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hts.c
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hts.c
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/* hts.c -- format-neutral I/O, indexing, and iterator API functions.
Copyright (C) 2008, 2009, 2012-2014 Genome Research Ltd.
Copyright (C) 2012, 2013 Broad Institute.
Author: Heng Li <[email protected]>
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 <zlib.h>
#include <ctype.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <fcntl.h>
#include <errno.h>
#include <sys/stat.h>
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "version.h"
#include "htslib/kseq.h"
#define KS_BGZF 1
#if KS_BGZF
// bgzf now supports gzip-compressed files, the gzFile branch can be removed
KSTREAM_INIT2(, BGZF*, bgzf_read, 65536)
#else
KSTREAM_INIT2(, gzFile, gzread, 16384)
#endif
#include "htslib/khash.h"
KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal)
int hts_verbose = 3;
const char *hts_version()
{
return HTS_VERSION;
}
const unsigned char seq_nt16_table[256] = {
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};
const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN";
/**********************
*** Basic file I/O ***
**********************/
static enum htsFormatCategory format_category(enum htsExactFormat fmt)
{
switch (fmt) {
case bam:
case sam:
case cram:
return sequence_data;
case vcf:
case bcfv1:
case bcf:
return variant_data;
case bai:
case crai:
case csi:
case gzi:
case tbi:
return index_file;
case bed:
return region_list;
case unknown_format:
case binary_format:
case text_format:
case format_maximum:
break;
}
return unknown_category;
}
// Decompress up to ten or so bytes by peeking at the file, which must be
// positioned at the start of a GZIP block.
static size_t decompress_peek(hFILE *fp, unsigned char *dest, size_t destsize)
{
// Typically at most a couple of hundred bytes of input are required
// to get a few bytes of output from inflate(), so hopefully this buffer
// size suffices in general.
unsigned char buffer[512];
z_stream zs;
ssize_t npeek = hpeek(fp, buffer, sizeof buffer);
if (npeek < 0) return 0;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_in = buffer;
zs.avail_in = npeek;
zs.next_out = dest;
zs.avail_out = destsize;
if (inflateInit2(&zs, 31) != Z_OK) return 0;
while (zs.total_out < destsize)
if (inflate(&zs, Z_SYNC_FLUSH) != Z_OK) break;
destsize = zs.total_out;
inflateEnd(&zs);
return destsize;
}
int hts_detect_format(hFILE *hfile, htsFormat *fmt)
{
unsigned char s[18];
ssize_t len = hpeek(hfile, s, 18);
if (len < 0) return -1;
if (len >= 2 && s[0] == 0x1f && s[1] == 0x8b) {
// The stream is either gzip-compressed or BGZF-compressed.
// Determine which, and decompress the first few bytes.
fmt->compression = (len >= 18 && (s[3] & 4) &&
memcmp(&s[12], "BC\2\0", 4) == 0)? bgzf : gzip;
len = decompress_peek(hfile, s, sizeof s);
}
else {
fmt->compression = no_compression;
len = hpeek(hfile, s, sizeof s);
}
if (len < 0) return -1;
if (len >= 6 && memcmp(s,"CRAM",4) == 0 && s[4]>=1 && s[4]<=3 && s[5]<=1) {
fmt->category = sequence_data;
fmt->format = cram;
fmt->compression = custom;
return 0;
}
else if (len >= 4 && s[3] <= '\4') {
if (memcmp(s, "BAM\1", 4) == 0) {
fmt->category = sequence_data;
fmt->format = bam;
return 0;
}
else if (memcmp(s, "BAI\1", 4) == 0) {
fmt->category = index_file;
fmt->format = bai;
return 0;
}
else if (memcmp(s, "BCF\4", 4) == 0) {
fmt->category = variant_data;
fmt->format = bcfv1;
return 0;
}
else if (memcmp(s, "BCF\2", 4) == 0) {
fmt->category = variant_data;
fmt->format = bcf;
return 0;
}
else if (memcmp(s, "CSI\1", 4) == 0) {
fmt->category = index_file;
fmt->format = csi;
return 0;
}
else if (memcmp(s, "TBI\1", 4) == 0) {
fmt->category = index_file;
fmt->format = tbi;
return 0;
}
}
else if (len >= 16 && memcmp(s, "##fileformat=VCF", 16) == 0) {
fmt->category = variant_data;
fmt->format = vcf;
return 0;
}
else if (len >= 4 && s[0] == '@' &&
(memcmp(s, "@HD\t", 4) == 0 || memcmp(s, "@SQ\t", 4) == 0 ||
memcmp(s, "@RG\t", 4) == 0 || memcmp(s, "@PG\t", 4) == 0)) {
fmt->category = sequence_data;
fmt->format = sam;
return 0;
}
else {
// Various possibilities for tab-delimited text:
// .crai (gzipped tab-delimited six columns: seqid 5*number)
// .bed ([3..12] tab-delimited columns)
// .bedpe (>= 10 tab-delimited columns)
// .sam (tab-delimited >= 11 columns: seqid number seqid...)
