ezbamqc: ezBAMQC/src/htslib/hts.c comparison

comparison ezBAMQC/src/htslib/hts.c @ 0:dfa3745e5fd8

Uploaded

author	youngkim
date	Thu, 24 Mar 2016 17:12:52 -0400
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:dfa3745e5fd8
+/*  hts.c -- format-neutral I/O, indexing, and iterator API functions.
+Copyright (C) 2008, 2009, 2012-2015 Genome Research Ltd.
+Copyright (C) 2012, 2013 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 <zlib.h>
+#include <ctype.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.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";
+const int seq_nt16_int[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+/**********************
+*** 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 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;
+}
+// Parse "x.y" text, taking care because the string is not NUL-terminated
+// and filling in major/minor only when the digits are followed by a delimiter,
+// so we don't misread "1.10" as "1.1" due to reaching the end of the buffer.
+static void
+parse_version(htsFormat *fmt, const unsigned char *u, const unsigned char *ulim)
+{
+const char *str  = (const char *) u;
+const char *slim = (const char *) ulim;
+const char *s;
+fmt->version.major = fmt->version.minor = -1;
+for (s = str; s < slim; s++) if (!isdigit(*s)) break;
+if (s < slim) {
+fmt->version.major = atoi(str);
+if (*s == '.') {
+str = &s[1];
+for (s = str; s < slim; s++) if (!isdigit(*s)) break;
+if (s < slim)
+fmt->version.minor = atoi(str);
+}
+else
+fmt->version.minor = 0;
+}
+}
+int hts_detect_format(hFILE *hfile, htsFormat *fmt)
+{
+unsigned char s[21];
+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;
+fmt->compression_level = -1;
+fmt->specific = NULL;
+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->version.major = s[4], fmt->version.minor = s[5];
+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;
+// TODO Decompress enough to pick version from @HD-VN header
+fmt->version.major = 1, fmt->version.minor = -1;
+return 0;
+}
+else if (memcmp(s, "BAI\1", 4) == 0) {
+fmt->category = index_file;
+fmt->format = bai;
+fmt->version.major = -1, fmt->version.minor = -1;
+return 0;
+}
+else if (memcmp(s, "BCF\4", 4) == 0) {
+fmt->category = variant_data;
+fmt->format = bcf;
+fmt->version.major = 1, fmt->version.minor = -1;
+return 0;
+}
+else if (memcmp(s, "BCF\2", 4) == 0) {
+fmt->category = variant_data;
+fmt->format = bcf;
+fmt->version.major = s[3];
+fmt->version.minor = (len >= 5 && s[4] <= 2)? s[4] : 0;
+return 0;
+}
+else if (memcmp(s, "CSI\1", 4) == 0) {
+fmt->category = index_file;
+fmt->format = csi;
+fmt->version.major = 1, fmt->version.minor = -1;
+return 0;
+}
+else if (memcmp(s, "TBI\1", 4) == 0) {
+fmt->category = index_file;
+fmt->format = tbi;
+fmt->version.major = -1, fmt->version.minor = -1;
+return 0;
+}
+}
+else if (len >= 16 && memcmp(s, "##fileformat=VCF", 16) == 0) {
+fmt->category = variant_data;
+fmt->format = vcf;
+if (len >= 21 && s[16] == 'v')
+parse_version(fmt, &s[17], &s[len]);
+else
+fmt->version.major = fmt->version.minor = -1;
+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;
+// @HD-VN is not guaranteed to be the first tag, but then @HD is
+// not guaranteed to be present at all...
