[med-svn] [Git][med-team/htslib][upstream] New upstream version 1.10.2
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Dec 21 20:33:14 GMT 2019
Michael R. Crusoe pushed to branch upstream at Debian Med / htslib
Commits:
beef2a3a by Michael R. Crusoe at 2019-12-20T17:54:00Z
New upstream version 1.10.2
- - - - -
9 changed files:
- NEWS
- bgzip.1
- configure
- htsfile.1
- htslib-s3-plugin.7
- htslib/hts.h
- − htslib/hts.h~
- tabix.1
- version.sh
Changes:
=====================================
NEWS
=====================================
@@ -1,5 +1,9 @@
-Noteworthy changes in release a.b
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Noteworthy changes in release 1.10.2 (19th December 2019)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is a release fix that corrects minor inconsistencies discovered in
+previous deliverables.
+
Noteworthy changes in release 1.10.1 (17th December 2019)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
=====================================
bgzip.1
=====================================
@@ -1,4 +1,4 @@
-.TH bgzip 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH bgzip 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
.SH NAME
.PP
bgzip \- Block compression/decompression utility
=====================================
configure
=====================================
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for HTSlib 1.10.1.
+# Generated by GNU Autoconf 2.68 for HTSlib 1.10.2.
#
# Report bugs to <samtools-help at lists.sourceforge.net>.
#
@@ -565,8 +565,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='HTSlib'
PACKAGE_TARNAME='htslib'
-PACKAGE_VERSION='1.10.1'
-PACKAGE_STRING='HTSlib 1.10.1'
+PACKAGE_VERSION='1.10.2'
+PACKAGE_STRING='HTSlib 1.10.2'
PACKAGE_BUGREPORT='samtools-help at lists.sourceforge.net'
PACKAGE_URL='http://www.htslib.org/'
@@ -1245,7 +1245,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures HTSlib 1.10.1 to adapt to many kinds of systems.
+\`configure' configures HTSlib 1.10.2 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1306,7 +1306,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of HTSlib 1.10.1:";;
+ short | recursive ) echo "Configuration of HTSlib 1.10.2:";;
esac
cat <<\_ACEOF
@@ -1413,7 +1413,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-HTSlib configure 1.10.1
+HTSlib configure 1.10.2
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1742,7 +1742,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by HTSlib $as_me 1.10.1, which was
+It was created by HTSlib $as_me 1.10.2, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -5804,7 +5804,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by HTSlib $as_me 1.10.1, which was
+This file was extended by HTSlib $as_me 1.10.2, which was
generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -5867,7 +5867,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-HTSlib config.status 1.10.1
+HTSlib config.status 1.10.2
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
=====================================
htsfile.1
=====================================
@@ -1,4 +1,4 @@
-.TH htsfile 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH htsfile 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
.SH NAME
htsfile \- identify high-throughput sequencing data files
.\"
=====================================
htslib-s3-plugin.7
=====================================
@@ -1,4 +1,4 @@
-.TH htslib-s3-plugin 7 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH htslib-s3-plugin 7 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
.SH NAME
s3 plugin \- htslib AWS S3 plugin
.\"
=====================================
htslib/hts.h
=====================================
@@ -421,7 +421,7 @@ const char *hts_version(void);
// Immediately after release, bump ZZ to 90 to distinguish in-development
// Git repository builds from the release; you may wish to increment this
// further when significant features are merged.
-#define HTS_VERSION 101001
+#define HTS_VERSION 101002
/*!
@abstract Determine format by peeking at the start of a file
=====================================
htslib/hts.h~ deleted
=====================================
@@ -1,1346 +0,0 @@
-/// @file htslib/hts.h
-/// Format-neutral I/O, indexing, and iterator API functions.
-/*
- Copyright (C) 2012-2019 Genome Research Ltd.
- Copyright (C) 2010, 2012 Broad Institute.
- Portions copyright (C) 2003-2006, 2008-2010 by Heng Li <lh3 at live.co.uk>
-
- Author: Heng Li <lh3 at 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. */
-
-#ifndef HTSLIB_HTS_H
-#define HTSLIB_HTS_H
-
-#include <stddef.h>
-#include <stdint.h>
-#include <inttypes.h>
-
-#include "hts_defs.h"
-#include "hts_log.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-// Separator used to split HTS_PATH (for plugins); REF_PATH (cram references)
-#if defined(_WIN32) || defined(__MSYS__)
-#define HTS_PATH_SEPARATOR_CHAR ';'
-#define HTS_PATH_SEPARATOR_STR ";"
-#else
-#define HTS_PATH_SEPARATOR_CHAR ':'
-#define HTS_PATH_SEPARATOR_STR ":"
-#endif
-
-#ifndef HTS_BGZF_TYPEDEF
-typedef struct BGZF BGZF;
-#define HTS_BGZF_TYPEDEF
-#endif
-struct cram_fd;
-struct hFILE;
-struct hts_tpool;
-struct sam_hdr_t;
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-/**
- * @hideinitializer
- * Deprecated macro to expand a dynamic array of a given type
- *
- * @param type_t The type of the array elements
- * @param[in] n Requested number of elements of type type_t
- * @param[in,out] m Size of memory allocated
- * @param[in,out] ptr Pointer to the array
- *
- * @discussion
- * Do not use this macro. Use hts_resize() instead as allows allocation
- * failures to be handled more gracefully.
- *
- * The array *ptr will be expanded if necessary so that it can hold @p n
- * or more elements. If the array is expanded then the new size will be
- * written to @p m and the value in @p ptr may change.
- *
- * It must be possible to take the address of @p ptr and @p m must be usable
- * as an lvalue.
- *
- * @bug
- * If the memory allocation fails, this will call exit(1). This is
- * not ideal behaviour in a library.
- */
-#define hts_expand(type_t, n, m, ptr) do { \
- if ((n) > (m)) { \
- size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \
- int, void **, const char *); \
- (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
- sizeof(type_t), 0, \
- (void **)&(ptr), __func__); \
- } \
- } while (0)
-
-/**
- * @hideinitializer
- * Macro to expand a dynamic array, zeroing any newly-allocated memory
- *
- * @param type_t The type of the array elements
- * @param[in] n Requested number of elements of type type_t
- * @param[in,out] m Size of memory allocated
- * @param[in,out] ptr Pointer to the array
- *
- * @discussion
- * Do not use this macro. Use hts_resize() instead as allows allocation
- * failures to be handled more gracefully.