// FIXME For now, assume it's SAM
fmt->category = sequence_data;
fmt->format = sam;
return 0;
}
fmt->category = unknown_category;
fmt->format = unknown_format;
fmt->compression = no_compression;
return 0;
}
const char *hts_format_description(const htsFormat *format)
{
switch (format->format) {
case sam: return "SAM-format sequence text";
case bam: return "BAM-format compressed sequence data";
case cram: return "CRAM-format compressed sequence data";
case vcf: return "VCF-format variant calling text";
case bcf: return "BCF-format compressed variant calling data";
case bcfv1: return "BCFv1-legacy-format compressed variant calling data";
case bai: return "BAI sequence index data";
case crai: return "CRAI compressed sequence index data";
case csi: return "CSI compressed sequence index data";
case tbi: return "Tabix compressed genomic region index data";
default: return "unknown";
}
}
htsFile *hts_open(const char *fn, const char *mode)
{
htsFile *fp = NULL;
hFILE *hfile = hopen(fn, mode);
if (hfile == NULL) goto error;
fp = hts_hopen(hfile, fn, mode);
if (fp == NULL) goto error;
return fp;
error:
if (hts_verbose >= 2)
fprintf(stderr, "[E::%s] fail to open file '%s'\n", __func__, fn);
if (hfile)
hclose_abruptly(hfile);
return NULL;
}
htsFile *hts_hopen(struct hFILE *hfile, const char *fn, const char *mode)
{
htsFile *fp = (htsFile*)calloc(1, sizeof(htsFile));
if (fp == NULL) goto error;
fp->fn = strdup(fn);
fp->is_be = ed_is_big();
if (strchr(mode, 'r')) {
if (hts_detect_format(hfile, &fp->format) < 0) goto error;
}
else if (strchr(mode, 'w') || strchr(mode, 'a')) {
htsFormat *fmt = &fp->format;
fp->is_write = 1;
if (strchr(mode, 'b')) fmt->format = binary_format;
else if (strchr(mode, 'c')) fmt->format = cram;
else fmt->format = text_format;
if (strchr(mode, 'z')) fmt->compression = bgzf;
else if (strchr(mode, 'g')) fmt->compression = gzip;
else if (strchr(mode, 'u')) fmt->compression = no_compression;
else {
// No compression mode specified, set to the default for the format
switch (fmt->format) {
case binary_format: fmt->compression = bgzf; break;
case cram: fmt->compression = custom; break;
case text_format: fmt->compression = no_compression; break;
default: abort();
}
}
// Fill in category (if determinable; e.g. 'b' could be BAM or BCF)
fmt->category = format_category(fmt->format);
}
else goto error;
switch (fp->format.format) {
case binary_format:
case bam:
case bcf:
fp->fp.bgzf = bgzf_hopen(hfile, mode);
if (fp->fp.bgzf == NULL) goto error;
fp->is_bin = 1;
break;
case cram:
fp->fp.cram = cram_dopen(hfile, fn, mode);
if (fp->fp.cram == NULL) goto error;
if (!fp->is_write)
cram_set_option(fp->fp.cram, CRAM_OPT_DECODE_MD, 1);
fp->is_cram = 1;
break;
case text_format:
case sam:
case vcf:
if (!fp->is_write) {
#if KS_BGZF
BGZF *gzfp = bgzf_hopen(hfile, mode);
#else
// TODO Implement gzip hFILE adaptor
hclose(hfile); // This won't work, especially for stdin
gzFile gzfp = strcmp(fn, "-")? gzopen(fn, "rb") : gzdopen(fileno(stdin), "rb");
#endif
if (gzfp) fp->fp.voidp = ks_init(gzfp);
else goto error;
}
else if (fp->format.compression != no_compression) {
fp->fp.bgzf = bgzf_hopen(hfile, mode);
if (fp->fp.bgzf == NULL) goto error;
