7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/tbx.c src/htslib/tbx.c deleted file mode 100644 index 3642d945706..00000000000 --- src/htslib/tbx.c +++ /dev/null @@ -1,334 +0,0 @@ -/* tbx.c -- tabix API functions. - - Copyright (C) 2009, 2010, 2012-2015 Genome Research Ltd. - Copyright (C) 2010-2012 Broad Institute. - - Author: Heng Li <lh3@sanger.ac.uk> - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -DEALINGS IN THE SOFTWARE. */ - -#include <config.h> - -#include <stdlib.h> -#include <string.h> -#include <ctype.h> -#include <stdio.h> -#include <assert.h> -#include "htslib/tbx.h" -#include "htslib/bgzf.h" - -#include "htslib/khash.h" -KHASH_DECLARE(s2i, kh_cstr_t, int64_t) - -tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 }; -tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 }; -tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 }; -tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 }; -tbx_conf_t tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 }; - -typedef struct { - int64_t beg, end; - char *ss, *se; - int tid; -} tbx_intv_t; - -static inline int get_tid(tbx_t *tbx, const char *ss, int is_add) -{ - khint_t k; - khash_t(s2i) *d; - if (tbx->dict == 0) tbx->dict = kh_init(s2i); - d = (khash_t(s2i)*)tbx->dict; - if (is_add) { - int absent; - k = kh_put(s2i, d, ss, &absent); - if (absent) { - kh_key(d, k) = strdup(ss); - kh_val(d, k) = kh_size(d) - 1; - } - } else k = kh_get(s2i, d, ss); - return k == kh_end(d)? -1 : kh_val(d, k); -} - -int tbx_name2id(tbx_t *tbx, const char *ss) -{ - return get_tid(tbx, ss, 0); -} - -int tbx_parse1(const tbx_conf_t *conf, int len, char *line, tbx_intv_t *intv) -{ - int i, b = 0, id = 1, ncols = 0; - char *s; - intv->ss = intv->se = 0; intv->beg = intv->end = -1; - for (i = 0; i <= len; ++i) { - if (line[i] == '\t' || line[i] == 0) { - ++ncols; - if (id == conf->sc) { - intv->ss = line + b; intv->se = line + i; - } else if (id == conf->bc) { - // here ->beg is 0-based. - intv->beg = intv->end = strtol(line + b, &s, 0); - if ( s==line+b ) return -1; // expected int - if (!(conf->preset&TBX_UCSC)) --intv->beg; - else ++intv->end; - if (intv->beg < 0) intv->beg = 0; - if (intv->end < 1) intv->end = 1; - } else { - if ((conf->preset&0xffff) == TBX_GENERIC) { - if (id == conf->ec) - { - intv->end = strtol(line + b, &s, 0); - if ( s==line+b ) return -1; // expected int - } - } else if ((conf->preset&0xffff) == TBX_SAM) { - if (id == 6) { // CIGAR - int l = 0, op; - char *t; - for (s = line + b; s < line + i;) { - long x = strtol(s, &t, 10); - op = toupper(*t); - if (op == 'M' || op == 'D' || op == 'N') l += x; - s = t + 1; - } - if (l == 0) l = 1; - intv->end = intv->beg + l; - } - } else if ((conf->preset&0xffff) == TBX_VCF) { - if (id == 4) { - if (b < i) intv->end = intv->beg + (i - b); - } else if (id == 8) { // look for "END=" - int c = line[i]; - line[i] = 0; - s = strstr(line + b, "END="); - if (s == line + b) s += 4; - else if (s) { - s = strstr(line + b, ";END="); - if (s) s += 5; - } - if (s) intv->end = strtol(s, &s, 0); - line[i] = c; - } - } - } - b = i + 1; - ++id; - } - } - if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; - return 0; -} - -static inline int get_intv(tbx_t *tbx, kstring_t *str, tbx_intv_t *intv, int is_add) -{ - if (tbx_parse1(&tbx->conf, str->l, str->s, intv) == 0) { - int c = *intv->se; - *intv->se = '\0'; intv->tid = get_tid(tbx, intv->ss, is_add); *intv->se = c; - return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1; - } else { - char *type = NULL; - switch (tbx->conf.preset&0xffff) - { - case TBX_SAM: type = "TBX_SAM"; break; - case TBX_VCF: type = "TBX_VCF"; break; - case TBX_UCSC: type = "TBX_UCSC"; break; - default: type = "TBX_GENERIC"; break; - } - if ((str->l > 0) && (*str->s != tbx->conf.meta_char)) - fprintf(stderr, "[E::%s] failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"\n", __func__, type, str->s); - return -1; - } -} - -int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end) -{ - tbx_t *tbx = (tbx_t *) tbxv; - kstring_t *s = (kstring_t *) sv; - int ret; - if ((ret = bgzf_getline(fp, '\n', s)) >= 0) { - tbx_intv_t