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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, 2012-2021 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. */
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>
#include <zlib.h>
#include <stdio.h>
#include <string.h>
#include <strings.h>
#include <stdlib.h>
#include <unistd.h>
#include <inttypes.h>
#include <limits.h>
#include <stdint.h>
#include <fcntl.h>
#include <errno.h>
#include <time.h>
#include <sys/stat.h>
#include <assert.h>
#include "htslib/hts.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "htslib/hts_endian.h"
#include "version.h"
#include "config_vars.h"
#include "hts_internal.h"
#include "hfile_internal.h"
#include "sam_internal.h"
#include "htslib/hts_expr.h"
#include "htslib/hts_os.h" // drand48
#include "htslib/khash.h"
#include "htslib/kseq.h"
#include "htslib/ksort.h"
#include "htslib/tbx.h"
#if defined(HAVE_EXTERNAL_LIBHTSCODECS)
#include <htscodecs/htscodecs.h>
#else
#include "htscodecs/htscodecs/htscodecs.h"
#endif
#ifndef EFTYPE
#define EFTYPE ENOEXEC
#endif
KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal)
HTSLIB_EXPORT
int hts_verbose = HTS_LOG_WARNING;
const char *hts_version()
{
return HTS_VERSION_TEXT;
}
unsigned int hts_features(void) {
unsigned int feat = HTS_FEATURE_HTSCODECS; // Always present
#ifdef PACKAGE_URL
feat |= HTS_FEATURE_CONFIGURE;
#endif
#ifdef ENABLE_PLUGINS
feat |= HTS_FEATURE_PLUGINS;
#endif
#ifdef HAVE_LIBCURL
feat |= HTS_FEATURE_LIBCURL;
#endif
#ifdef ENABLE_S3
feat |= HTS_FEATURE_S3;
#endif
#ifdef ENABLE_GCS
feat |= HTS_FEATURE_GCS;
#endif
#ifdef HAVE_LIBDEFLATE
feat |= HTS_FEATURE_LIBDEFLATE;
#endif
#ifdef HAVE_LIBLZMA
feat |= HTS_FEATURE_LZMA;
#endif
#ifdef HAVE_LIBBZ2
feat |= HTS_FEATURE_BZIP2;
#endif
return feat;
}
const char *hts_test_feature(unsigned int id) {
unsigned int feat = hts_features();
switch (id) {
case HTS_FEATURE_CONFIGURE:
return feat & HTS_FEATURE_CONFIGURE ? "yes" : NULL;
case HTS_FEATURE_PLUGINS:
return feat & HTS_FEATURE_PLUGINS ? "yes" : NULL;
case HTS_FEATURE_LIBCURL:
return feat & HTS_FEATURE_LIBCURL ? "yes" : NULL;
case HTS_FEATURE_S3:
return feat & HTS_FEATURE_S3 ? "yes" : NULL;
case HTS_FEATURE_GCS:
return feat & HTS_FEATURE_GCS ? "yes" : NULL;
case HTS_FEATURE_LIBDEFLATE:
return feat & HTS_FEATURE_LIBDEFLATE ? "yes" : NULL;
case HTS_FEATURE_BZIP2:
return feat & HTS_FEATURE_BZIP2 ? "yes" : NULL;
case HTS_FEATURE_LZMA:
return feat & HTS_FEATURE_LZMA ? "yes" : NULL;
case HTS_FEATURE_HTSCODECS:
return htscodecs_version();
case HTS_FEATURE_CC:
return HTS_CC;
case HTS_FEATURE_CFLAGS:
return HTS_CFLAGS;
case HTS_FEATURE_LDFLAGS:
return HTS_LDFLAGS;
case HTS_FEATURE_CPPFLAGS:
return HTS_CPPFLAGS;
default:
fprintf(stderr, "Unknown feature code: %u\n", id);
}
return NULL;
}
// Note this implementation also means we can just "strings" the library
// to find the configuration parameters.