}
else
fp->fp.hfile = hfile;
break;
default:
goto error;
}
return fp;
error:
if (hts_verbose >= 2)
fprintf(stderr, "[E::%s] fail to open file '%s'\n", __func__, fn);
if (fp) {
free(fp->fn);
free(fp->fn_aux);
free(fp);
}
return NULL;
}
int hts_close(htsFile *fp)
{
int ret, save;
switch (fp->format.format) {
case binary_format:
case bam:
case bcf:
ret = bgzf_close(fp->fp.bgzf);
break;
case cram:
if (!fp->is_write) {
switch (cram_eof(fp->fp.cram)) {
case 0:
fprintf(stderr, "[E::%s] Failed to decode sequence.\n", __func__);
return -1;
case 2:
fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
break;
default: /* case 1, expected EOF */
break;
}
}
ret = cram_close(fp->fp.cram);
break;
case text_format:
case sam:
case vcf:
if (!fp->is_write) {
#if KS_BGZF
BGZF *gzfp = ((kstream_t*)fp->fp.voidp)->f;
ret = bgzf_close(gzfp);
#else
gzFile gzfp = ((kstream_t*)fp->fp.voidp)->f;
ret = gzclose(gzfp);
#endif
ks_destroy((kstream_t*)fp->fp.voidp);
}
else if (fp->format.compression != no_compression)
ret = bgzf_close(fp->fp.bgzf);
else
ret = hclose(fp->fp.hfile);
break;
default:
ret = -1;
break;
}
save = errno;
free(fp->fn);
free(fp->fn_aux);
free(fp->line.s);
free(fp);
errno = save;
return ret;
}
const htsFormat *hts_get_format(htsFile *fp)
{
return fp? &fp->format : NULL;
}
int hts_set_opt(htsFile *fp, enum cram_option opt, ...) {
int r;
va_list args;
if (fp->format.format != cram)
return 0;
va_start(args, opt);
r = cram_set_voption(fp->fp.cram, opt, args);
va_end(args);
return r;
}
int hts_set_threads(htsFile *fp, int n)
{
if (fp->format.compression == bgzf) {
return bgzf_mt(fp->fp.bgzf, n, 256);
} else if (fp->format.format == cram) {
return hts_set_opt(fp, CRAM_OPT_NTHREADS, n);
}
else return 0;
}
int hts_set_fai_filename(htsFile *fp, const char *fn_aux)
{
free(fp->fn_aux);
if (fn_aux) {
fp->fn_aux = strdup(fn_aux);
if (fp->fn_aux == NULL) return -1;
}
else fp->fn_aux = NULL;
if (fp->format.format == cram)
cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, fp->fn_aux);
return 0;
}
// For VCF/BCF backward sweeper. Not exposing these functions because their
// future is uncertain. Things will probably have to change with hFILE...
BGZF *hts_get_bgzfp(htsFile *fp)
{
if ( fp->is_bin )
return fp->fp.bgzf;
else
return ((kstream_t*)fp->fp.voidp)->f;
}
int hts_useek(htsFile *fp, long uoffset, int where)
{
if ( fp->is_bin )
return bgzf_useek(fp->fp.bgzf, uoffset, where);
else
{
ks_rewind((kstream_t*)fp->fp.voidp);
((kstream_t*)fp->fp.voidp)->seek_pos = uoffset;
return bgzf_useek(((kstream_t*)fp->fp.voidp)->f, uoffset, where);
}
}
long hts_utell(htsFile *fp)
{
if ( fp->is_bin )
return bgzf_utell(fp->fp.bgzf);
else
return ((kstream_t*)fp->fp.voidp)->seek_pos;
}
int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
{
int ret, dret;
ret = ks_getuntil((kstream_t*)fp->fp.voidp, delimiter, str, &dret);
++fp->lineno;
return ret;
}
char **hts_readlist(const char *string, int is_file, int *_n)
{
int m = 0, n = 0, dret;
char **s = 0;
if ( is_file )
{
#if KS_BGZF
BGZF *fp = bgzf_open(string, "r");
#else
gzFile fp = gzopen(string, "r");
#endif
if ( !fp ) return NULL;
kstream_t *ks;
kstring_t str;
str.s = 0; str.l = str.m = 0;