intv; - get_intv(tbx, s, &intv, 0); - *tid = intv.tid; *beg = intv.beg; *end = intv.end; - } - return ret; -} - -void tbx_set_meta(tbx_t *tbx) -{ - int i, l = 0, l_nm; - uint32_t x[7]; - char **name; - uint8_t *meta; - khint_t k; - khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; - - memcpy(x, &tbx->conf, 24); - name = (char**)malloc(sizeof(char*) * kh_size(d)); - for (k = kh_begin(d), l = 0; k != kh_end(d); ++k) { - if (!kh_exist(d, k)) continue; - name[kh_val(d, k)] = (char*)kh_key(d, k); - l += strlen(kh_key(d, k)) + 1; // +1 to include '\0' - } - l_nm = x[6] = l; - meta = (uint8_t*)malloc(l_nm + 28); - if (ed_is_big()) - for (i = 0; i < 7; ++i) - x[i] = ed_swap_4(x[i]); - memcpy(meta, x, 28); - for (l = 28, i = 0; i < (int)kh_size(d); ++i) { - int x = strlen(name[i]) + 1; - memcpy(meta + l, name[i], x); - l += x; - } - free(name); - hts_idx_set_meta(tbx->idx, l, meta, 0); -} - -tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf) -{ - tbx_t *tbx; - kstring_t str; - int ret, first = 0, n_lvls, fmt; - int64_t lineno = 0; - uint64_t last_off = 0; - tbx_intv_t intv; - - str.s = 0; str.l = str.m = 0; - tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); - tbx->conf = *conf; - if (min_shift > 0) n_lvls = (TBX_MAX_SHIFT - min_shift + 2) / 3, fmt = HTS_FMT_CSI; - else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_TBI; - while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) { - ++lineno; - if (lineno <= tbx->conf.line_skip || str.s[0] == tbx->conf.meta_char) { - last_off = bgzf_tell(fp); - continue; - } - if (first == 0) { - tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); - first = 1; - } - get_intv(tbx, &str, &intv, 1); - ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1); - if (ret < 0) - { - free(str.s); - tbx_destroy(tbx); - return NULL; - } - } - if ( !tbx->idx ) tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls); // empty file - if ( !tbx->dict ) tbx->dict = kh_init(s2i); - hts_idx_finish(tbx->idx, bgzf_tell(fp)); - tbx_set_meta(tbx); - free(str.s); - return tbx; -} - -void tbx_destroy(tbx_t *tbx) -{ - khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; - if (d != NULL) - { - khint_t k; - for (k = kh_begin(d); k != kh_end(d); ++k) - if (kh_exist(d, k)) free((char*)kh_key(d, k)); - } - hts_idx_destroy(tbx->idx); - kh_destroy(s2i, d); - free(tbx); -} - -int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) -{ - tbx_t *tbx; - BGZF *fp; - int ret; - if ( bgzf_is_bgzf(fn)!=1 ) { fprintf(stderr,"Not a BGZF file: %s\n", fn); return -1; } - if ((fp = bgzf_open(fn, "r")) == 0) return -1; - if ( !fp->is_compressed ) { bgzf_close(fp); return -1; } - tbx = tbx_index(fp, min_shift, conf); - bgzf_close(fp); - if ( !tbx ) return -1; - ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); - tbx_destroy(tbx); - return ret; -} - -int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf) -{ - return tbx_index_build2(fn, NULL, min_shift, conf); -} - -tbx_t *tbx_index_load2(const char *fn, const char *fnidx) -{ - tbx_t *tbx; - uint8_t *meta; - char *nm, *p; - uint32_t x[7]; - int l_meta, l_nm; - tbx = (tbx_t*)calloc(1, sizeof(tbx_t)); - tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI); - if ( !tbx->idx ) - { - free(tbx); - return NULL; - } - meta = hts_idx_get_meta(tbx->idx, &l_meta); - if ( !meta ) - { - free(tbx); - return NULL; - } - memcpy(x, meta, 28); - memcpy(&tbx->conf, x, 24); - p = nm = (char*)meta + 28; - l_nm = x[6]; - for (; p - nm < l_nm; p += strlen(p) + 1) get_tid(tbx, p, 1); - return tbx; -} - -tbx_t *tbx_index_load(const char *fn) -{ - return tbx_index_load2(fn, NULL); -} - -const char **tbx_seqnames(tbx_t *tbx, int *n) -{ - khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict; - if (d == NULL) - { - *n = 0; - return NULL; - } - int tid, m = kh_size(d); - const char **names = (const char**) calloc(m,sizeof(const char*)); - khint_t k; - for (k=kh_begin(d); k<kh_end(d); k++) - { - if ( !kh_exist(d,k) ) continue; - tid = kh_val(d,k); - assert( tid<m ); - names[tid] = kh_key(d,k); - } - // sanity check: there should be no gaps - for (tid=0; tid<m; tid++) - assert(names[tid]); - *n = m; - return names; -} -