// Expands a output filename format string
static char* expand_format_string(const char* format_string, const char* basename, const char* rg_id, const int rg_idx)
{
kstring_t str = { 0, 0, NULL };
const char* pointer = format_string;
const char* next;
while ((next = strchr(pointer, '%')) != NULL) {
kputsn(pointer, next-pointer, &str);
++next;
switch (*next) {
case '%':
kputc('%', &str);
break;
case '*':
kputs(basename, &str);
break;
case '#':
kputl(rg_idx, &str);
break;
case '!':
kputs(rg_id, &str);
break;
case '\0':
// Error is: fprintf(pysamerr, "bad format string, trailing %%\n");
free(str.s);
return NULL;
default:
// Error is: fprintf(pysamerr, "bad format string, unknown format specifier\n");
free(str.s);
return NULL;
}
pointer = next + 1;
}
kputs(pointer, &str);
return ks_release(&str);
}
// Expands a output filename format string
static char* expand_format_string(const char* format_string, const char* basename, const char* rg_id, const int rg_idx, const htsFormat *format)
{
kstring_t str = { 0, 0, NULL };
const char* pointer = format_string;
const char* next;
while ((next = strchr(pointer, '%')) != NULL) {
kputsn(pointer, next-pointer, &str);
++next;
switch (*next) {
case '%':
kputc('%', &str);
break;
case '*':
kputs(basename, &str);
break;
case '#':
kputl(rg_idx, &str);
break;
case '!':
kputs(rg_id, &str);
break;
case '.':
// Only really need to cope with sam, bam, cram
if (format->format != unknown_format)
kputs(hts_format_file_extension(format), &str);
else
kputs("bam", &str);
break;
case '\0':
// Error is: fprintf(pysam_stderr, "bad format string, trailing %%\n");
free(str.s);
return NULL;
default:
// Error is: fprintf(pysam_stderr, "bad format string, unknown format specifier\n");
free(str.s);
return NULL;
}
pointer = next + 1;
}
kputs(pointer, &str);
return ks_release(&str);
}
int main_bedcov(int argc, char *argv[])
{
gzFile fp;
kstring_t str;
kstream_t *ks;
hts_idx_t **idx;
aux_t **aux;
int *n_plp, dret, i, n, c, min_mapQ = 0;
int64_t *cnt;
const bam_pileup1_t **plp;
int usage = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0),
{ NULL, 0, NULL, 0 }
};
while ((c = getopt_long(argc, argv, "Q:", lopts, NULL)) >= 0) {
switch (c) {
case 'Q': min_mapQ = atoi(optarg); break;
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
/* else fall-through */
case '?': usage = 1; break;
}
if (usage) break;
}
if (usage || optind + 2 > argc) {
fprintf(pysam_stderr, "Usage: samtools bedcov [options] <in.bed> <in1.bam> [...]\n\n");
fprintf(pysam_stderr, " -Q INT Only count bases of at least INT quality [0]\n");
sam_global_opt_help(pysam_stderr, "-.--.");
return 1;
}
memset(&str, 0, sizeof(kstring_t));
n = argc - optind - 1;
aux = calloc(n, sizeof(aux_t*));
idx = calloc(n, sizeof(hts_idx_t*));
for (i = 0; i < n; ++i) {
aux[i] = calloc(1, sizeof(aux_t));
aux[i]->min_mapQ = min_mapQ;
aux[i]->fp = sam_open_format(argv[i+optind+1], "r", &ga.in);
if (aux[i]->fp)
idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]);
if (aux[i]->fp == 0 || idx[i] == 0) {
fprintf(pysam_stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
return 2;
}
// TODO bgzf_set_cache_size(aux[i]->fp, 20);
aux[i]->header = sam_hdr_read(aux[i]->fp);
if (aux[i]->header == NULL) {
fprintf(pysam_stderr, "ERROR: failed to read header for '%s'\n",
argv[i+optind+1]);
return 2;
}
}
cnt = calloc(n, 8);
fp = gzopen(argv[optind], "rb");
ks = ks_init(fp);
n_plp = calloc(n, sizeof(int));
plp = calloc(n, sizeof(bam_pileup1_t*));
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
char *p, *q;
int tid, beg, end, pos;
bam_mplp_t mplp;
for (p = q = str.s; *p && *p != '\t'; ++p);