- *
- * As for hts_expand(), except the bytes that make up the array elements
- * between the old and new values of @p m are set to zero using memset().
- *
- * @bug
- * If the memory allocation fails, this will call exit(1). This is
- * not ideal behaviour in a library.
- */
-
-
-#define hts_expand0(type_t, n, m, ptr) do { \
- if ((n) > (m)) { \
- size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \
- int, void **, const char *); \
- (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \
- sizeof(type_t), 1, \
- (void **)&(ptr), __func__); \
- } \
- } while (0)
-
-// For internal use (by hts_resize()) only
-HTSLIB_EXPORT
-int hts_resize_array_(size_t, size_t, size_t, void *, void **, int,
- const char *);
-
-#define HTS_RESIZE_CLEAR 1
-
-/**
- * @hideinitializer
- * Macro to expand a dynamic array of a given type
- *
- * @param type_t The type of the array elements
- * @param[in] num Requested number of elements of type type_t
- * @param[in,out] size_ptr Pointer to where the size (in elements) of the
- array is stored.
- * @param[in,out] ptr Location of the pointer to the array
- * @param[in] flags Option flags
- *
- * @return 0 for success, or negative if an error occurred.
- *
- * @discussion
- * The array *ptr will be expanded if necessary so that it can hold @p num
- * or more elements. If the array is expanded then the new size will be
- * written to @p *size_ptr and the value in @p *ptr may change.
- *
- * If ( @p flags & HTS_RESIZE_CLEAR ) is set, any newly allocated memory will
- * be cleared.
- */
-
-#define hts_resize(type_t, num, size_ptr, ptr, flags) \
- ((num) > (*(size_ptr)) \
- ? hts_resize_array_(sizeof(type_t), (num), \
- sizeof(*(size_ptr)), (size_ptr), \
- (void **)(ptr), (flags), __func__) \
- : 0)
-
-/**
- * Wrapper function for free(). Enables memory deallocation across DLL
- * boundary. Should be used by all applications, which are compiled
- * with a different standard library than htslib and call htslib
- * methods that return dynamically allocated data.
- */
-HTSLIB_EXPORT
-void hts_free(void *ptr);
-
-/************
- * File I/O *
- ************/
-
-// Add new entries only at the end (but before the *_maximum entry)
-// of these enums, as their numbering is part of the htslib ABI.
-
-enum htsFormatCategory {
- unknown_category,
- sequence_data, // Sequence data -- SAM, BAM, CRAM, etc
- variant_data, // Variant calling data -- VCF, BCF, etc
- index_file, // Index file associated with some data file
- region_list, // Coordinate intervals or regions -- BED, etc
- category_maximum = 32767
-};
-
-enum htsExactFormat {
- unknown_format,
- binary_format, text_format,
- sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed,
- htsget,
- json HTS_DEPRECATED_ENUM("Use htsExactFormat 'htsget' instead") = htsget,
- empty_format, // File is empty (or empty after decompression)
- fasta_format, fastq_format, fai_format, fqi_format,
- format_maximum = 32767
-};
-
-enum htsCompression {
- no_compression, gzip, bgzf, custom, bzip2_compression,
- compression_maximum = 32767
-};
-
-typedef struct htsFormat {
- enum htsFormatCategory category;
- enum htsExactFormat format;
- struct { short major, minor; } version;
- enum htsCompression compression;
- short compression_level; // currently unused
- void *specific; // format specific options; see struct hts_opt.
-} htsFormat;
-
-struct __hts_idx_t;
-typedef struct __hts_idx_t hts_idx_t;
-
-// Maintainers note htsFile cannot be an opaque structure because some of its
-// fields are part of libhts.so's ABI (hence these fields must not be moved):
-// - fp is used in the public sam_itr_next()/etc macros
-// - is_bin is used directly in samtools <= 1.1 and bcftools <= 1.1
-// - is_write and is_cram are used directly in samtools <= 1.1
-// - fp is used directly in samtools (up to and including current develop)
-// - line is used directly in bcftools (up to and including current develop)
-typedef struct {
- uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, is_bgzf:1, dummy:27;
- int64_t lineno;
- kstring_t line;
- char *fn, *fn_aux;
- union {
- BGZF *bgzf;
- struct cram_fd *cram;
- struct hFILE *hfile;
- } fp;
- void *state; // format specific state information
- htsFormat format;
- hts_idx_t *idx;
- const char *fnidx;
- struct sam_hdr_t *bam_header;
-} htsFile;
-
-// A combined thread pool and queue allocation size.
-// The pool should already be defined, but qsize may be zero to
-// indicate an appropriate queue size is taken from the pool.
-//
-// Reasons for explicitly setting it could be where many more file
-// descriptors are in use than threads, so keeping memory low is
-// important.
-typedef struct {
- struct hts_tpool *pool; // The shared thread pool itself
- int qsize; // Size of I/O queue to use for this fp
-} htsThreadPool;
-
-// REQUIRED_FIELDS
-enum sam_fields {
- SAM_QNAME = 0x00000001,
- SAM_FLAG = 0x00000002,
- SAM_RNAME = 0x00000004,
- SAM_POS = 0x00000008,
- SAM_MAPQ = 0x00000010,
- SAM_CIGAR = 0x00000020,
- SAM_RNEXT = 0x00000040,
- SAM_PNEXT = 0x00000080,
- SAM_TLEN = 0x00000100,
- SAM_SEQ = 0x00000200,
- SAM_QUAL = 0x00000400,
- SAM_AUX = 0x00000800,
- SAM_RGAUX = 0x00001000,
-};
-
-// Mostly CRAM only, but this could also include other format options
-enum hts_fmt_option {
- // CRAM specific
- CRAM_OPT_DECODE_MD,
- CRAM_OPT_PREFIX,
- CRAM_OPT_VERBOSITY, // obsolete, use hts_set_log_level() instead
- CRAM_OPT_SEQS_PER_SLICE,
- CRAM_OPT_SLICES_PER_CONTAINER,
- CRAM_OPT_RANGE,
- CRAM_OPT_VERSION, // rename to cram_version?
