#include <unistd.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
#include "faidx.h"
-#include "bam.h"
+#include "sam.h"
#include "kstring.h"
+#include "kaln.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);
bam1_core_t *c = &b->core;
- int i, x, y, u = 0, has_md = 0;
+ int i, x, y, u = 0;
kstring_t *str;
+ uint8_t *old_md, *old_nm;
+ int32_t old_nm_i = -1, nm = 0;
- if (bam_aux_get(b, "MD")) has_md = 1;
- if (has_md == 1 && !is_equal) return; // no need to add MD
str = (kstring_t*)calloc(1, sizeof(kstring_t));
- if (c->flag & BAM_FUNMAP) return;
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) {
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;
if (ref[x+j] == 0) break;
kputc(ref[x+j], str);
}
+ 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);
- if (!has_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+ // 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);
+}
+
+// local realignment
+
+#define MIN_REF_LEN 10
+
+int bam_realn(bam1_t *b, const char *ref)
+{
+ int k, l_ref, score, n_cigar;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *s_ref = 0, *s_read = 0, *seq;
+ ka_param_t par;
+ bam1_core_t *c = &b->core;
+ // set S/W parameters
+ par = ka_param_blast; par.gap_open = 4; par.gap_ext = 1; par.gap_end_open = par.gap_end_ext = 0;
+ // calculate the length of the reference in the alignment
+ for (k = l_ref = 0; k < c->n_cigar; ++k) {
+ if ((cigar[k]&0xf) == BAM_CREF_SKIP) break; // do not do realignment if there is an `N' operation
+ if ((cigar[k]&0xf) == BAM_CMATCH || (cigar[k]&0xf) == BAM_CDEL)
+ l_ref += cigar[k]>>4;
+ }
+ if (k != c->n_cigar || l_ref < MIN_REF_LEN) return -1;
+ for (k = 0; k < l_ref; ++k)
+ if (ref[c->pos + k] == 0) return -1; // the read stands out of the reference
+ // allocate
+ s_ref = calloc(l_ref, 1);
+ s_read = calloc(c->l_qseq, 1);
+ for (k = 0, seq = bam1_seq(b); k < c->l_qseq; ++k)
+ s_read[k] = bam_nt16_nt4_table[bam1_seqi(seq, k)];
+ for (k = 0; k < l_ref; ++k)
+ s_ref[k] = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[c->pos + k]]];
+ // do alignment
+ cigar = ka_global_core(s_ref, l_ref, s_read, c->l_qseq, &par, &score, &n_cigar);
+ if (score <= 0) { // realignment failed
+ free(cigar); free(s_ref); free(s_read);
+ return -1;
+ }
+ // copy over the alignment
+ if (4 * (n_cigar - (int)c->n_cigar) + b->data_len > b->m_data) { // enlarge b->data
+ b->m_data = 4 * (n_cigar - (int)c->n_cigar) + b->data_len;
+ kroundup32(b->m_data);
+ b->data = realloc(b->data, b->m_data);
+ }
+ if (n_cigar != (int)c->n_cigar) // move data
+ memmove(b->data + c->l_qname + 4 * n_cigar, bam1_seq(b), b->data_len - c->l_qseq - 4 * c->n_cigar);
+ memcpy(bam1_cigar(b), cigar, n_cigar * 4);
+ c->n_cigar = n_cigar;
+ free(s_ref); free(s_read); free(cigar);
+ return 0;
+}
+
int bam_fillmd(int argc, char *argv[])
{
- int c, is_equal = 0, tid = -1, 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, max_nm = 0, is_realn;
+ 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 = is_realn = 0;
+ mode_w[0] = mode_r[0] = 0;
+ strcpy(mode_r, "r"); strcpy(mode_w, "w");
+ while ((c = getopt(argc, argv, "reubSn:")) >= 0) {
switch (c) {
+ case 'r': is_realn = 1; break;
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, "Usage: bam fillmd [-e] <aln.bam> <ref.fasta>\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools fillmd [-eubrS] <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");
+ fprintf(stderr, " -r read-independent local realignment\n\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);
+ 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 = bam_read1(fp, b)) >= 0) {
- if (tid != b->core.tid)
- ref = fai_fetch(fai, header->target_name[b->core.tid], &len);
- bam_fillmd1(b, ref, is_equal);
- bam_write1(fpout, b);
+ 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 (is_realn) bam_realn(b, ref);
+ if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
+ }
+ 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;
}
projects / samtools.git / blobdiff