const char *hts_feature_string(void) {
static char config[1200];
const char *fmt=
#ifdef PACKAGE_URL
"build=configure "
#else
"build=Makefile "
#endif
#ifdef ENABLE_PLUGINS
"plugins=yes, plugin-path=%.1000s "
#else
"plugins=no "
#endif
#ifdef HAVE_LIBCURL
"libcurl=yes "
#else
"libcurl=no "
#endif
#ifdef ENABLE_S3
"S3=yes "
#else
"S3=no "
#endif
#ifdef ENABLE_GCS
"GCS=yes "
#else
"GCS=no "
#endif
#ifdef HAVE_LIBDEFLATE
"libdeflate=yes "
#else
"libdeflate=no "
#endif
#ifdef HAVE_LIBLZMA
"lzma=yes "
#else
"lzma=no "
#endif
#ifdef HAVE_LIBBZ2
"bzip2=yes "
#else
"bzip2=no "
#endif
"htscodecs=%.40s";
#ifdef ENABLE_PLUGINS
snprintf(config, sizeof(config), fmt,
hts_plugin_path(), htscodecs_version());
#else
snprintf(config, sizeof(config), fmt, htscodecs_version());
#endif
return config;
}
HTSLIB_EXPORT
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
};
HTSLIB_EXPORT
const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN";
HTSLIB_EXPORT
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:
case fastq_format:
case fasta_format:
return sequence_data;
case vcf:
case bcf:
return variant_data;
case bai:
case crai:
case csi:
case fai_format:
case fqi_format:
case gzi:
case tbi:
return index_file;
case bed:
return region_list;
case htsget:
case hts_crypt4gh_format:
return unknown_category;
case unknown_format:
case binary_format:
case text_format:
case empty_format:
case format_maximum:
break;
}
return unknown_category;
}
// Decompress several hundred 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)
{
unsigned char buffer[2048];
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 *s = (const char *) u;
const char *slim = (const char *) ulim;
short v;
fmt->version.major = fmt->version.minor = -1;
for (v = 0; s < slim && isdigit_c(*s); s++)
v = 10 * v + *s - '0';
if (s < slim) {
fmt->version.major = v;
if (*s == '.') {
s++;
for (v = 0; s < slim && isdigit_c(*s); s++)
v = 10 * v + *s - '0';
if (s < slim)
fmt->version.minor = v;
}
else
fmt->version.minor = 0;
}
}
static int
cmp_nonblank(const char *key, const unsigned char *u, const unsigned char *ulim)
{
const unsigned char *ukey = (const unsigned char *) key;
while (*ukey)
if (u >= ulim) return +1;
else if (isspace_c(*u)) u++;
else if (*u != *ukey) return (*ukey < *u)? -1 : +1;
else u++, ukey++;
return 0;
}
static int is_text_only(const unsigned char *u, const unsigned char *ulim)
{
for (; u < ulim; u++)
if (! (*u >= ' ' || *u == '\t' || *u == '\r' || *u == '\n'))
return 0;
return 1;
}
static int
secondline_is_bases(const unsigned char *u, const unsigned char *ulim)
{
// Skip to second line, returning false if there isn't one
u = memchr(u, '\n', ulim - u);
if (u == NULL || ++u == ulim) return 0;
// Scan over all base-encoding letters (including 'N' but not SEQ's '=')
while (u < ulim && (seq_nt16_table[*u] != 15 || toupper(*u) == 'N')) {
if (*u == '=') return 0;
u++;
}
return (u == ulim || *u == '\r' || *u == '\n')? 1 : 0;
}
// Parse tab-delimited text, filling in a string of column types and returning
// the number of columns spotted (within [u,ulim), and up to column_len) or -1
// if non-printable characters were seen. Column types:
// i: integer, s: strand sign, C: CIGAR, O: SAM optional field, Z: anything
static int
parse_tabbed_text(char *columns, int column_len,
const unsigned char *u, const unsigned char *ulim,
int *complete)
{
const char *str = (const char *) u;
const char *slim = (const char *) ulim;
const char *s;
int ncolumns = 0;
enum { digit = 1, leading_sign = 2, cigar_operator = 4, other = 8 };
unsigned seen = 0;
*complete = 0;
for (s = str; s < slim; s++)
if (*s >= ' ') {
if (isdigit_c(*s))
seen |= digit;
else if ((*s == '+' || *s == '-') && s == str)
seen |= leading_sign;
else if (strchr(BAM_CIGAR_STR, *s) && s > str && isdigit_c(s[-1]))
seen |= cigar_operator;
else
seen |= other;
}
else if (*s == '\t' || *s == '\r' || *s == '\n') {
size_t len = s - str;
char type;
if (seen == digit || seen == (leading_sign|digit)) type = 'i';
else if (seen == (digit|cigar_operator)) type = 'C';
else if (len == 1)
switch (str[0]) {
case '*': type = 'C'; break;
case '+': case '-': case '.': type = 's'; break;
default: type = 'Z'; break;
}
else if (len >= 5 && str[2] == ':' && str[4] == ':') type = 'O';
else type = 'Z';
columns[ncolumns++] = type;
if (*s != '\t' || ncolumns >= column_len - 1) {
*complete = 1; // finished the line or more columns than needed
break;
}
str = s + 1;
seen = 0;
}
else return -1;
columns[ncolumns] = '\0';
return ncolumns;
}
// Match COLUMNS as a prefix against PATTERN (so COLUMNS may run out first).