- CRAM_OPT_EMBED_REF,
- CRAM_OPT_IGNORE_MD5,
- CRAM_OPT_REFERENCE, // make general
- CRAM_OPT_MULTI_SEQ_PER_SLICE,
- CRAM_OPT_NO_REF,
- CRAM_OPT_USE_BZIP2,
- CRAM_OPT_SHARED_REF,
- CRAM_OPT_NTHREADS, // deprecated, use HTS_OPT_NTHREADS
- CRAM_OPT_THREAD_POOL,// make general
- CRAM_OPT_USE_LZMA,
- CRAM_OPT_USE_RANS,
- CRAM_OPT_REQUIRED_FIELDS,
- CRAM_OPT_LOSSY_NAMES,
- CRAM_OPT_BASES_PER_SLICE,
- CRAM_OPT_STORE_MD,
- CRAM_OPT_STORE_NM,
-
- // General purpose
- HTS_OPT_COMPRESSION_LEVEL = 100,
- HTS_OPT_NTHREADS,
- HTS_OPT_THREAD_POOL,
- HTS_OPT_CACHE_SIZE,
- HTS_OPT_BLOCK_SIZE,
-};
-
-// For backwards compatibility
-#define cram_option hts_fmt_option
-
-typedef struct hts_opt {
- char *arg; // string form, strdup()ed
- enum hts_fmt_option opt; // tokenised key
- union { // ... and value
- int i;
- char *s;
- } val;
- struct hts_opt *next;
-} hts_opt;
-
-#define HTS_FILE_OPTS_INIT {{0},0}
-
-/*
- * Explicit index file name delimiter, see below
- */
-#define HTS_IDX_DELIM "##idx##"
-
-
-/**********************
- * Exported functions *
- **********************/
-
-/*
- * Parses arg and appends it to the option list.
- *
- * Returns 0 on success;
- * -1 on failure.
- */
-HTSLIB_EXPORT
-int hts_opt_add(hts_opt **opts, const char *c_arg);
-
-/*
- * Applies an hts_opt option list to a given htsFile.
- *
- * Returns 0 on success
- * -1 on failure
- */
-HTSLIB_EXPORT
-int hts_opt_apply(htsFile *fp, hts_opt *opts);
-
-/*
- * Frees an hts_opt list.
- */
-HTSLIB_EXPORT
-void hts_opt_free(hts_opt *opts);
-
-/*
- * Accepts a string file format (sam, bam, cram, vcf, bam) optionally
- * followed by a comma separated list of key=value options and splits
- * these up into the fields of htsFormat struct.
- *
- * Returns 0 on success
- * -1 on failure.
- */
-HTSLIB_EXPORT
-int hts_parse_format(htsFormat *opt, const char *str);
-
-/*
- * Tokenise options as (key(=value)?,)*(key(=value)?)?
- * NB: No provision for ',' appearing in the value!
- * Add backslashing rules?
- *
- * This could be used as part of a general command line option parser or
- * as a string concatenated onto the file open mode.
- *
- * Returns 0 on success
- * -1 on failure.
- */
-HTSLIB_EXPORT
-int hts_parse_opt_list(htsFormat *opt, const char *str);
-
-/*! @abstract Table for converting a nucleotide character to 4-bit encoding.
-The input character may be either an IUPAC ambiguity code, '=' for 0, or
-'0'/'1'/'2'/'3' for a result of 1/2/4/8. The result is encoded as 1/2/4/8
-for A/C/G/T or combinations of these bits for ambiguous bases.
-*/
-extern const unsigned char seq_nt16_table[256];
-
-/*! @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC
-ambiguity code letter (or '=' when given 0).
-*/
-extern const char seq_nt16_str[];
-
-/*! @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.
-Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).
-*/
-extern const int seq_nt16_int[];
-
-/*!
- @abstract Get the htslib version number
- @return For released versions, a string like "N.N[.N]"; or git describe
- output if using a library built within a Git repository.
-*/
-HTSLIB_EXPORT
-const char *hts_version(void);
-
-/*!
- @abstract Compile-time HTSlib version number, for use in #if checks
- @return For released versions X.Y[.Z], an integer of the form XYYYZZ;
- useful for preprocessor conditionals such as
- #if HTS_VERSION >= 101000 // Check for v1.10 or later
-*/
-// Maintainers: Bump this in the final stage of preparing a new release.
-// Immediately after release, bump ZZ to 90 to distinguish in-development
-// Git repository builds from the release; you may wish to increment this
-// further when significant features are merged.
-#define HTS_VERSION 101000
-
-/*!
- @abstract Determine format by peeking at the start of a file
- @param fp File opened for reading, positioned at the beginning
- @param fmt Format structure that will be filled out on return
- @return 0 for success, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_detect_format(struct hFILE *fp, htsFormat *fmt);
-
-/*!
- @abstract Get a human-readable description of the file format
- @param fmt Format structure holding type, version, compression, etc.
- @return Description string, to be freed by the caller after use.
-*/
-HTSLIB_EXPORT
-char *hts_format_description(const htsFormat *format);
-
-/*!
- @abstract Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF)
- or possibly-compressed textual line-orientated file
- @param fn The file name or "-" for stdin/stdout. For indexed files
- with a non-standard naming, the file name can include the
- name of the index file delimited with HTS_IDX_DELIM
- @param mode Mode matching / [rwa][bceguxz0-9]* /
- @discussion
- With 'r' opens for reading; any further format mode letters are ignored
- as the format is detected by checking the first few bytes or BGZF blocks
- of the file. With 'w' or 'a' opens for writing or appending, with format
- specifier letters:
- b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)
- c CRAM format
- g gzip compressed
- u uncompressed
- z bgzf compressed
- [0-9] zlib compression level
- and with non-format option letters (for any of 'r'/'w'/'a'):
- e close the file on exec(2) (opens with O_CLOEXEC, where supported)
- x create the file exclusively (opens with O_EXCL, where supported)
- Note that there is a distinction between 'u' and '0': the first yields
- plain uncompressed output whereas the latter outputs uncompressed data
- wrapped in the zlib format.
