tbx.c

#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;
        }
		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_build(const char *fn, int min_shift, const tbx_conf_t *conf)
{
	tbx_t *tbx;
	BGZF *fp;
    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;
	hts_idx_save(tbx->idx, fn, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI);
	tbx_destroy(tbx);
	return 0;
}

tbx_t *tbx_index_load(const char *fn)
{
	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 = hts_idx_load(fn, HTS_FMT_TBI);
	if ( !tbx->idx ) 
    {
        free(tbx);
        return NULL;
    }
	meta = hts_idx_get_meta(tbx->idx, &l_meta);
	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;
}

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;
}