// Returns len(COLUMNS) (modulo '+'), or 0 if there is a mismatched entry.
static int colmatch(const char *columns, const char *pattern)
{
int i;
for (i = 0; columns[i] != '\0'; i++) {
if (pattern[i] == '+') return i;
if (! (columns[i] == pattern[i] || pattern[i] == 'Z')) return 0;
}
return i;
}
int hts_detect_format(hFILE *hfile, htsFormat *fmt)
{
char columns[24];
unsigned char s[1024];
int complete = 0;
ssize_t len = hpeek(hfile, s, 18);
if (len < 0) return -1;
fmt->category = unknown_category;
fmt->format = unknown_format;
fmt->version.major = fmt->version.minor = -1;
fmt->compression = no_compression;
fmt->compression_level = -1;
fmt->specific = NULL;
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 records or lines.
fmt->compression = gzip;
if (len >= 18 && (s[3] & 4)) {
if (memcmp(&s[12], "BC\2\0", 4) == 0)
fmt->compression = bgzf;
else if (memcmp(&s[12], "RAZF", 4) == 0)
fmt->compression = razf_compression;
}
if (len >= 9 && s[2] == 8)
fmt->compression_level = (s[8] == 2)? 9 : (s[8] == 4)? 1 : -1;
len = decompress_peek(hfile, s, sizeof s);
}
else if (len >= 10 && memcmp(s, "BZh", 3) == 0 &&
(memcmp(&s[4], "\x31\x41\x59\x26\x53\x59", 6) == 0 ||
memcmp(&s[4], "\x17\x72\x45\x38\x50\x90", 6) == 0)) {
fmt->compression = bzip2_compression;
fmt->compression_level = s[3] - '0';
// Decompressing via libbz2 produces no output until it has a whole
// block (of size 100Kb x level), which is too large for peeking.
// So unfortunately we can recognise bzip2 but not the contents,
// except that \x1772... magic indicates the stream is empty.
if (s[4] == '\x31') return 0;
else len = 0;
}
else {
len = hpeek(hfile, s, sizeof s);
}
if (len < 0) return -1;
if (len == 0) {
fmt->format = empty_format;
return 0;
}
if (len >= 6 && memcmp(s,"CRAM",4) == 0 && s[4]>=1 && s[4]<=7 && s[5]<=7) {
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;
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]);
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 ||
memcmp(s, "@CO\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 if (cmp_nonblank("{\"htsget\":", s, &s[len]) == 0) {
fmt->category = unknown_category;
fmt->format = htsget;
return 0;
}
else if (len > 8 && memcmp(s, "crypt4gh", 8) == 0) {
fmt->category = unknown_category;
fmt->format = hts_crypt4gh_format;
return 0;
}
else if (len >= 1 && s[0] == '>' && secondline_is_bases(s, &s[len])) {
fmt->category = sequence_data;
fmt->format = fasta_format;
return 0;
}
else if (len >= 1 && s[0] == '@' && secondline_is_bases(s, &s[len])) {
fmt->category = sequence_data;
fmt->format = fastq_format;
return 0;
}
else if (parse_tabbed_text(columns, sizeof columns, s,
&s[len], &complete) > 0) {
// A complete SAM line is at least 11 columns. On unmapped long reads may
// be missing two. (On mapped long reads we must have an @ header so long
// CIGAR is irrelevant.)