- @example
- [rw]b .. compressed BCF, BAM, FAI
- [rw]bu .. uncompressed BCF
- [rw]z .. compressed VCF
- [rw] .. uncompressed VCF
-*/
-HTSLIB_EXPORT
-htsFile *hts_open(const char *fn, const char *mode);
-
-/*!
- @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file
- @param fn The file name or "-" for stdin/stdout
- @param mode Open mode, as per hts_open()
- @param fmt Optional format specific parameters
- @discussion
- See hts_open() for description of fn and mode.
- // TODO Update documentation for s/opts/fmt/
- Opts contains a format string (sam, bam, cram, vcf, bcf) which will,
- if defined, override mode. Opts also contains a linked list of hts_opt
- structures to apply to the open file handle. These can contain things
- like pointers to the reference or information on compression levels,
- block sizes, etc.
-*/
-HTSLIB_EXPORT
-htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt);
-
-/*!
- @abstract Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
- @param fn The already-open file handle
- @param mode Open mode, as per hts_open()
-*/
-HTSLIB_EXPORT
-htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);
-
-/*!
- @abstract Close a file handle, flushing buffered data for output streams
- @param fp The file handle to be closed
- @return 0 for success, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_close(htsFile *fp);
-
-/*!
- @abstract Returns the file's format information
- @param fp The file handle
- @return Read-only pointer to the file's htsFormat.
-*/
-HTSLIB_EXPORT
-const htsFormat *hts_get_format(htsFile *fp);
-
-/*!
- @ abstract Returns a string containing the file format extension.
- @ param format Format structure containing the file type.
- @ return A string ("sam", "bam", etc) or "?" for unknown formats.
- */
-HTSLIB_EXPORT
-const char *hts_format_file_extension(const htsFormat *format);
-
-/*!
- @abstract Sets a specified CRAM option on the open file handle.
- @param fp The file handle open the open file.
- @param opt The CRAM_OPT_* option.
- @param ... Optional arguments, dependent on the option used.
- @return 0 for success, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...);
-
-HTSLIB_EXPORT
-int hts_getline(htsFile *fp, int delimiter, kstring_t *str);
-HTSLIB_EXPORT
-char **hts_readlines(const char *fn, int *_n);
-/*!
- @abstract Parse comma-separated list or read list from a file
- @param list File name or comma-separated list
- @param is_file
- @param _n Size of the output array (number of items read)
- @return NULL on failure or pointer to newly allocated array of
- strings
-*/
-HTSLIB_EXPORT
-char **hts_readlist(const char *fn, int is_file, int *_n);
-
-/*!
- @abstract Create extra threads to aid compress/decompression for this file
- @param fp The file handle
- @param n The number of worker threads to create
- @return 0 for success, or negative if an error occurred.
- @notes This function creates non-shared threads for use solely by fp.
- The hts_set_thread_pool function is the recommended alternative.
-*/
-HTSLIB_EXPORT
-int hts_set_threads(htsFile *fp, int n);
-
-/*!
- @abstract Create extra threads to aid compress/decompression for this file
- @param fp The file handle
- @param p A pool of worker threads, previously allocated by hts_create_threads().
- @return 0 for success, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_set_thread_pool(htsFile *fp, htsThreadPool *p);
-
-/*!
- @abstract Adds a cache of decompressed blocks, potentially speeding up seeks.
- This may not work for all file types (currently it is bgzf only).
- @param fp The file handle
- @param n The size of cache, in bytes
-*/
-HTSLIB_EXPORT
-void hts_set_cache_size(htsFile *fp, int n);
-
-/*!
- @abstract Set .fai filename for a file opened for reading
- @return 0 for success, negative on failure
- @discussion
- Called before *_hdr_read(), this provides the name of a .fai file
- used to provide a reference list if the htsFile contains no @SQ headers.
-*/
-HTSLIB_EXPORT
-int hts_set_fai_filename(htsFile *fp, const char *fn_aux);
-
-
-/*!
- @abstract Determine whether a given htsFile contains a valid EOF block
- @return 3 for a non-EOF checkable filetype;
- 2 for an unseekable file type where EOF cannot be checked;
- 1 for a valid EOF block;
- 0 for if the EOF marker is absent when it should be present;
- -1 (with errno set) on failure
- @discussion
- Check if the BGZF end-of-file (EOF) marker is present
-*/
-HTSLIB_EXPORT
-int hts_check_EOF(htsFile *fp);
-
-/************
- * Indexing *
- ************/
-
-/*!
-These HTS_IDX_* macros are used as special tid values for hts_itr_query()/etc,
-producing iterators operating as follows:
- - HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file
- - HTS_IDX_START iterates over the entire file
- - HTS_IDX_REST iterates from the current position to the end of the file
- - HTS_IDX_NONE always returns "no more alignment records"
-When one of these special tid values is used, beg and end are ignored.
-When REST or NONE is used, idx is also ignored and may be NULL.
-*/
-#define HTS_IDX_NOCOOR (-2)
-#define HTS_IDX_START (-3)
-#define HTS_IDX_REST (-4)
-#define HTS_IDX_NONE (-5)
-
-#define HTS_FMT_CSI 0
-#define HTS_FMT_BAI 1
-#define HTS_FMT_TBI 2
-#define HTS_FMT_CRAI 3
-
-// Almost INT64_MAX, but when cast into a 32-bit int it's
-// also INT_MAX instead of -1. This avoids bugs with old code
-// using the new hts_pos_t data type.