+if (len >= 9 && memcmp(s, "@HD\tVN:", 7) == 0)
+parse_version(fmt, &s[7], &s[len]);
+else
+fmt->version.major = 1, fmt->version.minor = -1;
+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;
+fmt->version.major = 1, fmt->version.minor = -1;
+return 0;
+}
+fmt->category = unknown_category;
+fmt->format = unknown_format;
+fmt->version.major = fmt->version.minor = -1;
+fmt->compression = no_compression;
+return 0;
+}
+char *hts_format_description(const htsFormat *format)
+{
+kstring_t str = { 0, 0, NULL };
+switch (format->format) {
+case sam:   kputs("SAM", &str); break;
+case bam:   kputs("BAM", &str); break;
+case cram:  kputs("CRAM", &str); break;
+case vcf:   kputs("VCF", &str); break;
+case bcf:
+if (format->version.major == 1) kputs("Legacy BCF", &str);
+else kputs("BCF", &str);
+break;
+case bai:   kputs("BAI", &str); break;
+case crai:  kputs("CRAI", &str); break;
+case csi:   kputs("CSI", &str); break;
+case tbi:   kputs("Tabix", &str); break;
+default:    kputs("unknown", &str); break;
+}
+if (format->version.major >= 0) {
+kputs(" version ", &str);
+kputw(format->version.major, &str);
+if (format->version.minor >= 0) {
+kputc('.', &str);
+kputw(format->version.minor, &str);
+}
+}
+switch (format->compression) {
+case custom: kputs(" compressed", &str); break;
+case gzip:   kputs(" gzip-compressed", &str); break;
+case bgzf:
+switch (format->format) {
+case bam:
+case bcf:
+case csi:
+case tbi:
+// These are by definition BGZF, so just use the generic term
+kputs(" compressed", &str);
+break;
+default:
+kputs(" BGZF-compressed", &str);
+break;
+}
+break;
+default: break;
+}
+switch (format->category) {
+case sequence_data: kputs(" sequence", &str); break;
+case variant_data:  kputs(" variant calling", &str); break;
+case index_file:    kputs(" index", &str); break;
+case region_list:   kputs(" genomic region", &str); break;
+default: break;
+}
+if (format->compression == no_compression)
+switch (format->format) {
+case sam:
+case crai:
+case vcf:
+case bed:
+kputs(" text", &str);
+break;
+default:
+kputs(" data", &str);
+break;
+}
+else
+kputs(" data", &str);
+return ks_release(&str);
+}
+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);
+fmt->version.major = fmt->version.minor = -1;
+fmt->compression_level = -1;
+fmt->specific = NULL;
+}
+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;
+}
+// DEPRECATED: To be removed in a future HTSlib release
+int hts_file_type(const char *fname)
+{
+int len = strlen(fname);
+if ( !strcasecmp(".vcf.gz",fname+len-7) ) return FT_VCF_GZ;
+if ( !strcasecmp(".vcf",fname+len-4) ) return FT_VCF;
+if ( !strcasecmp(".bcf",fname+len-4) ) return FT_BCF_GZ;
+if ( !strcmp("-",fname) ) return FT_STDIN;
+hFILE *f = hopen(fname, "r");
+if (f == NULL) return 0;
+htsFormat fmt;
+if (hts_detect_format(f, &fmt) < 0) { hclose_abruptly(f); return 0; }
+if (hclose(f) < 0) return 0;
+switch (fmt.format) {
+case vcf: return (fmt.compression == no_compression)? FT_VCF : FT_VCF_GZ;
+case bcf: return (fmt.compression == no_compression)? FT_BCF : FT_BCF_GZ;
+default:  return 0;
+}
+}
+/****************
+*** 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, sizeof(hts_pair64_t));
+}
+if (l->n == l->m) {
+l->m <<= 1;