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0)
{
if (str.l == 0) continue;
n++;
hts_expand(char*,n,m,s);
s[n-1] = strdup(str.s);
}
ks_destroy(ks);
#if KS_BGZF
bgzf_close(fp);
#else
gzclose(fp);
#endif
free(str.s);
}
else
{
const char *q = string, *p = string;
while ( 1 )
{
if (*p == ',' || *p == 0)
{
n++;
hts_expand(char*,n,m,s);
s[n-1] = (char*)calloc(p - q + 1, 1);
strncpy(s[n-1], q, p - q);
q = p + 1;
}
if ( !*p ) break;
p++;
}
}
s = (char**)realloc(s, n * sizeof(char*));
*_n = n;
return s;
}
char **hts_readlines(const char *fn, int *_n)
{
int m = 0, n = 0, dret;
char **s = 0;
#if KS_BGZF
BGZF *fp = bgzf_open(fn, "r");
#else
gzFile fp = gzopen(fn, "r");
#endif
if ( fp ) { // read from file
kstream_t *ks;
kstring_t str;
str.s = 0; str.l = str.m = 0;
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
if (str.l == 0) continue;
if (m == n) {
m = m? m<<1 : 16;
s = (char**)realloc(s, m * sizeof(char*));
}
s[n++] = strdup(str.s);
}
ks_destroy(ks);
#if KS_BGZF
bgzf_close(fp);
#else
gzclose(fp);
#endif
s = (char**)realloc(s, n * sizeof(char*));
free(str.s);
} else if (*fn == ':') { // read from string
const char *q, *p;
for (q = p = fn + 1;; ++p)
if (*p == ',' || *p == 0) {
if (m == n) {
m = m? m<<1 : 16;
s = (char**)realloc(s, m * sizeof(char*));
}
s[n] = (char*)calloc(p - q + 1, 1);
strncpy(s[n++], q, p - q);
q = p + 1;
if (*p == 0) break;
}
} else return 0;
s = (char**)realloc(s, n * sizeof(char*));
*_n = n;
return s;
}
/****************
*** Indexing ***
****************/
#define HTS_MIN_MARKER_DIST 0x10000
// Finds the special meta bin
// ((1<<(3 * n_lvls + 3)) - 1) / 7 + 1
#define META_BIN(idx) ((idx)->n_bins + 1)
#define pair64_lt(a,b) ((a).u < (b).u)
#include "htslib/ksort.h"
KSORT_INIT(_off, hts_pair64_t, pair64_lt)
typedef struct {
int32_t m, n;
uint64_t loff;
hts_pair64_t *list;
} bins_t;
#include "htslib/khash.h"
KHASH_MAP_INIT_INT(bin, bins_t)
typedef khash_t(bin) bidx_t;
typedef struct {
int32_t n, m;
uint64_t *offset;
} lidx_t;
struct __hts_idx_t {
int fmt, min_shift, n_lvls, n_bins;
uint32_t l_meta;
int32_t n, m;
uint64_t n_no_coor;
bidx_t **bidx;
lidx_t *lidx;
uint8_t *meta;
struct {
uint32_t last_bin, save_bin;
int last_coor, last_tid, save_tid, finished;
uint64_t last_off, save_off;
uint64_t off_beg, off_end;
uint64_t n_mapped, n_unmapped;
} z; // keep internal states
};
static inline void insert_to_b(bidx_t *b, int bin, uint64_t beg, uint64_t end)
{
khint_t k;
bins_t *l;
int absent;
k = kh_put(bin, b, bin, &absent);
l = &kh_value(b, k);
if (absent) {
l->m = 1; l->n = 0;
l->list = (hts_pair64_t*)calloc(l->m, 16);
}
if (l->n == l->m) {
l->m <<= 1;
l->list = (hts_pair64_t*)realloc(l->list, l->m * 16);
}
l->list[l->n].u = beg;
l->list[l->n++].v = end;
}
static inline void insert_to_l(lidx_t *l, int64_t _beg, int64_t _end, uint64_t offset, int min_shift)
{
int i, beg, end;
beg = _beg >> min_shift;
end = (_end - 1) >> min_shift;
if (l->m < end + 1) {
int old_m = l->m;
l->m = end + 1;
kroundup32(l->m);
l->offset = (uint64_t*)realloc(l->offset, l->m * 8);
memset(l->offset + old_m, 0xff, 8 * (l->m - old_m)); // fill l->offset with (uint64_t)-1
}
if (beg == end) { // to save a loop in this case