-#define HTS_POS_MAX ((((int64_t)INT_MAX)<<32)|INT_MAX)
-#define HTS_POS_MIN INT64_MIN
-#define PRIhts_pos PRId64
-typedef int64_t hts_pos_t;
-
-// For comparison with previous release:
-//
-// #define HTS_POS_MAX INT_MAX
-// #define HTS_POS_MIN INT_MIN
-// #define PRIhts_pos PRId32
-// typedef int32_t hts_pos_t;
-
-typedef struct {
- hts_pos_t beg, end;
-} hts_pair_pos_t;
-
-typedef hts_pair_pos_t hts_pair32_t; // For backwards compatibility
-
-typedef struct {
- uint64_t u, v;
-} hts_pair64_t;
-
-typedef struct {
- uint64_t u, v;
- uint64_t max;
-} hts_pair64_max_t;
-
-typedef struct {
- const char *reg;
- hts_pair_pos_t *intervals;
- int tid;
- uint32_t count;
- hts_pos_t min_beg, max_end;
-} hts_reglist_t;
-
-typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, hts_pos_t *beg, hts_pos_t *end);
-typedef int hts_seek_func(void *fp, int64_t offset, int where);
-typedef int64_t hts_tell_func(void *fp);
-
-typedef struct {
- uint32_t read_rest:1, finished:1, is_cram:1, nocoor:1, multi:1, dummy:27;
- int tid, n_off, i, n_reg;
- hts_pos_t beg, end;
- hts_reglist_t *reg_list;
- int curr_tid, curr_reg, curr_intv;
- hts_pos_t curr_beg, curr_end;
- uint64_t curr_off, nocoor_off;
- hts_pair64_max_t *off;
- hts_readrec_func *readrec;
- hts_seek_func *seek;
- hts_tell_func *tell;
- struct {
- int n, m;
- int *a;
- } bins;
-} hts_itr_t;
-
-typedef struct {
- int key;
- uint64_t min_off, max_off;
-} aux_key_t;
-
-typedef hts_itr_t hts_itr_multi_t;
-
- #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7)
- #define hts_bin_parent(l) (((l) - 1) >> 3)
-
-///////////////////////////////////////////////////////////
-// Low-level API for building indexes.
-
-/// Create a BAI/CSI/TBI type index structure
-/** @param n Initial number of targets
- @param fmt Format, one of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI
- @param offset0 Initial file offset
- @param min_shift Number of bits for the minimal interval
- @param n_lvls Number of levels in the binning index
- @return An initialised hts_idx_t struct on success; NULL on failure
-
-The struct returned by a successful call should be freed via hts_idx_destroy()
-when it is no longer needed.
-*/
-HTSLIB_EXPORT
-hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls);
-
-/// Free a BAI/CSI/TBI type index
-/** @param idx Index structure to free
- */
-HTSLIB_EXPORT
-void hts_idx_destroy(hts_idx_t *idx);
-
-/// Push an index entry
-/** @param idx Index
- @param tid Target id
- @param beg Range start (zero-based)
- @param end Range end (zero-based, half-open)
- @param offset File offset
- @param is_mapped Range corresponds to a mapped read
- @return 0 on success; -1 on failure
-
-The @p is_mapped parameter is used to update the n_mapped / n_unmapped counts
-stored in the meta-data bin.
- */
-HTSLIB_EXPORT
-int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped);
-
-/// Finish building an index
-/** @param idx Index
- @param final_offset Last file offset
- @return 0 on success; non-zero on failure.
-*/
-HTSLIB_EXPORT
-int hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);
-
-/// Returns index format
-/** @param idx Index
- @return One of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI
-*/
-HTSLIB_EXPORT
-int hts_idx_fmt(hts_idx_t *idx);
-
-/// Add name to TBI index meta-data
-/** @param idx Index
- @param tid Target identifier
- @param name Target name
- @return Index number of name in names list on success; -1 on failure.
-*/
-HTSLIB_EXPORT
-int hts_idx_tbi_name(hts_idx_t *idx, int tid, const char *name);
-
-// Index loading and saving
-
-/// Save an index to a file
-/** @param idx Index to be written
- @param fn Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added
- @param fmt One of the HTS_FMT_* index formats
- @return 0 if successful, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) HTS_RESULT_USED;
-
-/// Save an index to a specific file
-/** @param idx Index to be written
- @param fn Input BAM/BCF/etc filename
- @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn
- @param fmt One of the HTS_FMT_* index formats
- @return 0 if successful, or negative if an error occurred.
-*/
-HTSLIB_EXPORT
-int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) HTS_RESULT_USED;
-
-/// Load an index file
-/** @param fn BAM/BCF/etc filename, to which .bai/.csi/etc will be added or
- the extension substituted, to search for an existing index file.
- In case of a non-standard naming, the file name can include the
- name of the index file delimited with HTS_IDX_DELIM.
- @param fmt One of the HTS_FMT_* index formats
- @return The index, or NULL if an error occurred.
-
-If @p fn contains the string "##idx##" (HTS_IDX_DELIM), the part before
-the delimiter will be used as the name of the data file and the part after
-it will be used as the name of the index.
-
-Otherwise, this function tries to work out the index name as follows:
-
- It will try appending ".csi" to @p fn
- It will try substituting an existing suffix (e.g. .bam, .vcf) with ".csi"
- Then, if @p fmt is HTS_FMT_BAI:
- It will try appending ".bai" to @p fn
- To will substituting the existing suffix (e.g. .bam) with ".bai"
- else if @p fmt is HTS_FMT_TBI:
- It will try appending ".tbi" to @p fn
- To will substituting the existing suffix (e.g. .vcf) with ".tbi"
-
-If the index file is remote (served over a protocol like https), first a check
-is made to see is a locally cached copy is available. This is done for all
-of the possible names listed above. If a cached copy is not available then
-the index will be downloaded and stored in the current working directory,
-with the same name as the remote index.
-
- Equivalent to hts_idx_load3(fn, NULL, fmt, HTS_IDX_SAVE_REMOTE);
-*/
-HTSLIB_EXPORT
-hts_idx_t *hts_idx_load(const char *fn, int fmt);
-
-/// Load a specific index file
-/** @param fn Input BAM/BCF/etc filename
- @param fnidx The input index filename
- @return The index, or NULL if an error occurred.
-
- Equivalent to hts_idx_load3(fn, fnidx, 0, 0);
-
- This function will not attempt to save index files locally.
-*/
-HTSLIB_EXPORT
-hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
-
-/// Load a specific index file
-/** @param fn Input BAM/BCF/etc filename
- @param fnidx The input index filename
- @param fmt One of the HTS_FMT_* index formats
- @param flags Flags to alter behaviour (see description)
- @return The index, or NULL if an error occurred.
-
- If @p fnidx is NULL, the index name will be derived from @p fn in the
- same way as hts_idx_load().
-
- If @p fnidx is not NULL, @p fmt is ignored.