+l->list = (hts_pair64_t*)realloc(l->list, l->m * sizeof(hts_pair64_t));
+}
+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 * sizeof(uint64_t));
+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 * sizeof(hts_pair64_t));
+}
+memcpy(q->list + q->n, p->list, p->n * sizeof(hts_pair64_t));
+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<0) beg = -1, end = 0;
+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);
+if (idx->l_meta) bgzf_write(fp, idx->meta, idx->l_meta);
+hts_idx_save_core(idx, fp, HTS_FMT_CSI);
+bgzf_close(fp);
+} else if (fmt == HTS_FMT_TBI) {
+BGZF *fp;
+fp = bgzf_open(strcat(fnidx, ".tbi"), "w");
+bgzf_write(fp, "TBI\1", 4);
+hts_idx_save_core(idx, fp, HTS_FMT_TBI);
+bgzf_close(fp);
+} else if (fmt == HTS_FMT_BAI) {
+FILE *fp;
+fp = fopen(strcat(fnidx, ".bai"), "w");
+fwrite("BAI\1", 1, 4, fp);
+hts_idx_save_core(idx, fp, HTS_FMT_BAI);
+fclose(fp);
+} else abort();
+free(fnidx);
+}
+static int hts_idx_load_core(hts_idx_t *idx, void *fp, int fmt)
+{
+int32_t i, n, is_be;
+int is_bgzf = (fmt != HTS_FMT_BAI);
+is_be = ed_is_big();
+if (idx == NULL) return -4;
+for (i = 0; i < idx->n; ++i) {
+bidx_t *h;
+lidx_t *l = &idx->lidx[i];
+uint32_t key;
+int j, absent;
+bins_t *p;
+h = idx->bidx[i] = kh_init(bin);
+if (idx_read(is_bgzf, fp, &n, 4) != 4) return -1;
+if (is_be) ed_swap_4p(&n);
+for (j = 0; j < n; ++j) {
+khint_t k;
+if (idx_read(is_bgzf, fp, &key, 4) != 4) return -1;
+if (is_be) ed_swap_4p(&key);
+k = kh_put(bin, h, key, &absent);
+if (absent <= 0) return -3; // Duplicate bin number
+p = &kh_val(h, k);
+if (fmt == HTS_FMT_CSI) {
+if (idx_read(is_bgzf, fp, &p->loff, 8) != 8) return -1;
+if (is_be) ed_swap_8p(&p->loff);
+} else p->loff = 0;
+if (idx_read(is_bgzf, fp, &p->n, 4) != 4) return -1;
+if (is_be) ed_swap_4p(&p->n);
+p->m = p->n;
+p->list = (hts_pair64_t*)malloc(p->m * sizeof(hts_pair64_t));
+if (p->list == NULL) return -2;
+if (idx_read(is_bgzf, fp, p->list, p->n<<4) != p->n<<4) return -1;
+if (is_be) swap_bins(p);
+}
+if (fmt != HTS_FMT_CSI) { // load linear index
+int j;
+if (idx_read(is_bgzf, fp, &l->n, 4) != 4) return -1;
+if (is_be) ed_swap_4p(&l->n);
+l->m = l->n;
+l->offset = (uint64_t*)malloc(l->n * sizeof(uint64_t));
+if (l->offset == NULL) return -2;
+if (idx_read(is_bgzf, fp, l->offset, l->n << 3) != l->n << 3) return -1;
+if (is_be) for (j = 0; j < l->n; ++j) ed_swap_8p(&l->offset[j]);
+for (j = 1; j < l->n; ++j) // fill missing values; may happen given older samtools and tabix
+if (l->offset[j] == 0) l->offset[j] = l->offset[j-1];
+update_loff(idx, i, 1);
+}
+}
+if (idx_read(is_bgzf, fp, &idx->n_no_coor, 8) != 8) idx->n_no_coor = 0;
+if (is_be) ed_swap_8p(&idx->n_no_coor);
+return 0;
+}
+hts_idx_t *hts_idx_load_local(const char *fn, int fmt)
+{
+uint8_t magic[4];
+int i, is_be;
+hts_idx_t *idx = NULL;
+is_be = ed_is_big();
+if (fmt == HTS_FMT_CSI) {
+BGZF *fp;
+uint32_t x[3], n;
+uint8_t *meta = 0;
+if ((fp = bgzf_open(fn, "r")) == 0) return NULL;
+if (bgzf_read(fp, magic, 4) != 4) goto csi_fail;
+if (memcmp(magic, "CSI\1", 4) != 0) goto csi_fail;
+if (bgzf_read(fp, x, 12) != 12) goto csi_fail;
+if (is_be) for (i = 0; i < 3; ++i) ed_swap_4p(&x[i]);
+if (x[2]) {
+if ((meta = (uint8_t*)malloc(x[2])) == NULL) goto csi_fail;