if (l->offset[beg] == (uint64_t)-1) l->offset[beg] = offset;
} else {
for (i = beg; i <= end; ++i)
if (l->offset[i] == (uint64_t)-1) l->offset[i] = offset;
}
if (l->n < end + 1) l->n = end + 1;
}
hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls)
{
hts_idx_t *idx;
idx = (hts_idx_t*)calloc(1, sizeof(hts_idx_t));
if (idx == NULL) return NULL;
idx->fmt = fmt;
idx->min_shift = min_shift;
idx->n_lvls = n_lvls;
idx->n_bins = ((1<<(3 * n_lvls + 3)) - 1) / 7;
idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
idx->z.save_off = idx->z.last_off = idx->z.off_beg = idx->z.off_end = offset0;
idx->z.last_coor = 0xffffffffu;
if (n) {
idx->n = idx->m = n;
idx->bidx = (bidx_t**)calloc(n, sizeof(bidx_t*));
if (idx->bidx == NULL) { free(idx); return NULL; }
idx->lidx = (lidx_t*) calloc(n, sizeof(lidx_t));
if (idx->lidx == NULL) { free(idx->bidx); free(idx); return NULL; }
}
return idx;
}
static void update_loff(hts_idx_t *idx, int i, int free_lidx)
{
bidx_t *bidx = idx->bidx[i];
lidx_t *lidx = &idx->lidx[i];
khint_t k;
int l;
uint64_t offset0 = 0;
if (bidx) {
k = kh_get(bin, bidx, META_BIN(idx));
if (k != kh_end(bidx))
offset0 = kh_val(bidx, k).list[0].u;
for (l = 0; l < lidx->n && lidx->offset[l] == (uint64_t)-1; ++l)
lidx->offset[l] = offset0;
} else l = 1;
for (; l < lidx->n; ++l) // fill missing values
if (lidx->offset[l] == (uint64_t)-1)
lidx->offset[l] = lidx->offset[l-1];
if (bidx == 0) return;
for (k = kh_begin(bidx); k != kh_end(bidx); ++k) // set loff
if (kh_exist(bidx, k))
{
if ( kh_key(bidx, k) < idx->n_bins )
{
int bot_bin = hts_bin_bot(kh_key(bidx, k), idx->n_lvls);
// disable linear index if bot_bin out of bounds
kh_val(bidx, k).loff = bot_bin < lidx->n ? lidx->offset[bot_bin] : 0;
}
else
kh_val(bidx, k).loff = 0;
}
if (free_lidx) {
free(lidx->offset);
lidx->m = lidx->n = 0;
lidx->offset = 0;
}
}
static void compress_binning(hts_idx_t *idx, int i)
{
bidx_t *bidx = idx->bidx[i];
khint_t k;
int l, m;
if (bidx == 0) return;
// merge a bin to its parent if the bin is too small
for (l = idx->n_lvls; l > 0; --l) {
unsigned start = hts_bin_first(l);
for (k = kh_begin(bidx); k != kh_end(bidx); ++k) {
bins_t *p, *q;
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
p = &kh_value(bidx, k);
if (l < idx->n_lvls && p->n > 1) ks_introsort(_off, p->n, p->list);
if ((p->list[p->n - 1].v>>16) - (p->list[0].u>>16) < HTS_MIN_MARKER_DIST) {
khint_t kp;
kp = kh_get(bin, bidx, hts_bin_parent(kh_key(bidx, k)));
if (kp == kh_end(bidx)) continue;
q = &kh_val(bidx, kp);
if (q->n + p->n > q->m) {
q->m = q->n + p->n;
kroundup32(q->m);
q->list = (hts_pair64_t*)realloc(q->list, q->m * 16);
}
memcpy(q->list + q->n, p->list, p->n * 16);
q->n += p->n;
free(p->list);
kh_del(bin, bidx, k);
}
}
}
k = kh_get(bin, bidx, 0);
if (k != kh_end(bidx)) ks_introsort(_off, kh_val(bidx, k).n, kh_val(bidx, k).list);
// merge adjacent chunks that start from the same BGZF block
for (k = kh_begin(bidx); k != kh_end(bidx); ++k) {
bins_t *p;
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
p = &kh_value(bidx, k);
for (l = 1, m = 0; l < p->n; ++l) {
if (p->list[m].v>>16 >= p->list[l].u>>16) {
if (p->list[m].v < p->list[l].v) p->list[m].v = p->list[l].v;