-
- The @p flags parameter can be set to a combination of the following
- values:
-
- HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes
- HTS_IDX_SILENT_FAIL Fail silently if the index is not present
-
- The index struct returned by a successful call should be freed
- via hts_idx_destroy() when it is no longer needed.
-*/
-HTSLIB_EXPORT
-hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags);
-
-/// Flags for hts_idx_load3() ( and also sam_idx_load3(), tbx_idx_load3() )
-#define HTS_IDX_SAVE_REMOTE 1
-#define HTS_IDX_SILENT_FAIL 2
-
-///////////////////////////////////////////////////////////
-// Functions for accessing meta-data stored in indexes
-
-/// Get extra index meta-data
-/** @param idx The index
- @param l_meta Pointer to where the length of the extra data is stored
- @return Pointer to the extra data if present; NULL otherwise
-
- Indexes (both .tbi and .csi) made by tabix include extra data about
- the indexed file. The returns a pointer to this data. Note that the
- data is stored exactly as it is in the index. Callers need to interpret
- the results themselves, including knowing what sort of data to expect;
- byte swapping etc.
-*/
-HTSLIB_EXPORT
-uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta);
-
-/// Set extra index meta-data
-/** @param idx The index
- @param l_meta Length of data
- @param meta Pointer to the extra data
- @param is_copy If not zero, a copy of the data is taken
- @return 0 on success; -1 on failure (out of memory).
-
- Sets the data that is returned by hts_idx_get_meta().
-
- If is_copy != 0, a copy of the input data is taken. If not, ownership of
- the data pointed to by *meta passes to the index.
-*/
-HTSLIB_EXPORT
-int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int is_copy);
-
-/// Get number of mapped and unmapped reads from an index
-/** @param idx Index
- @param tid Target ID
- @param[out] mapped Location to store number of mapped reads
- @param[out] unmapped Location to store number of unmapped reads
- @return 0 on success; -1 on failure (data not available)
-
- BAI and CSI indexes store information on the number of reads for each
- target that were mapped or unmapped (unmapped reads will generally have
- a paired read that is mapped to the target). This function returns this
- infomation if it is available.
-
- @note Cram CRAI indexes do not include this information.
-*/
-HTSLIB_EXPORT
-int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped);
-
-/// Return the number of unplaced reads from an index
-/** @param idx Index
- @return Unplaced reads count
-
- Unplaced reads are not linked to any reference (e.g. RNAME is '*' in SAM
- files).
-*/
-HTSLIB_EXPORT
-uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx);
-
-///////////////////////////////////////////////////////////
-// Region parsing
-
-#define HTS_PARSE_THOUSANDS_SEP 1 ///< Ignore ',' separators within numbers
-#define HTS_PARSE_ONE_COORD 2 ///< chr:pos means chr:pos-pos and not chr:pos-end
-#define HTS_PARSE_LIST 4 ///< Expect a comma separated list of regions. (Disables HTS_PARSE_THOUSANDS_SEP)
-
-/// Parse a numeric string
-/** The number may be expressed in scientific notation, and optionally may
- contain commas in the integer part (before any decimal point or E notation).
- @param str String to be parsed
- @param strend If non-NULL, set on return to point to the first character
- in @a str after those forming the parsed number
- @param flags Or'ed-together combination of HTS_PARSE_* flags
- @return Converted value of the parsed number.
-
- When @a strend is NULL, a warning will be printed (if hts_verbose is HTS_LOG_WARNING
- or more) if there are any trailing characters after the number.
-*/
-HTSLIB_EXPORT
-long long hts_parse_decimal(const char *str, char **strend, int flags);
-
-typedef int (*hts_name2id_f)(void*, const char*);
-typedef const char *(*hts_id2name_f)(void*, int);
-
-/// Parse a "CHR:START-END"-style region string
-/** @param str String to be parsed
- @param beg Set on return to the 0-based start of the region
- @param end Set on return to the 1-based end of the region
- @return Pointer to the colon or '\0' after the reference sequence name,
- or NULL if @a str could not be parsed.
-
- NOTE: For compatibility with hts_parse_reg only.
- Please use hts_parse_region instead.
-*/
-HTSLIB_EXPORT
-const char *hts_parse_reg64(const char *str, hts_pos_t *beg, hts_pos_t *end);
-
-/// Parse a "CHR:START-END"-style region string
-/** @param str String to be parsed
- @param beg Set on return to the 0-based start of the region
- @param end Set on return to the 1-based end of the region
- @return Pointer to the colon or '\0' after the reference sequence name,
- or NULL if @a str could not be parsed.
-*/
-HTSLIB_EXPORT
-const char *hts_parse_reg(const char *str, int *beg, int *end);
-
-/// Parse a "CHR:START-END"-style region string
-/** @param str String to be parsed
- @param tid Set on return (if not NULL) to be reference index (-1 if invalid)
- @param beg Set on return to the 0-based start of the region
- @param end Set on return to the 1-based end of the region
- @param getid Function pointer. Called if not NULL to set tid.
- @param hdr Caller data passed to getid.
- @param flags Bitwise HTS_PARSE_* flags listed above.
- @return Pointer to the byte after the end of the entire region
- specifier (including any trailing comma) on success,
- or NULL if @a str could not be parsed.
-
- A variant of hts_parse_reg which is reference-id aware. It uses
- the iterator name2id callbacks to validate the region tokenisation works.
-
- This is necessary due to GRCh38 HLA additions which have reference names
- like "HLA-DRB1*12:17".
-
- To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200"
- are reference names, quote using curly braces.
- Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example.
-
- Flags are used to control how parsing works, and can be one of the below.
-
- HTS_PARSE_THOUSANDS_SEP:
- Ignore commas in numbers. For example with this flag 1,234,567
- is interpreted as 1234567.
-
- HTS_PARSE_LIST:
- If present, the region is assmed to be a comma separated list and
- position parsing will not contain commas (this implicitly
- clears HTS_PARSE_THOUSANDS_SEP in the call to hts_parse_decimal).
- On success the return pointer will be the start of the next region, ie
- the character after the comma. (If *ret != '\0' then the caller can
- assume another region is present in the list.)
