#include <string.h>
#include <ctype.h>
#include "faidx.h"
-#include "bam.h"
+#include "sam.h"
#include "kstring.h"
void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
bam1_core_t *c = &b->core;
int i, x, y, u = 0;
kstring_t *str;
- uint8_t *old_md;
+ uint8_t *old_md, *old_nm;
+ int32_t old_nm_i = -1, nm = 0;
- old_md = bam_aux_get(b, "MD");
- if (c->flag & BAM_FUNMAP) return;
- if (old_md && !is_equal) return; // no need to add MD
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;
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) {
+ 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;
+ u = 0; ++nm;
}
}
if (j < l) break;
}
u = 0;
if (j < l) break;
- x += l;
+ 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);
+ // 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;
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);
+ 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);
}
int bam_fillmd(int argc, char *argv[])
{
- int c, is_equal = 0, tid = -2, ret, len;
- bamFile fp, fpout = 0;
- bam_header_t *header;
+ int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed;
+ samfile_t *fp, *fpout = 0;
faidx_t *fai;
- char *ref = 0;
+ char *ref = 0, mode_w[8], mode_r[8];
bam1_t *b;
- while ((c = getopt(argc, argv, "e")) >= 0) {
+ 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) {
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;
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, "Usage: bam fillmd [-e] <aln.bam> <ref.fasta>\n");
+ 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;
}
- fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
- assert(fp);
- header = bam_header_read(fp);
- fpout = bam_dopen(fileno(stdout), "w");
- bam_header_write(fpout, header);
+ fpout = samopen("-", mode_w, fp->header);
fai = fai_load(argv[optind+1]);
b = bam_init1();
- while ((ret = bam_read1(fp, b)) >= 0) {
+ while ((ret = samread(fp, b)) >= 0) {
if (b->core.tid >= 0) {
if (tid != b->core.tid) {
free(ref);
- ref = fai_fetch(fai, header->target_name[b->core.tid], &len);
+ 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(b, ref, is_equal);
}
- bam_write1(fpout, b);
+ samwrite(fpout, b);
}
bam_destroy1(b);
free(ref);
fai_destroy(fai);
- bam_header_destroy(header);
- bam_close(fp); bam_close(fpout);
+ samclose(fp); samclose(fpout);
return 0;
}
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