;
- x += l; nm += l;
- } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
- y += l;
- if (op == BAM_CINS) nm += l;
- } else if (op == BAM_CREF_SKIP) {
- x += l;
- }
- }
- 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;
- if (old_nm) old_nm_i = bam_aux2i(old_nm);
- if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
- else if (nm != old_nm_i) {
- fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
- bam_aux_del(b, old_nm);
- bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
- }
- // update MD
- old_md = bam_aux_get(b, "MD");
- if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
- else {
- int is_diff = 0;
- if (strlen((char*)old_md+1) == str->l) {
- for (i = 0; i < str->l; ++i)
- if (toupper(old_md[i+1]) != toupper(str->s[i]))
- break;
- if (i < str->l) is_diff = 1;
- } else is_diff = 1;
- if (is_diff) {
- fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
- bam_aux_del(b, old_md);
- bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
- }
- }
- 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, max_nm = 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 = 0;
- mode_w[0] = mode_r[0] = 0;
- strcpy(mode_r, "r"); strcpy(mode_w, "w");
- 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;
- }
- }
- if (!is_sam_in) strcat(mode_r, "b");
- if (is_bam_out) strcat(mode_w, "b");
- else strcat(mode_w, "h");
- if (is_uncompressed) strcat(mode_w, "u");
- if (optind + 1 >= argc) {
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: samtools fillmd [-eubS] <aln.bam> <ref.fasta>\n\n");
- fprintf(stderr, "Options: -e change identical bases to '='\n");
- fprintf(stderr, " -u uncompressed BAM output (for piping)\n");
- fprintf(stderr, " -b compressed BAM output\n");
- fprintf(stderr, " -S the input is SAM with header\n\n");
- return 1;
- }
- fp = samopen(argv[optind], mode_r, 0);
- if (fp == 0) return 1;
- if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
- fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
- return 1;
- }
- fpout = samopen("-", mode_w, fp->header);
- fai = fai_load(argv[optind+1]);
-
- b = bam_init1();
- while ((ret = samread(fp, b)) >= 0) {
- if (b->core.tid >= 0) {
- if (tid != b->core.tid) {
- 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]);
- }
- if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
- }
- samwrite(fpout, b);
- }
- bam_destroy1(b);
-
- free(ref);
- fai_destroy(fai);
- samclose(fp); samclose(fpout);
- return 0;
-}
projects / pysam.git / blobdiff