if (colmatch(columns, "ZiZiiCZiiZZOOOOOOOOOOOOOOOOOOOO+")
>= 9 + 2*complete) {
fmt->category = sequence_data;
fmt->format = sam;
fmt->version.major = 1, fmt->version.minor = -1;
return 0;
}
else if (fmt->compression == gzip && colmatch(columns, "iiiiii") == 6) {
fmt->category = index_file;
fmt->format = crai;
return 0;
}
else if (colmatch(columns, "Ziiiii") == 6) {
fmt->category = index_file;
fmt->format = fqi_format;
return 0;
}
else if (colmatch(columns, "Ziiii") == 5) {
fmt->category = index_file;
fmt->format = fai_format;
return 0;
}
else if (colmatch(columns, "Zii+") >= 3) {
fmt->category = region_list;
fmt->format = bed;
return 0;
}
}
// Arbitrary text files can be read using hts_getline().
if (is_text_only(s, &s[len])) fmt->format = text_format;
// Nothing recognised: leave unset fmt-> fields as unknown.
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 fasta_format: kputs("FASTA", &str); break;
case fastq_format: kputs("FASTQ", &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 fai_format: kputs("FASTA-IDX", &str); break;
case fqi_format: kputs("FASTQ-IDX", &str); break;
case gzi: kputs("GZI", &str); break;
case tbi: kputs("Tabix", &str); break;
case bed: kputs("BED", &str); break;
case htsget: kputs("htsget", &str); break;
case hts_crypt4gh_format: kputs("crypt4gh", &str); break;
case empty_format: kputs("empty", &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 bzip2_compression: kputs(" bzip2-compressed", &str); break;
case razf_compression: kputs(" legacy-RAZF-compressed", &str); break;
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 text_format:
case sam:
case crai:
case vcf:
case bed:
case fai_format:
case fqi_format:
case fasta_format:
case fastq_format:
case htsget:
kputs(" text", &str);
break;
case empty_format:
break;
default:
kputs(" data", &str);
break;
}
else
kputs(" data", &str);
return ks_release(&str);
}
htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
{
char smode[101], *cp, *cp2, *mode_c;
htsFile *fp = NULL;
hFILE *hfile = NULL;
char fmt_code = '\0';
// see enum htsExactFormat in htslib/hts.h
const char format_to_mode[] = "\0g\0\0b\0c\0\0b\0g\0\0\0\0\0Ff\0\0";
strncpy(smode, mode, 99);
smode[99]=0;
if ((cp = strchr(smode, ',')))
*cp = '\0';
// Migrate format code (b or c) to the end of the smode buffer.
for (cp2 = cp = smode; *cp; cp++) {
if (*cp == 'b')
fmt_code = 'b';
else if (*cp == 'c')
fmt_code = 'c';
else
*cp2++ = *cp;
}
mode_c = cp2;
*cp2++ = fmt_code;
*cp2++ = 0;
// Set or reset the format code if opts->format is used
if (fmt && fmt->format > unknown_format
&& fmt->format < sizeof(format_to_mode)) {
*mode_c = format_to_mode[fmt->format];
}
// If we really asked for a compressed text format then mode_c above will
// point to nul. We set to 'z' to enable bgzf.
if (strchr(mode, 'w') && fmt && fmt->compression == bgzf) {
if (fmt->format == sam || fmt->format == vcf || fmt->format == text_format)
*mode_c = 'z';
}
char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM);
if ( fnidx ) {
rmme = strdup(fn);
if ( !rmme ) goto error;
rmme[fnidx-fn] = 0;
fn = rmme;
}
hfile = hopen(fn, smode);
if (hfile == NULL) goto error;
fp = hts_hopen(hfile, fn, smode);
if (fp == NULL) goto error;
// Compensate for the loss of exactness in htsExactFormat.