+if (bgzf_read(fp, meta, x[2]) != x[2]) goto csi_fail;
+}
+if (bgzf_read(fp, &n, 4) != 4) goto csi_fail;
+if (is_be) ed_swap_4p(&n);
+if ((idx = hts_idx_init(n, fmt, 0, x[0], x[1])) == NULL) goto csi_fail;
+idx->l_meta = x[2];
+idx->meta = meta;
+meta = NULL;
+if (hts_idx_load_core(idx, fp, HTS_FMT_CSI) < 0) goto csi_fail;
+bgzf_close(fp);
+return idx;
+csi_fail:
+bgzf_close(fp);
+hts_idx_destroy(idx);
+free(meta);
+return NULL;
+} else if (fmt == HTS_FMT_TBI) {
+BGZF *fp;
+uint32_t x[8];
+if ((fp = bgzf_open(fn, "r")) == 0) return NULL;
+if (bgzf_read(fp, magic, 4) != 4) goto tbi_fail;
+if (memcmp(magic, "TBI\1", 4) != 0) goto tbi_fail;
+if (bgzf_read(fp, x, 32) != 32) goto tbi_fail;
+if (is_be) for (i = 0; i < 8; ++i) ed_swap_4p(&x[i]);
+if ((idx = hts_idx_init(x[0], fmt, 0, 14, 5)) == NULL) goto tbi_fail;
+idx->l_meta = 28 + x[7];
+if ((idx->meta = (uint8_t*)malloc(idx->l_meta)) == NULL) goto tbi_fail;
+memcpy(idx->meta, &x[1], 28);
+if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto tbi_fail;
+if (hts_idx_load_core(idx, fp, HTS_FMT_TBI) < 0) goto tbi_fail;
+bgzf_close(fp);
+return idx;
+tbi_fail:
+bgzf_close(fp);
+hts_idx_destroy(idx);
+return NULL;
+} else if (fmt == HTS_FMT_BAI) {
+uint32_t n;
+FILE *fp;
+if ((fp = fopen(fn, "rb")) == 0) return NULL;
+if (fread(magic, 1, 4, fp) != 4) goto bai_fail;
+if (memcmp(magic, "BAI\1", 4) != 0) goto bai_fail;
+if (fread(&n, 4, 1, fp) != 1) goto bai_fail;
+if (is_be) ed_swap_4p(&n);
+idx = hts_idx_init(n, fmt, 0, 14, 5);
+if (hts_idx_load_core(idx, fp, HTS_FMT_BAI) < 0) goto bai_fail;
+fclose(fp);
+return idx;
+bai_fail:
+fclose(fp);
+hts_idx_destroy(idx);
+return NULL;
+} else abort();
+}
+void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy)
+{
+if (idx->meta) free(idx->meta);
+idx->l_meta = l_meta;
+if (is_copy) {
+idx->meta = (uint8_t*)malloc(l_meta);
+memcpy(idx->meta, meta, l_meta);
+} else idx->meta = meta;
+}
+uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta)
+{
+*l_meta = idx->l_meta;
+return idx->meta;
+}
+const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr)
+{
+if ( !idx->n )
+{
+*n = 0;
+return NULL;
+}
+int tid = 0, i;
+const char **names = (const char**) calloc(idx->n,sizeof(const char*));
+for (i=0; i<idx->n; i++)
+{
+bidx_t *bidx = idx->bidx[i];
+if ( !bidx ) continue;
+names[tid++] = getid(hdr,i);
+}
+*n = tid;
+return names;
+}
+int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped)
+{
+if ( idx->fmt == HTS_FMT_CRAI ) {
+*mapped = 0; *unmapped = 0;
+return -1;
+}
+bidx_t *h = idx->bidx[tid];
+khint_t k = kh_get(bin, h, META_BIN(idx));
+if (k != kh_end(h)) {
+*mapped = kh_val(h, k).list[1].u;
+*unmapped = kh_val(h, k).list[1].v;
+return 0;
+} else {
+*mapped = 0; *unmapped = 0;
+return -1;
+}
+}
+uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx)
+{
+return idx->n_no_coor;
+}
+/****************
+*** Iterator ***
+****************/
+static inline int reg2bins(int64_t beg, int64_t end, hts_itr_t *itr, int min_shift, int n_lvls)
+{
+int l, t, s = min_shift + (n_lvls<<1) + n_lvls;
+if (beg >= end) return 0;
+if (end >= 1LL<<s) end = 1LL<<s;
+for (--end, l = 0, t = 0; l <= n_lvls; s -= 3, t += 1<<((l<<1)+l), ++l) {
+int b, e, n, i;
+b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