} else p->list[++m] = p->list[l];
}
p->n = m + 1;
}
}
void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset)
{
int i;
if (idx == NULL || idx->z.finished) return; // do not run this function on an empty index or multiple times
if (idx->z.save_tid >= 0) {
insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, final_offset);
insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, final_offset);
insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped);
}
for (i = 0; i < idx->n; ++i) {
update_loff(idx, i, (idx->fmt == HTS_FMT_CSI));
compress_binning(idx, i);
}
idx->z.finished = 1;
}
int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped)
{
int bin;
if (tid >= idx->m) { // enlarge the index
int32_t oldm = idx->m;
idx->m = idx->m? idx->m<<1 : 2;
idx->bidx = (bidx_t**)realloc(idx->bidx, idx->m * sizeof(bidx_t*));
idx->lidx = (lidx_t*) realloc(idx->lidx, idx->m * sizeof(lidx_t));
memset(&idx->bidx[oldm], 0, (idx->m - oldm) * sizeof(bidx_t*));
memset(&idx->lidx[oldm], 0, (idx->m - oldm) * sizeof(lidx_t));
}
if (idx->n < tid + 1) idx->n = tid + 1;
if (idx->z.finished) return 0;
if (idx->z.last_tid != tid || (idx->z.last_tid >= 0 && tid < 0)) { // change of chromosome
if ( tid>=0 && idx->n_no_coor )
{
if (hts_verbose >= 1) fprintf(stderr,"[E::%s] NO_COOR reads not in a single block at the end %d %d\n", __func__, tid,idx->z.last_tid);
return -1;
}
if (tid>=0 && idx->bidx[tid] != 0)
{
if (hts_verbose >= 1) fprintf(stderr, "[E::%s] chromosome blocks not continuous\n", __func__);
return -1;
}
idx->z.last_tid = tid;
idx->z.last_bin = 0xffffffffu;
} else if (tid >= 0 && idx->z.last_coor > beg) { // test if positions are out of order
if (hts_verbose >= 1) fprintf(stderr, "[E::%s] unsorted positions\n", __func__);
return -1;
}
if ( tid>=0 )
{
if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin);
if ( is_mapped)
insert_to_l(&idx->lidx[tid], beg, end, idx->z.last_off, idx->min_shift); // last_off points to the start of the current record
}
else idx->n_no_coor++;
bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls);
if ((int)idx->z.last_bin != bin) { // then possibly write the binning index
if (idx->z.save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, idx->z.last_off);
if (idx->z.last_bin == 0xffffffffu && idx->z.save_bin != 0xffffffffu) { // change of chr; keep meta information
idx->z.off_end = idx->z.last_off;
insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, idx->z.off_end);
insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped);
idx->z.n_mapped = idx->z.n_unmapped = 0;
idx->z.off_beg = idx->z.off_end;
}
idx->z.save_off = idx->z.last_off;
idx->z.save_bin = idx->z.last_bin = bin;
idx->z.save_tid = tid;
}
if (is_mapped) ++idx->z.n_mapped;
else ++idx->z.n_unmapped;
idx->z.last_off = offset;
idx->z.last_coor = beg;
return 0;
}
void hts_idx_destroy(hts_idx_t *idx)
{
khint_t k;
int i;
if (idx == 0) return;
// For HTS_FMT_CRAI, idx actually points to a different type -- see sam.c
if (idx->fmt == HTS_FMT_CRAI) { free(idx); return; }
for (i = 0; i < idx->m; ++i) {
bidx_t *bidx = idx->bidx[i];
free(idx->lidx[i].offset);
if (bidx == 0) continue;