// hts_hopen returns generics such as binary or text, but we
// have been given something explicit here so use that instead.
if (fp->is_write && fmt &&
(fmt->format == bam || fmt->format == sam ||
fmt->format == vcf || fmt->format == bcf ||
fmt->format == bed || fmt->format == fasta_format ||
fmt->format == fastq_format))
fp->format.format = fmt->format;
if (fmt && fmt->specific)
if (hts_opt_apply(fp, fmt->specific) != 0)
goto error;
if ( rmme ) free(rmme);
return fp;
error:
hts_log_error("Failed to open file \"%s\"%s%s", fn,
errno ? " : " : "", errno ? strerror(errno) : "");
if ( rmme ) free(rmme);
if (hfile)
hclose_abruptly(hfile);
return NULL;
}
htsFile *hts_open(const char *fn, const char *mode) {
return hts_open_format(fn, mode, NULL);
}
/*
* Splits str into a prefix, delimiter ('\0' or delim), and suffix, writing
* the prefix in lowercase into buf and returning a pointer to the suffix.
* On return, buf is always NUL-terminated; thus assumes that the "keyword"
* prefix should be one of several known values of maximum length buflen-2.
* (If delim is not found, returns a pointer to the '\0'.)
*/
static const char *
scan_keyword(const char *str, char delim, char *buf, size_t buflen)
{
size_t i = 0;
while (*str && *str != delim) {
if (i < buflen-1) buf[i++] = tolower_c(*str);
str++;
}
buf[i] = '\0';
return *str? str+1 : str;
}
/*
* Parses arg and appends it to the option list.
*
* Returns 0 on success;
* -1 on failure.
*/
int hts_opt_add(hts_opt **opts, const char *c_arg) {
hts_opt *o, *t;
char *val;
/*
* IMPORTANT!!!
* If you add another string option here, don't forget to also add
* it to the case statement in hts_opt_apply.
*/
if (!c_arg)
return -1;
if (!(o = malloc(sizeof(*o))))
return -1;
if (!(o->arg = strdup(c_arg))) {
free(o);
return -1;
}
if (!(val = strchr(o->arg, '=')))
val = "1"; // assume boolean
else
*val++ = '\0';
if (strcmp(o->arg, "decode_md") == 0 ||
strcmp(o->arg, "DECODE_MD") == 0)
o->opt = CRAM_OPT_DECODE_MD, o->val.i = atoi(val);
else if (strcmp(o->arg, "verbosity") == 0 ||
strcmp(o->arg, "VERBOSITY") == 0)
o->opt = CRAM_OPT_VERBOSITY, o->val.i = atoi(val);
else if (strcmp(o->arg, "seqs_per_slice") == 0 ||
strcmp(o->arg, "SEQS_PER_SLICE") == 0)
o->opt = CRAM_OPT_SEQS_PER_SLICE, o->val.i = atoi(val);
else if (strcmp(o->arg, "bases_per_slice") == 0 ||
strcmp(o->arg, "BASES_PER_SLICE") == 0)
o->opt = CRAM_OPT_BASES_PER_SLICE, o->val.i = atoi(val);
else if (strcmp(o->arg, "slices_per_container") == 0 ||
strcmp(o->arg, "SLICES_PER_CONTAINER") == 0)
o->opt = CRAM_OPT_SLICES_PER_CONTAINER, o->val.i = atoi(val);
else if (strcmp(o->arg, "embed_ref") == 0 ||
strcmp(o->arg, "EMBED_REF") == 0)
o->opt = CRAM_OPT_EMBED_REF, o->val.i = atoi(val);
else if (strcmp(o->arg, "no_ref") == 0 ||
strcmp(o->arg, "NO_REF") == 0)
o->opt = CRAM_OPT_NO_REF, o->val.i = atoi(val);
else if (strcmp(o->arg, "pos_delta") == 0 ||
strcmp(o->arg, "POS_DELTA") == 0)
o->opt = CRAM_OPT_POS_DELTA, o->val.i = atoi(val);