+if (itr->bins.n + n > itr->bins.m) {
+itr->bins.m = itr->bins.n + n;
+kroundup32(itr->bins.m);
+itr->bins.a = (int*)realloc(itr->bins.a, sizeof(int) * itr->bins.m);
+}
+for (i = b; i <= e; ++i) itr->bins.a[itr->bins.n++] = i;
+}
+return itr->bins.n;
+}
+hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
+{
+int i, n_off, l, bin;
+hts_pair64_t *off;
+khint_t k;
+bidx_t *bidx;
+uint64_t min_off;
+hts_itr_t *iter = 0;
+if (tid < 0) {
+int finished0 = 0;
+uint64_t off0 = (uint64_t)-1;
+khint_t k;
+switch (tid) {
+case HTS_IDX_START:
+// Find the smallest offset, note that sequence ids may not be ordered sequentially
+for (i=0; i<idx->n; i++)
+{
+bidx = idx->bidx[i];
+k = kh_get(bin, bidx, META_BIN(idx));
+if (k == kh_end(bidx)) continue;
+if ( off0 > kh_val(bidx, k).list[0].u ) off0 = kh_val(bidx, k).list[0].u;
+}
+if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam
+break;
+case HTS_IDX_NOCOOR:
+if ( idx->n>0 )
+{
+bidx = idx->bidx[idx->n - 1];
+k = kh_get(bin, bidx, META_BIN(idx));
+if (k != kh_end(bidx)) off0 = kh_val(bidx, k).list[0].v;
+}
+if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam
+break;
+case HTS_IDX_REST:
+off0 = 0;
+break;
+case HTS_IDX_NONE:
+finished0 = 1;
+off0 = 0;
+break;
+default:
+return 0;
+}
+if (off0 != (uint64_t)-1) {
+iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t));
+iter->read_rest = 1;
+iter->finished = finished0;
+iter->curr_off = off0;
+iter->readrec = readrec;
+return iter;
+} else return 0;
+}
+if (beg < 0) beg = 0;
+if (end < beg) return 0;
+if (tid >= idx->n || (bidx = idx->bidx[tid]) == NULL) return 0;
+iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t));
+iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+iter->readrec = readrec;
+// compute min_off
+bin = hts_bin_first(idx->n_lvls) + (beg>>idx->min_shift);
+do {
+int first;
+k = kh_get(bin, bidx, bin);
+if (k != kh_end(bidx)) break;
+first = (hts_bin_parent(bin)<<3) + 1;
+if (bin > first) --bin;
+else bin = hts_bin_parent(bin);
+} while (bin);
+if (bin == 0) k = kh_get(bin, bidx, bin);
+min_off = k != kh_end(bidx)? kh_val(bidx, k).loff : 0;
+// retrieve bins
+reg2bins(beg, end, iter, idx->min_shift, idx->n_lvls);
+for (i = n_off = 0; i < iter->bins.n; ++i)
+if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx))
+n_off += kh_value(bidx, k).n;
+if (n_off == 0) return iter;
+off = (hts_pair64_t*)calloc(n_off, sizeof(hts_pair64_t));
+for (i = n_off = 0; i < iter->bins.n; ++i) {
+if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) {
+int j;
+bins_t *p = &kh_value(bidx, k);
+for (j = 0; j < p->n; ++j)
+if (p->list[j].v > min_off) off[n_off++] = p->list[j];
+}
+}
+if (n_off == 0) {
+free(off); return iter;
+}
+ks_introsort(_off, n_off, off);
+// resolve completely contained adjacent blocks
+for (i = 1, l = 0; i < n_off; ++i)
+if (off[l].v < off[i].v) off[++l] = off[i];
+n_off = l + 1;
+// resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
+for (i = 1; i < n_off; ++i)
+if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
+// merge adjacent blocks
+for (i = 1, l = 0; i < n_off; ++i) {
+if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+else off[++l] = off[i];
+}
+n_off = l + 1;
+iter->n_off = n_off; iter->off = off;