if (*p != '\t') goto bed_error;
*p = 0; tid = bam_name2id(aux[0]->header, q); *p = '\t';
if (tid < 0) goto bed_error;
for (q = p = p + 1; isdigit(*p); ++p);
if (*p != '\t') goto bed_error;
*p = 0; beg = atoi(q); *p = '\t';
for (q = p = p + 1; isdigit(*p); ++p);
if (*p == '\t' || *p == 0) {
int c = *p;
*p = 0; end = atoi(q); *p = c;
} else goto bed_error;
for (i = 0; i < n; ++i) {
if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end);
}
mplp = bam_mplp_init(n, read_bam, (void**)aux);
bam_mplp_set_maxcnt(mplp, 64000);
memset(cnt, 0, 8 * n);
while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0)
if (pos >= beg && pos < end)
for (i = 0; i < n; ++i) cnt[i] += n_plp[i];
for (i = 0; i < n; ++i) {
kputc('\t', &str);
kputl(cnt[i], &str);
}
fputs(str.s, pysam_stdout) & fputc('\n', pysam_stdout);
bam_mplp_destroy(mplp);
continue;
bed_error:
fprintf(pysam_stderr, "Errors in BED line '%s'\n", str.s);
}
free(n_plp); free(plp);
ks_destroy(ks);
gzclose(fp);
free(cnt);
for (i = 0; i < n; ++i) {
if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
hts_idx_destroy(idx[i]);
bam_hdr_destroy(aux[i]->header);
sam_close(aux[i]->fp);
free(aux[i]);
}
free(aux); free(idx);
free(str.s);
sam_global_args_free(&ga);
return 0;
}
int main_bedcov(int argc, char *argv[])
{
gzFile fp;
kstring_t str;
kstream_t *ks;
hts_idx_t **idx;
aux_t **aux;
int *n_plp, dret, i, n, c, min_mapQ = 0;
int64_t *cnt;
const bam_pileup1_t **plp;
while ((c = getopt(argc, argv, "Q:")) >= 0) {
switch (c) {
case 'Q': min_mapQ = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "Usage: samtools bedcov <in.bed> <in1.bam> [...]\n");
return 1;
}
memset(&str, 0, sizeof(kstring_t));
n = argc - optind - 1;
aux = calloc(n, sizeof(aux_t*));
idx = calloc(n, sizeof(hts_idx_t*));
for (i = 0; i < n; ++i) {
aux[i] = calloc(1, sizeof(aux_t));
aux[i]->min_mapQ = min_mapQ;
aux[i]->fp = sam_open(argv[i+optind+1], "r");
idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]);
if (aux[i]->fp == 0 || idx[i] == 0) {
fprintf(stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
return 2;
}
// TODO bgzf_set_cache_size(aux[i]->fp, 20);
aux[i]->header = sam_hdr_read(aux[i]->fp);
}
cnt = calloc(n, 8);
fp = gzopen(argv[optind], "rb");
ks = ks_init(fp);
n_plp = calloc(n, sizeof(int));
plp = calloc(n, sizeof(bam_pileup1_t*));
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
char *p, *q;
int tid, beg, end, pos;
bam_mplp_t mplp;
for (p = q = str.s; *p && *p != '\t'; ++p);
if (*p != '\t') goto bed_error;
*p = 0; tid = bam_name2id(aux[0]->header, q); *p = '\t';
if (tid < 0) goto bed_error;
for (q = p = p + 1; isdigit(*p); ++p);
if (*p != '\t') goto bed_error;
*p = 0; beg = atoi(q); *p = '\t';
for (q = p = p + 1; isdigit(*p); ++p);
if (*p == '\t' || *p == 0) {
int c = *p;
*p = 0; end = atoi(q); *p = c;
} else goto bed_error;
for (i = 0; i < n; ++i) {
if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end);
}
mplp = bam_mplp_init(n, read_bam, (void**)aux);
bam_mplp_set_maxcnt(mplp, 64000);
memset(cnt, 0, 8 * n);
while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0)
if (pos >= beg && pos < end)
for (i = 0; i < n; ++i) cnt[i] += n_plp[i];
for (i = 0; i < n; ++i) {
kputc('\t', &str);
kputl(cnt[i], &str);
}
puts(str.s);
bam_mplp_destroy(mplp);
continue;
bed_error:
fprintf(stderr, "Errors in BED line '%s'\n", str.s);
}
free(n_plp); free(plp);
ks_destroy(ks);
gzclose(fp);
free(cnt);
for (i = 0; i < n; ++i) {
if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
hts_idx_destroy(idx[i]);
bam_hdr_destroy(aux[i]->header);
sam_close(aux[i]->fp);
free(aux[i]);
}
free(aux); free(idx);
free(str.s);
return 0;
}