else if (strcmp(o->arg, "ignore_md5") == 0 ||
strcmp(o->arg, "IGNORE_MD5") == 0)
o->opt = CRAM_OPT_IGNORE_MD5, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_bzip2") == 0 ||
strcmp(o->arg, "USE_BZIP2") == 0)
o->opt = CRAM_OPT_USE_BZIP2, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_rans") == 0 ||
strcmp(o->arg, "USE_RANS") == 0)
o->opt = CRAM_OPT_USE_RANS, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_lzma") == 0 ||
strcmp(o->arg, "USE_LZMA") == 0)
o->opt = CRAM_OPT_USE_LZMA, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_tok") == 0 ||
strcmp(o->arg, "USE_TOK") == 0)
o->opt = CRAM_OPT_USE_TOK, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_fqz") == 0 ||
strcmp(o->arg, "USE_FQZ") == 0)
o->opt = CRAM_OPT_USE_FQZ, o->val.i = atoi(val);
else if (strcmp(o->arg, "use_arith") == 0 ||
strcmp(o->arg, "USE_ARITH") == 0)
o->opt = CRAM_OPT_USE_ARITH, o->val.i = atoi(val);
else if (strcmp(o->arg, "fast") == 0 ||
strcmp(o->arg, "FAST") == 0)
o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_FAST;
else if (strcmp(o->arg, "normal") == 0 ||
strcmp(o->arg, "NORMAL") == 0)
o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_NORMAL;
else if (strcmp(o->arg, "small") == 0 ||
strcmp(o->arg, "SMALL") == 0)
o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_SMALL;
else if (strcmp(o->arg, "archive") == 0 ||
strcmp(o->arg, "ARCHIVE") == 0)
o->opt = HTS_OPT_PROFILE, o->val.i = HTS_PROFILE_ARCHIVE;
else if (strcmp(o->arg, "reference") == 0 ||
strcmp(o->arg, "REFERENCE") == 0)
o->opt = CRAM_OPT_REFERENCE, o->val.s = val;
else if (strcmp(o->arg, "version") == 0 ||
strcmp(o->arg, "VERSION") == 0)
o->opt = CRAM_OPT_VERSION, o->val.s =val;
else if (strcmp(o->arg, "multi_seq_per_slice") == 0 ||
strcmp(o->arg, "MULTI_SEQ_PER_SLICE") == 0)
o->opt = CRAM_OPT_MULTI_SEQ_PER_SLICE, o->val.i = atoi(val);
else if (strcmp(o->arg, "nthreads") == 0 ||
strcmp(o->arg, "NTHREADS") == 0)
o->opt = HTS_OPT_NTHREADS, o->val.i = atoi(val);
else if (strcmp(o->arg, "cache_size") == 0 ||
strcmp(o->arg, "CACHE_SIZE") == 0) {
char *endp;
o->opt = HTS_OPT_CACHE_SIZE;
o->val.i = strtol(val, &endp, 0);
// NB: Doesn't support floats, eg 1.5g
// TODO: extend hts_parse_decimal? See also samtools sort.
switch (*endp) {
case 'g': case 'G': o->val.i *= 1024; // fall through
case 'm': case 'M': o->val.i *= 1024; // fall through
case 'k': case 'K': o->val.i *= 1024; break;
case '\0': break;
default:
hts_log_error("Unrecognised cache size suffix '%c'", *endp);
free(o->arg);
free(o);
return -1;
}
}
else if (strcmp(o->arg, "required_fields") == 0 ||
strcmp(o->arg, "REQUIRED_FIELDS") == 0)
o->opt = CRAM_OPT_REQUIRED_FIELDS, o->val.i = strtol(val, NULL, 0);
else if (strcmp(o->arg, "lossy_names") == 0 ||
strcmp(o->arg, "LOSSY_NAMES") == 0)
o->opt = CRAM_OPT_LOSSY_NAMES, o->val.i = strtol(val, NULL, 0);
else if (strcmp(o->arg, "name_prefix") == 0 ||
strcmp(o->arg, "NAME_PREFIX") == 0)
o->opt = CRAM_OPT_PREFIX, o->val.s = val;