-
- If not set then positions may contain commas. In this case the return
- value should point to the end of the string, or NULL on failure.
-
- HTS_PARSE_ONE_COORD:
- If present, X:100 is treated as the single base pair region X:100-100.
- In this case X:-100 is shorthand for X:1-100 and X:100- is X:100-<end>.
- (This is the standard bcftools region convention.)
-
- When not set X:100 is considered to be X:100-<end> where <end> is
- the end of chromosome X (set to INT_MAX here). X:100- and X:-100 are
- invalid.
- (This is the standard samtools region convention.)
-
- Note the supplied string expects 1 based inclusive coordinates, but the
- returned coordinates start from 0 and are half open, so pos0 is valid
- for use in e.g. "for (pos0 = beg; pos0 < end; pos0++) {...}"
-
- If NULL is returned, the value in tid mat give additional information
- about the error:
-
- -2 Failed to parse @p hdr; or out of memory
- -1 The reference in @p str has mismatched braces, or does not
- exist in @p hdr
- >= 0 The specified range in @p str could not be parsed
-*/
-HTSLIB_EXPORT
-const char *hts_parse_region(const char *s, int *tid, hts_pos_t *beg,
- hts_pos_t *end, hts_name2id_f getid, void *hdr,
- int flags);
-
-
-///////////////////////////////////////////////////////////
-// Generic iterators
-//
-// These functions provide the low-level infrastructure for iterators.
-// Wrappers around these are used to make iterators for specific file types.
-// See:
-// htslib/sam.h for SAM/BAM/CRAM iterators
-// htslib/vcf.h for VCF/BCF iterators
-// htslib/tbx.h for files indexed by tabix
-
-/// Create a single-region iterator
-/** @param idx Index
- @param tid Target ID
- @param beg Start of region
- @param end End of region
- @param readrec Callback to read a record from the input file
- @return An iterator on success; NULL on failure
-
- The iterator struct returned by a successful call should be freed
- via hts_itr_destroy() when it is no longer needed.
- */
-HTSLIB_EXPORT
-hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec);
-
-/// Free an iterator
-/** @param iter Iterator to free
- */
-HTSLIB_EXPORT
-void hts_itr_destroy(hts_itr_t *iter);
-
-typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec);
-
-/// Create a single-region iterator from a text region specification
-/** @param idx Index
- @param reg Region specifier
- @param getid Callback function to return the target ID for a name
- @param hdr Input file header
- @param itr_query Callback function returning an iterator for a numeric tid,
- start and end position
- @param readrec Callback to read a record from the input file
- @return An iterator on success; NULL on error
-
- The iterator struct returned by a successful call should be freed
- via hts_itr_destroy() when it is no longer needed.
- */
-HTSLIB_EXPORT
-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);
-
-/// Return the next record from an iterator
-/** @param fp Input file handle
- @param iter Iterator
- @param r Pointer to record placeholder
- @param data Data passed to the readrec callback
- @return >= 0 on success, -1 when there is no more data, < -1 on error
- */
-HTSLIB_EXPORT
-int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) HTS_RESULT_USED;
-
-/// Return a list of target names from an index
-/** @param idx Index
- @param[out] n Location to store the number of targets
- @param getid Callback function to get the name for a target ID
- @param hdr Header from indexed file
- @return An array of pointers to the names on success; NULL on failure
-
- @note The names are pointers into the header data structure. When cleaning
- up, only the array should be freed, not the names.
- */
-HTSLIB_EXPORT
-const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
-
-/**********************************
- * Iterator with multiple regions *
- **********************************/
-
-typedef int hts_itr_multi_query_func(const hts_idx_t *idx, hts_itr_t *itr);
-HTSLIB_EXPORT
-int hts_itr_multi_bam(const hts_idx_t *idx, hts_itr_t *iter);
-HTSLIB_EXPORT
-int hts_itr_multi_cram(const hts_idx_t *idx, hts_itr_t *iter);
-
-/// Create a multi-region iterator from a region list
-/** @param idx Index
- @param reglist Region list
- @param count Number of items in region list
- @param getid Callback to convert names to target IDs
- @param hdr Indexed file header (passed to getid)
- @param itr_specific Filetype-specific callback function
- @param readrec Callback to read an input file record
- @param seek Callback to seek in the input file
- @param tell Callback to return current input file location
- @return An iterator on success; NULL on failure
-
- The iterator struct returned by a successful call should be freed
- via hts_itr_destroy() when it is no longer needed.
- */
-HTSLIB_EXPORT
-hts_itr_t *hts_itr_regions(const hts_idx_t *idx, hts_reglist_t *reglist, int count, hts_name2id_f getid, void *hdr, hts_itr_multi_query_func *itr_specific, hts_readrec_func *readrec, hts_seek_func *seek, hts_tell_func *tell);
-
-/// Return the next record from an iterator
-/** @param fp Input file handle
- @param iter Iterator
- @param r Pointer to record placeholder
- @return >= 0 on success, -1 when there is no more data, < -1 on error
- */
-HTSLIB_EXPORT
-int hts_itr_multi_next(htsFile *fd, hts_itr_t *iter, void *r);
-
-/// Create a region list from a char array
-/** @param argv Char array of target:interval elements, e.g. chr1:2500-3600, chr1:5100, chr2
- @param argc Number of items in the array
- @param r_count Pointer to the number of items in the resulting region list
- @param hdr Header for the sam/bam/cram file
- @param getid Callback to convert target names to target ids.
- @return A region list on success, NULL on failure
-
- The hts_reglist_t struct returned by a successful call should be freed
- via hts_reglist_free() when it is no longer needed.
- */
-HTSLIB_EXPORT
-hts_reglist_t *hts_reglist_create(char **argv, int argc, int *r_count, void *hdr, hts_name2id_f getid);
-
-/// Free a region list
-/** @param reglist Region list
- @param count Number of items in the list
- */
-HTSLIB_EXPORT
-void hts_reglist_free(hts_reglist_t *reglist, int count);
-
-/// Free a multi-region iterator
-/** @param iter Iterator to free
- */
-#define hts_itr_multi_destroy(iter) hts_itr_destroy(iter)
-
-
- /**
- * hts_file_type() - Convenience function to determine file type
- * DEPRECATED: This function has been replaced by hts_detect_format().
