#include "faidx.h"
#include "bam_maqcns.h"
#include "khash.h"
+#include "glf.h"
KHASH_SET_INIT_INT64(64)
-#define BAM_PLF_SIMPLE 0x01
-#define BAM_PLF_CNS 0x02
+#define BAM_PLF_SIMPLE 0x01
+#define BAM_PLF_CNS 0x02
+#define BAM_PLF_INDEL_ONLY 0x04
+#define BAM_PLF_GLF 0x08
typedef struct {
bam_header_t *h;
khash_t(64) *hash;
uint32_t format;
int tid, len;
+ int mask;
char *ref;
+ glfFile fp; // for glf output only
} pu_data_t;
char **bam_load_pos(const char *fn, int *_n);
return hash;
}
+// an analogy to pileup_func() below
+static int glt_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
+{
+ pu_data_t *d = (pu_data_t*)data;
+ bam_maqindel_ret_t *r = 0;
+ int rb;
+ glf1_t *g;
+ glf2_t g2;
+ if (d->fai == 0) {
+ fprintf(stderr, "[glt_func] reference sequence is required for generating GLT. Abort!\n");
+ exit(1);
+ }
+ if (d->hash && kh_get(64, d->hash, (uint64_t)tid<<32|pos) == kh_end(d->hash)) return 0;
+ if (d->fai && (int)tid != d->tid) {
+ if (d->ref) { // then write the end mark
+ memset(&g2, 0, sizeof(glf2_t));
+ g2.type = GLF_TYPE_END;
+ bgzf_write(d->fp, &g2, sizeof(glf2_t));
+ }
+ glf_ref_write(d->fp, d->h->target_name[tid]); // write reference
+ free(d->ref);
+ d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
+ d->tid = tid;
+ }
+ rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
+ g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
+ memcpy(&g2, g, sizeof(glf1_t));
+ g2.type = GLF_TYPE_NORMAL;
+ g2.pos = pos;
+ bgzf_write(d->fp, &g2, sizeof(glf2_t));
+ r = bam_maqindel(n, pos, d->ido, pu, d->ref);
+ if (r) { // then write indel line
+ int g3 = 3 * n, min;
+ min = g3;
+ if (min > r->gl[0]) min = r->gl[0];
+ if (min > r->gl[1]) min = r->gl[1];
+ g3 -= min;
+ g2.ref_base = 0;
+ g2.type = GLF_TYPE_INDEL;
+ memset(g2.lk, 0, 10);
+ g2.lk[0] = r->gl[0] < 255? r->gl[0] : 255;
+ g2.lk[1] = r->gl[1] < 255? r->gl[1] : 255;
+ g2.lk[2] = g3 < 255? g3 : 255;
+ *(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
+ *(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
+ g2.min_lk = min < 255? min : 255;
+ bgzf_write(d->fp, &g2, sizeof(glf2_t));
+ if (r->indel1) bgzf_write(d->fp, r->s[0]+1, r->indel1>0? r->indel1 : -r->indel1);
+ if (r->indel2) bgzf_write(d->fp, r->s[1]+1, r->indel2>0? r->indel2 : -r->indel2);
+ bam_maqindel_ret_destroy(r);
+ }
+ free(g);
+ return 0;
+}
+
static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
{
pu_data_t *d = (pu_data_t*)data;
int i, j, rb;
uint32_t x;
if (d->hash && kh_get(64, d->hash, (uint64_t)tid<<32|pos) == kh_end(d->hash)) return 0;
+ if (d->format & BAM_PLF_GLF) return glt_func(tid, pos, n, pu, data);
if (d->fai && (int)tid != d->tid) {
free(d->ref);
d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
d->tid = tid;
}
rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
+ if (d->format & BAM_PLF_INDEL_ONLY) {
+ for (i = 0; i < n; ++i)
+ if (pu[i].indel != 0) break;
+ if (i == n) return 0;
+ }
printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
if (d->format & BAM_PLF_CNS) { // consensus
int ref_q, rb4 = bam_nt16_table[rb];
if (ref_q > 255) ref_q = 255;
}
printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[x>>28], x>>8&0xff, ref_q, x>>16&0xff);
+ }
+ if (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) {
if (d->ref) // indel calling
r = bam_maqindel(n, pos, d->ido, pu, d->ref);
}
}
putchar('\n');
if (r) { // then print indel line
- printf("%s\t%d\t*\t%s/%s\t", d->h->target_name[tid], pos + 1, r->s1, r->s2);
+ printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1);
+ if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]);