+return iter;
+}
+void hts_itr_destroy(hts_itr_t *iter)
+{
+if (iter) { free(iter->off); free(iter->bins.a); free(iter); }
+}
+const char *hts_parse_reg(const char *s, int *beg, int *end)
+{
+int i, k, l, name_end;
+*beg = *end = -1;
+name_end = l = strlen(s);
+// determine the sequence name
+for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+if (i >= 0) name_end = i;
+if (name_end < l) { // check if this is really the end
+int n_hyphen = 0;
+for (i = name_end + 1; i < l; ++i) {
+if (s[i] == '-') ++n_hyphen;
+else if (!isdigit(s[i]) && s[i] != ',') break;
+}
+if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+}
+// parse the interval
+if (name_end < l) {
+char *tmp;
+tmp = (char*)alloca(l - name_end + 1);
+for (i = name_end + 1, k = 0; i < l; ++i)
+if (s[i] != ',') tmp[k++] = s[i];
+tmp[k] = 0;
+if ((*beg = strtol(tmp, &tmp, 10) - 1) < 0) *beg = 0;
+*end = *tmp? strtol(tmp + 1, &tmp, 10) : INT_MAX;
+if (*beg > *end) name_end = l;
+}
+if (name_end == l) *beg = 0, *end = INT_MAX;
+return s + name_end;
+}
+hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec)
+{
+int tid, beg, end;
+char *q, *tmp;
+if (strcmp(reg, ".") == 0)
+return itr_query(idx, HTS_IDX_START, 0, 0, readrec);
+else if (strcmp(reg, "*") != 0) {
+q = (char*)hts_parse_reg(reg, &beg, &end);
+tmp = (char*)alloca(q - reg + 1);
+strncpy(tmp, reg, q - reg);
+tmp[q - reg] = 0;
+if ((tid = getid(hdr, tmp)) < 0)
+tid = getid(hdr, reg);
+if (tid < 0) return 0;
+return itr_query(idx, tid, beg, end, readrec);
+} else return itr_query(idx, HTS_IDX_NOCOOR, 0, 0, readrec);
+}
+int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data)
+{
+int ret, tid, beg, end;
+if (iter == NULL || iter->finished) return -1;
+if (iter->read_rest) {
+if (iter->curr_off) { // seek to the start
+bgzf_seek(fp, iter->curr_off, SEEK_SET);
+iter->curr_off = 0; // only seek once
+}
+ret = iter->readrec(fp, data, r, &tid, &beg, &end);
+if (ret < 0) iter->finished = 1;
+iter->curr_tid = tid;
+iter->curr_beg = beg;
+iter->curr_end = end;
+return ret;
+}
+if (iter->off == 0) return -1;
+for (;;) {
+if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks
+if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+iter->curr_off = bgzf_tell(fp);
+}
+++iter->i;
+}
+if ((ret = iter->readrec(fp, data, r, &tid, &beg, &end)) >= 0) {
+iter->curr_off = bgzf_tell(fp);
+if (tid != iter->tid || beg >= iter->end) { // no need to proceed
+ret = -1; break;
+} else if (end > iter->beg && iter->end > beg) {
+iter->curr_tid = tid;
+iter->curr_beg = beg;
+iter->curr_end = end;
+return ret;
+}
+} else break; // end of file or error
+}
+iter->finished = 1;
+return ret;
+}
+/**********************
+*** Retrieve index ***
+**********************/
+static char *test_and_fetch(const char *fn)
+{
+FILE *fp;
+if (hisremote(fn)) {
+const int buf_size = 1 * 1024 * 1024;
+hFILE *fp_remote;
+uint8_t *buf;
+int l;
+const char *p;
+for (p = fn + strlen(fn) - 1; p >= fn; --p)
+if (*p == '/') break;
+++p; // p now points to the local file name
+// Attempt to open local file first
+if ((fp = fopen((char*)p, "rb")) != 0)
+{
+fclose(fp);
+return (char*)p;
+}
+// Attempt to open remote file. Stay quiet on failure, it is OK to fail when trying first .csi then .tbi index.