- * It and these FT_* macros will be removed in a future HTSlib release.
- */
- #define FT_UNKN 0
- #define FT_GZ 1
- #define FT_VCF 2
- #define FT_VCF_GZ (FT_GZ|FT_VCF)
- #define FT_BCF (1<<2)
- #define FT_BCF_GZ (FT_GZ|FT_BCF)
- #define FT_STDIN (1<<3)
- HTSLIB_EXPORT
- int hts_file_type(const char *fname);
-
-
-/***************************
- * Revised MAQ error model *
- ***************************/
-
-struct errmod_t;
-typedef struct errmod_t errmod_t;
-
-HTSLIB_EXPORT
-errmod_t *errmod_init(double depcorr);
-HTSLIB_EXPORT
-void errmod_destroy(errmod_t *em);
-
-/*
- n: number of bases
- m: maximum base
- bases[i]: qual:6, strand:1, base:4
- q[i*m+j]: phred-scaled likelihood of (i,j)
- */
-HTSLIB_EXPORT
-int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
-
-
-/*****************************************************
- * Probabilistic banded glocal alignment *
- * See https://doi.org/10.1093/bioinformatics/btr076 *
- *****************************************************/
-
-typedef struct probaln_par_t {
- float d, e;
- int bw;
-} probaln_par_t;
-
-/// Perform probabilistic banded glocal alignment
-/** @param ref Reference sequence
- @param l_ref Length of reference
- @param query Query sequence
- @param l_query Length of query sequence
- @param iqual Query base qualities
- @param c Alignment parameters
- @param[out] state Output alignment
- @param[out] q Phred scaled posterior probability of state[i] being wrong
- @return Phred-scaled likelihood score, or INT_MIN on failure.
-
-The reference and query sequences are coded using integers 0,1,2,3,4 for
-bases A,C,G,T,N respectively (N here is for any ambiguity code).
-
-On output, state and q are arrays of length l_query. The higher 30
-bits give the reference position the query base is matched to and the
-lower two bits can be 0 (an alignment match) or 1 (an
-insertion). q[i] gives the phred scaled posterior probability of
-state[i] being wrong.
-
-On failure, errno will be set to EINVAL if the values of l_ref or l_query
-were invalid; or ENOMEM if a memory allocation failed.
-*/
-
-HTSLIB_EXPORT
-int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q);
-
-
- /**********************
- * MD5 implementation *
- **********************/
-
- struct hts_md5_context;
- typedef struct hts_md5_context hts_md5_context;
-
- /*! @abstract Intialises an MD5 context.
- * @discussion
- * The expected use is to allocate an hts_md5_context using
- * hts_md5_init(). This pointer is then passed into one or more calls
- * of hts_md5_update() to compute successive internal portions of the
- * MD5 sum, which can then be externalised as a full 16-byte MD5sum
- * calculation by calling hts_md5_final(). This can then be turned
- * into ASCII via hts_md5_hex().
- *
- * To dealloate any resources created by hts_md5_init() call the
- * hts_md5_destroy() function.
- *
- * @return hts_md5_context pointer on success, NULL otherwise.
- */
- HTSLIB_EXPORT
- hts_md5_context *hts_md5_init(void);
-
- /*! @abstract Updates the context with the MD5 of the data. */
- HTSLIB_EXPORT
- void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size);
-
- /*! @abstract Computes the final 128-bit MD5 hash from the given context */
- HTSLIB_EXPORT
- void hts_md5_final(unsigned char *digest, hts_md5_context *ctx);
-
- /*! @abstract Resets an md5_context to the initial state, as returned
- * by hts_md5_init().
- */
- HTSLIB_EXPORT
- void hts_md5_reset(hts_md5_context *ctx);
-
- /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated
- * hex string.
- */
- HTSLIB_EXPORT
- void hts_md5_hex(char *hex, const unsigned char *digest);
-
- /*! @abstract Deallocates any memory allocated by hts_md5_init. */
- HTSLIB_EXPORT
- void hts_md5_destroy(hts_md5_context *ctx);
-
-static inline int hts_reg2bin(hts_pos_t beg, hts_pos_t end, int min_shift, int n_lvls)
-{
- int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7;
- for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l))
- if (beg>>s == end>>s) return t + (beg>>s);
- return 0;
-}
-
-static inline int hts_bin_bot(int bin, int n_lvls)
-{
- int l, b;
- for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); // compute the level of bin
- return (bin - hts_bin_first(l)) << (n_lvls - l) * 3;
-}
-
-/**************
- * Endianness *
- **************/
-
-static inline int ed_is_big(void)
-{
- long one= 1;
- return !(*((char *)(&one)));
-}
-static inline uint16_t ed_swap_2(uint16_t v)
-{
- return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
-}
-static inline void *ed_swap_2p(void *x)
-{
- *(uint16_t*)x = ed_swap_2(*(uint16_t*)x);
- return x;
-}
-static inline uint32_t ed_swap_4(uint32_t v)
-{
- v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
- return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
-}
-static inline void *ed_swap_4p(void *x)
-{
- *(uint32_t*)x = ed_swap_4(*(uint32_t*)x);
- return x;
-}
-static inline uint64_t ed_swap_8(uint64_t v)
-{
- v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
- v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
- return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
-}
-static inline void *ed_swap_8p(void *x)
-{
- *(uint64_t*)x = ed_swap_8(*(uint64_t*)x);
- return x;
-}
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
=====================================
tabix.1
=====================================
@@ -1,4 +1,4 @@
-.TH tabix 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH tabix 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
.SH NAME
.PP
tabix \- Generic indexer for TAB-delimited genome position files
=====================================
version.sh
=====================================
@@ -24,7 +24,7 @@
# DEALINGS IN THE SOFTWARE.
# Master version, for use in tarballs or non-git source copies
-VERSION=1.10.1
+VERSION=1.10.2
# If we have a git clone, then check against the current tag
if [ -e .git ]
View it on GitLab: https://salsa.debian.org/med-team/htslib/commit/beef2a3aeafd0d7a08dc3c74dff23c36843ca77f
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/commit/beef2a3aeafd0d7a08dc3c74dff23c36843ca77f
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