+ else printf("%s/%s\t", r->s[0], r->s[1]);
+ printf("%d\t%d\t", r->q_cns, r->q_ref);
+ printf("%s\t%s\t", r->s[0], r->s[1]);
+ //printf("%d\t%d\t", r->gl[0], r->gl[1]);
printf("%d\t%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_ambi, r->cnt_anti);
bam_maqindel_ret_destroy(r);
}
int c;
char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
- d->tid = -1;
+ d->tid = -1; d->mask = BAM_DEF_MASK;
d->c = bam_maqcns_init();
- while ((c = getopt(argc, argv, "st:f:cT:N:r:l:")) >= 0) {
+ d->ido = bam_maqindel_opt_init();
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:")) >= 0) {
switch (c) {
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'N': d->c->n_hap = atoi(optarg); break;
case 'r': d->c->het_rate = atoi(optarg); break;
case 'c': d->format |= BAM_PLF_CNS; break;
+ case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
+ case 'm': d->mask = atoi(optarg); break;
+ case 'g': d->format |= BAM_PLF_GLF; break;
+ case 'I': d->ido->q_indel = atoi(optarg); break;
+ case 'G': d->ido->r_indel = atof(optarg); break;
default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
}
}
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bamtk pileup [options] <in.bam>|<in.sam>\n\n");
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
+ fprintf(stderr, " -i only show lines/consensus with indels\n");
+ fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
fprintf(stderr, " -t FILE list of reference sequences (assume the input is in SAM)\n");
fprintf(stderr, " -l FILE list of sites at which pileup is output\n");
fprintf(stderr, " -f FILE reference sequence in the FASTA format\n\n");
fprintf(stderr, " -c output the maq consensus sequence\n");
- fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c only) [%f]\n", d->c->theta);
- fprintf(stderr, " -N INT number of haplotypes in the sample (for -c only) [%d]\n", d->c->n_hap);
- fprintf(stderr, " -r FLOAT prior of a difference between any two haplotypes (for -c only) [%f]\n\n",
- d->c->het_rate);
+ fprintf(stderr, " -g output in the extended GLT format (suppressing -c/-i/-s)\n");
+ fprintf(stderr, " -T FLOAT theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
+ fprintf(stderr, " -N INT number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
+ fprintf(stderr, " -r FLOAT prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
+ fprintf(stderr, " -G FLOAT prior of an indel between two haplotypes (for -c/-g) [%f]\n", d->ido->r_indel);
+ fprintf(stderr, " -I INT phred prob. of an indel in sequencing/prep. (for -c/-g) [%d]\n", d->ido->q_indel);
+ fprintf(stderr, "\n");
free(fn_list); free(fn_fa); free(d);
return 1;
}
if (fn_fa) d->fai = fai_load(fn_fa);
free(fn_fa);
bam_maqcns_prepare(d->c);
- d->ido = bam_maqindel_opt_init();
+ if (d->format & BAM_PLF_GLF) {
+ glf_header_t *h;
+ h = glf_header_init();
+ d->fp = bgzf_fdopen(fileno(stdout), "w");
+ glf_header_write(d->fp, h);
+ glf_header_destroy(h);
+ }
if (fn_list) {
tamFile fp;
bam1_t *b;
int ret;
bam_plbuf_t *buf = bam_plbuf_init(pileup_func, d);
+ bam_plbuf_set_mask(buf, d->mask);
d->h = sam_header_read2(fn_list);
if (fn_pos) d->hash = load_pos(fn_pos, d->h);
fp = sam_open(argv[optind]);
fp = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
d->h = bam_header_read(fp);
if (fn_pos) d->hash = load_pos(fn_pos, d->h);
- bam_pileup_file(fp, pileup_func, d);
+ bam_pileup_file(fp, d->mask, pileup_func, d);
bam_close(fp);
}
+ if (d->format & BAM_PLF_GLF) bgzf_close(d->fp);
free(fn_pos); free(fn_list);
kh_destroy(64, d->hash);
bam_header_destroy(d->h);
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