+if ((fp_remote = hopen(fn, "r")) == 0) return 0;
+if ((fp = fopen(p, "w")) == 0) {
+if (hts_verbose >= 1) fprintf(stderr, "[E::%s] fail to create file '%s' in the working directory\n", __func__, p);
+hclose_abruptly(fp_remote);
+return 0;
+}
+if (hts_verbose >= 3) fprintf(stderr, "[M::%s] downloading file '%s' to local directory\n", __func__, fn);
+buf = (uint8_t*)calloc(buf_size, 1);
+while ((l = hread(fp_remote, buf, buf_size)) > 0) fwrite(buf, 1, l, fp);
+free(buf);
+fclose(fp);
+if (hclose(fp_remote) != 0) fprintf(stderr, "[E::%s] fail to close remote file '%s'\n", __func__, fn);
+return (char*)p;
+} else {
+if ((fp = fopen(fn, "rb")) == 0) return 0;
+fclose(fp);
+return (char*)fn;
+}
+}
+char *hts_idx_getfn(const char *fn, const char *ext)
+{
+int i, l_fn, l_ext;
+char *fnidx, *ret;
+l_fn = strlen(fn); l_ext = strlen(ext);
+fnidx = (char*)calloc(l_fn + l_ext + 1, 1);
+strcpy(fnidx, fn); strcpy(fnidx + l_fn, ext);
+if ((ret = test_and_fetch(fnidx)) == 0) {
+for (i = l_fn - 1; i > 0; --i)
+if (fnidx[i] == '.') break;
+strcpy(fnidx + i, ext);
+ret = test_and_fetch(fnidx);
+}
+if (ret == 0) {
+free(fnidx);
+return 0;
+}
+l_fn = strlen(ret);
+memmove(fnidx, ret, l_fn + 1);
+return fnidx;
+}
+hts_idx_t *hts_idx_load(const char *fn, int fmt)
+{
+char *fnidx;
+hts_idx_t *idx;
+fnidx = hts_idx_getfn(fn, ".csi");
+if (fnidx) fmt = HTS_FMT_CSI;
+else fnidx = hts_idx_getfn(fn, fmt == HTS_FMT_BAI? ".bai" : ".tbi");
+if (fnidx == 0) return 0;
+// Check that the index file is up to date, the main file might have changed
+struct stat stat_idx,stat_main;
+if ( !stat(fn, &stat_main) && !stat(fnidx, &stat_idx) )
+{
+if ( stat_idx.st_mtime < stat_main.st_mtime )
+fprintf(stderr, "Warning: The index file is older than the data file: %s\n", fnidx);
+}
+idx = hts_idx_load_local(fnidx, fmt);
+free(fnidx);
+return idx;
+}

Mercurial > repos > youngkim > ezbamqc

comparison ezBAMQC/src/htslib/hts.c @ 0:dfa3745e5fd8