for (k = kh_begin(bidx); k != kh_end(bidx); ++k)
if (kh_exist(bidx, k))
free(kh_value(bidx, k).list);
kh_destroy(bin, bidx);
}
free(idx->bidx); free(idx->lidx); free(idx->meta);
free(idx);
}
static inline long idx_read(int is_bgzf, void *fp, void *buf, long l)
{
if (is_bgzf) return bgzf_read((BGZF*)fp, buf, l);
else return (long)fread(buf, 1, l, (FILE*)fp);
}
static inline long idx_write(int is_bgzf, void *fp, const void *buf, long l)
{
if (is_bgzf) return bgzf_write((BGZF*)fp, buf, l);
else return (long)fwrite(buf, 1, l, (FILE*)fp);
}
static inline void swap_bins(bins_t *p)
{
int i;
for (i = 0; i < p->n; ++i) {
ed_swap_8p(&p->list[i].u);
ed_swap_8p(&p->list[i].v);
}
}
static void hts_idx_save_core(const hts_idx_t *idx, void *fp, int fmt)
{
int32_t i, size, is_be;
int is_bgzf = (fmt != HTS_FMT_BAI);
is_be = ed_is_big();
if (is_be) {
uint32_t x = idx->n;
idx_write(is_bgzf, fp, ed_swap_4p(&x), 4);
} else idx_write(is_bgzf, fp, &idx->n, 4);
if (fmt == HTS_FMT_TBI && idx->l_meta) idx_write(is_bgzf, fp, idx->meta, idx->l_meta);
for (i = 0; i < idx->n; ++i) {
khint_t k;
bidx_t *bidx = idx->bidx[i];
lidx_t *lidx = &idx->lidx[i];
// write binning index
size = bidx? kh_size(bidx) : 0;
if (is_be) { // big endian
uint32_t x = size;
idx_write(is_bgzf, fp, ed_swap_4p(&x), 4);
} else idx_write(is_bgzf, fp, &size, 4);
if (bidx == 0) goto write_lidx;
for (k = kh_begin(bidx); k != kh_end(bidx); ++k) {
bins_t *p;
if (!kh_exist(bidx, k)) continue;
p = &kh_value(bidx, k);
if (is_be) { // big endian
uint32_t x;
x = kh_key(bidx, k); idx_write(is_bgzf, fp, ed_swap_4p(&x), 4);
if (fmt == HTS_FMT_CSI) {
uint64_t y = kh_val(bidx, k).loff;
idx_write(is_bgzf, fp, ed_swap_4p(&y), 8);
}
x = p->n; idx_write(is_bgzf, fp, ed_swap_4p(&x), 4);
swap_bins(p);
idx_write(is_bgzf, fp, p->list, 16 * p->n);
swap_bins(p);
} else {
idx_write(is_bgzf, fp, &kh_key(bidx, k), 4);
if (fmt == HTS_FMT_CSI) idx_write(is_bgzf, fp, &kh_val(bidx, k).loff, 8);
//int j;for(j=0;j<p->n;++j)fprintf(stderr,"%d,%llx,%d,%llx:%llx\n",kh_key(bidx,k),kh_val(bidx, k).loff,j,p->list[j].u,p->list[j].v);
idx_write(is_bgzf, fp, &p->n, 4);
idx_write(is_bgzf, fp, p->list, p->n << 4);
}
}
write_lidx:
if (fmt != HTS_FMT_CSI) {
if (is_be) {
int32_t x = lidx->n;
idx_write(is_bgzf, fp, ed_swap_4p(&x), 4);
for (x = 0; x < lidx->n; ++x) ed_swap_8p(&lidx->offset[x]);
idx_write(is_bgzf, fp, lidx->offset, lidx->n << 3);
for (x = 0; x < lidx->n; ++x) ed_swap_8p(&lidx->offset[x]);
} else {
idx_write(is_bgzf, fp, &lidx->n, 4);
idx_write(is_bgzf, fp, lidx->offset, lidx->n << 3);
}
}
}
if (is_be) { // write the number of reads without coordinates
uint64_t x = idx->n_no_coor;
idx_write(is_bgzf, fp, &x, 8);
} else idx_write(is_bgzf, fp, &idx->n_no_coor, 8);
}
void hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt)
{
char *fnidx;
fnidx = (char*)calloc(1, strlen(fn) + 5);
strcpy(fnidx, fn);
if (fmt == HTS_FMT_CSI) {
BGZF *fp;
uint32_t x[3];
int is_be, i;
is_be = ed_is_big();
fp = bgzf_open(strcat(fnidx, ".csi"), "w");
bgzf_write(fp, "CSI\1", 4);
x[0] = idx->min_shift; x[1] = idx->n_lvls; x[2] = idx->l_meta;
if (is_be) {
for (i = 0; i < 3; ++i)
bgzf_write(fp, ed_swap_4p(&x[i]), 4);
} else bgzf_write(fp, &x, 12);