#include "sam.h"
#include "faidx.h"
#include "bam_maqcns.h"
+#include "bam_mcns.h"
#include "khash.h"
#include "glf.h"
#include "kstring.h"
***********/
typedef struct {
- char *reg;
+ int vcf, max_mq, min_mq;
+ char *reg, *fn_pos;
faidx_t *fai;
+ kh_64_t *hash;
} mplp_conf_t;
typedef struct {
bamFile fp;
bam_iter_t iter;
+ int min_mq;
} mplp_aux_t;
static int mplp_func(void *data, bam1_t *b)
{
mplp_aux_t *ma = (mplp_aux_t*)data;
- if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
- return bam_read1(ma->fp, b);
+ int ret;
+ do {
+ ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
+ } while (b->core.qual < ma->min_mq && ret >= 0);
+ return ret;
}
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
mplp_aux_t **data;
+ mc_aux_t *ma = 0;
int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
char *ref;
+ khash_t(64) *hash = 0;
// allocate
data = calloc(n, sizeof(void*));
plp = calloc(n, sizeof(void*));
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
+ data[i]->min_mq = conf->min_mq;
data[i]->fp = bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
if (conf->reg) {
bam_header_destroy(h_tmp);
}
}
+ if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
+ // write the VCF header
+ if (conf->vcf) {
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
+ for (i = 0; i < n; ++i) {
+ const char *p;
+ kputc('\t', &s);
+ if ((p = strstr(fn[i], ".bam")) != 0)
+ kputsn(fn[i], p - fn[i], &s);
+ else kputs(fn[i], &s);
+ }
+ puts(s.s);
+ free(s.s);
+ }
// mpileup
+ if (conf->vcf) ma = mc_init(n);
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+ if (hash) {
+ khint_t k;
+ k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
+ if (k == kh_end(hash)) continue;
+ }
if (tid != ref_tid) {
free(ref);
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
ref_tid = tid;
}
- printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
- for (i = 0; i < n; ++i) {
- int j;
- printf("\t%d\t", n_plp[i]);
- if (n_plp[i] == 0) printf("*\t*");
- else {
- for (j = 0; j < n_plp[i]; ++j)
- pileup_seq(plp[i] + j, pos, ref_len, ref);
- putchar('\t');
+ if (conf->vcf) {
+ double f0, f; // the reference allele frequency
+ int j, _ref, _alt, _ref0, depth, rms_q, _ref0b;
+ uint64_t sqr_sum;
+ _ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
+ _ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
+ f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
+ if (f >= 0.0) {
+ double flast = f;
+ for (j = 0; j < 10; ++j) {
+ f = mc_freq_iter(flast, ma);
+ if (fabs(f - flast) < 1e-3) break;
+ flast = f;
+ }
+ }
+ printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
+ if (_ref0 == _ref) putchar("ACGTN"[_alt]);
+ else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
+ printf("\t0\t"); // FIXME: currently these not available
+ if (f0 < 0.) printf("Q13\t");
+ else printf(".\t");
+ for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
+ depth += n_plp[i];
for (j = 0; j < n_plp[i]; ++j) {
- const bam_pileup1_t *p = plp[i] + j;
- int c = bam1_qual(p->b)[p->qpos] + 33;
- if (c > 126) c = 126;
- putchar(c);
+ int q = plp[i][j].b->core.qual;
+ if (q > conf->max_mq) q = conf->max_mq;
+ sqr_sum += q * q;
+ }
+ }
+ rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
+ printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f);
+ printf("\tDP");
+ // output genotype information; FIXME: to be implmented...
+ for (i = 0; i < n; ++i)
+ printf("\t%d", n_plp[i]);
+ putchar('\n');
+ } else {
+ printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+ for (i = 0; i < n; ++i) {
+ int j;
+ printf("\t%d\t", n_plp[i]);
+ if (n_plp[i] == 0) printf("*\t*");
+ else {
+ for (j = 0; j < n_plp[i]; ++j)
+ pileup_seq(plp[i] + j, pos, ref_len, ref);
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ int c = bam1_qual(p->b)[p->qpos] + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
}
}
+ putchar('\n');
}
- putchar('\n');
}
+ if (hash) { // free the hash table
+ khint_t k;
+ for (k = kh_begin(hash); k < kh_end(hash); ++k)
+ if (kh_exist(hash, k)) free(kh_val(hash, k));
+ kh_destroy(64, hash);
+ }
+ mc_destroy(ma);
bam_mplp_destroy(iter);
bam_header_destroy(h);
for (i = 0; i < n; ++i) {
int c;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
- while ((c = getopt(argc, argv, "f:r:")) >= 0) {
+ mplp.max_mq = 60;
+ while ((c = getopt(argc, argv, "f:r:l:VM:q:")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
break;
- case 'r': mplp.reg = strdup(optarg);
+ case 'r': mplp.reg = strdup(optarg); break;
+ case 'l': mplp.fn_pos = strdup(optarg); break;
+ case 'V': mplp.vcf = 1; break;
+ case 'M': mplp.max_mq = atoi(optarg); break;
+ case 'q': mplp.min_mq = atoi(optarg); break;
}
}
if (argc == 1) {
- fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] in1.bam [in2.bam [...]]\n");
+ fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
return 1;
}
mpileup(&mplp, argc - optind, argv + optind);
projects / samtools.git / blobdiff