tbx.c

/*  tbx.c -- tabix API functions.

    Copyright (C) 2009, 2010, 2012-2015, 2017 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 <stdio.h>
#include <assert.h>
#include <errno.h>
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/hts_endian.h"
#include "hts_internal.h"

#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)

const tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 };
const tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 };
const tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 };
const tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 };
const 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 < 0) {
            return -1; // Out of memory
        } else if (absent) {
            char *ss_dup = strdup(ss);
            if (ss_dup) {
                kh_key(d, k) = ss_dup;
                kh_val(d, k) = kh_size(d) - 1;
            } else {
                kh_del(s2i, d, k);
                return -1; // Out of memory
            }
        }
    } 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;
                        char *t;
                        for (s = line + b; s < line + i;) {
                            long x = strtol(s, &t, 10);
                            char op = toupper_c(*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;
        }
        hts_log_error("Failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"",
            type, str->s);
        return -1;
    }
}

/*
 * Called by tabix iterator to read the next record.
 * Returns    >=  0 on success
 *               -1 on EOF
 *            <= -2 on error
 */
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;
        if (get_intv(tbx, s, &intv, 0) < 0)
            return -2;
        *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_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf)
{
    tbx_t *tbx;
    BGZF *fp;
    int ret;
    if ((fp = bgzf_open(fn, "r")) == 0) return -1;
    if ( n_threads ) bgzf_mt(fp, n_threads, 256);
    if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -2; }
    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_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf)
{
    return tbx_index_build3(fn, fnidx, min_shift, 0, conf);
}

int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf)
{
    return tbx_index_build3(fn, NULL, min_shift, 0, conf);
}

tbx_t *tbx_index_load2(const char *fn, const char *fnidx)
{
    tbx_t *tbx;
    uint8_t *meta;
    char *nm, *p;
    uint32_t 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 || l_meta < 28) goto invalid;

    tbx->conf.preset = le_to_i32(&meta[0]);
    tbx->conf.sc = le_to_i32(&meta[4]);
    tbx->conf.bc = le_to_i32(&meta[8]);
    tbx->conf.ec = le_to_i32(&meta[12]);
    tbx->conf.meta_char = le_to_i32(&meta[16]);
    tbx->conf.line_skip = le_to_i32(&meta[20]);
    l_nm = le_to_u32(&meta[24]);
    if (l_nm > l_meta - 28) goto invalid;

    p = nm = (char*)meta + 28;
    // This assumes meta is NUL-terminated, so we can merrily strlen away.
    // hts_idx_load_local() assures this for us by adding a NUL on the end
    // of whatever it reads.
    for (; p - nm < l_nm; p += strlen(p) + 1) {
        if (get_tid(tbx, p, 1) < 0) {
            hts_log_error("%s", strerror(errno));
            goto fail;
        }
    }
    return tbx;

 invalid:
    hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn);

 fail:
    tbx_destroy(tbx);
    return NULL;
}

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 calloc(1, sizeof(char *));
    }
    int tid, m = kh_size(d);
    const char **names = (const char**) calloc(m,sizeof(const char*));
    khint_t k;
    if (!names) {
        *n = 0;
        return NULL;
    }
    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;
}