[med-svn] [Git][med-team/htslib][master] 5 commits: New upstream version 1.10.1
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 17 13:50:07 GMT 2019
Andreas Tille pushed to branch master at Debian Med / htslib
Commits:
581cbb1d by Andreas Tille at 2019-12-17T13:37:11Z
New upstream version 1.10.1
- - - - -
1e5ac9f6 by Andreas Tille at 2019-12-17T13:37:13Z
Update upstream source from tag 'upstream/1.10.1'
Update to upstream version '1.10.1'
with Debian dir bdfed011fc46b46a73f03e9f40bd476b264ccbf8
- - - - -
c438eba1 by Andreas Tille at 2019-12-17T13:37:39Z
Refresh patches
- - - - -
feed9d29 by Andreas Tille at 2019-12-17T13:38:35Z
Fix syntax
- - - - -
df4af758 by Andreas Tille at 2019-12-17T13:48:36Z
Upload to unstable
- - - - -
16 changed files:
- Makefile
- NEWS
- README.large_positions.md
- configure
- debian/changelog
- debian/patches/fPIC.patch
- debian/patches/no_git_version
- debian/rules
- htslib/hts.h
- + htslib/hts.h~
- htslib/vcf.h
- test/longrefs/index.expected2.vcf
- test/longrefs/index.vcf
- test/test.pl
- vcf.c
- version.sh
Changes:
=====================================
Makefile
=====================================
@@ -30,6 +30,8 @@ RANLIB = ranlib
htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
CPPFLAGS =
+# TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
+# to CFLAGS manually, here or in config.mk if the latter exists.
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
=====================================
NEWS
=====================================
@@ -1,3 +1,15 @@
+Noteworthy changes in release a.b
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Noteworthy changes in release 1.10.1 (17th December 2019)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The support for 64-bit coordinates in VCF brought problems for files
+not conforming to VCF/BCF specification. While previous versions would
+make out-of-range values silently overflow creating nonsense values
+but parseable file, the version 1.10 would silently create an invalid BCF.
+
+
Noteworthy changes in release 1.10 (6th December 2019)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
=====================================
README.large_positions.md
=====================================
@@ -9,7 +9,9 @@ which have, or are expected to have, chromosomes longer than two gigabases.
Currently 64 bit positions can only be stored in SAM and VCF format files.
Binary BAM, CRAM and BCF cannot be used due to limitations in the formats
themselves. As SAM and VCF are text formats, they have no limit on the
-size of numeric values.
+size of numeric values. Note that while 64 bit positions are supported by
+default for SAM, for VCF they must be enabled explicitly at compile time
+by editing Makefile and adding -DVCF_ALLOW_INT64=1 to CFLAGS.
# Compatibility issues to check
=====================================
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.
+# Generated by GNU Autoconf 2.68 for HTSlib 1.10.1.
#
# 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'
-PACKAGE_STRING='HTSlib 1.10'
+PACKAGE_VERSION='1.10.1'
+PACKAGE_STRING='HTSlib 1.10.1'
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 to adapt to many kinds of systems.
+\`configure' configures HTSlib 1.10.1 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 $ac_init_help in
- short | recursive ) echo "Configuration of HTSlib 1.10:";;
+ short | recursive ) echo "Configuration of HTSlib 1.10.1:";;
esac
cat <<\_ACEOF
@@ -1413,7 +1413,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-HTSlib configure 1.10
+HTSlib configure 1.10.1
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, which was
+It was created by HTSlib $as_me 1.10.1, 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, which was
+This file was extended by HTSlib $as_me 1.10.1, 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
+HTSlib config.status 1.10.1
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-htslib (1.10-3) UNRELEASED; urgency=medium
+htslib (1.10.1-1) unstable; urgency=medium
+ * New upstream version
* for some very strange reason /usr/include/htslib/cram/cram.h is using the
private interface header.h. This is provided now in the
libhts-private-dev package rather than htslib-test
@@ -10,7 +11,7 @@ htslib (1.10-3) UNRELEASED; urgency=medium
* Fix Perl interpreter path
* Fix permissions of script
- -- Andreas Tille <tille at debian.org> Tue, 17 Dec 2019 11:31:46 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 17 Dec 2019 14:38:13 +0100
htslib (1.10-2) unstable; urgency=medium
=====================================
debian/patches/fPIC.patch
=====================================
@@ -3,9 +3,9 @@ Description: Build with -fPIC instead of -fpic
linking the library on s390x and sparc64.
Author: Adrian Bunk <bunk at debian.org>
---- htslib.orig/Makefile
-+++ htslib/Makefile
-@@ -34,7 +34,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -36,7 +36,7 @@ CPPFLAGS =
# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
CFLAGS = -g -Wall -O2 -fvisibility=hidden
=====================================
debian/patches/no_git_version
=====================================
@@ -1,9 +1,9 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Don't check git tags for versioning
---- htslib.orig/version.sh
-+++ htslib/version.sh
+--- a/version.sh
++++ b/version.sh
@@ -27,11 +27,11 @@
- VERSION=1.10
+ VERSION=1.10.1
# If we have a git clone, then check against the current tag
-if [ -e .git ]
=====================================
debian/rules
=====================================
@@ -85,7 +85,7 @@ override_dh_link:
find debian/htslib-test -name header.h
dh_link -phtslib-test usr/include/htslib/cram/header.h usr/share/htslib-test/header.h
-override_dh_fixperms
+override_dh_fixperms:
dh_fixperms
find debian -name simple_test_driver.sh -exec chmod +x \{\} \;
=====================================
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 101000
+#define HTS_VERSION 101001
/*!
@abstract Determine format by peeking at the start of a file
=====================================
htslib/hts.h~
=====================================
@@ -0,0 +1,1346 @@
+/// @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
=====================================
htslib/vcf.h
=====================================
@@ -1390,10 +1390,10 @@ static inline int bcf_enc_int1(kstring_t *s, int32_t x)
@param[out] q Location to store an updated value for p
@return The integer value, or zero if @p type is not valid.
-If @p type is not one of BCF_BT_INT8, BCF_BT_INT16 or BCF_BT_INT32, zero
-will be returned and @p *q will not be updated. Otherwise, the integer
-value will be returned and @p *q will be set to the memory location
-immediately following the integer value.
+If @p type is not one of BCF_BT_INT8, BCF_BT_INT16, BCF_BT_INT32 or
+BCF_BT_INT64, zero will be returned and @p *q will not be updated.
+Otherwise, the integer value will be returned and @p *q will be set
+to the memory location immediately following the integer value.
Cautious callers can detect invalid type codes by checking that *q has
actually been updated.
@@ -1411,7 +1411,7 @@ static inline int64_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q)
*q = (uint8_t*)p + 4;
return le_to_i32(p);
} else if (type == BCF_BT_INT64) {
- *q = (uint8_t*)p + 4;
+ *q = (uint8_t*)p + 8;
return le_to_i64(p);
} else { // Invalid type.
return 0;
=====================================
test/longrefs/index.expected2.vcf
=====================================
@@ -1 +1 @@
-1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000 PL 0,1,45
+1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000;QS=1,0 PL 0,1,45
=====================================
test/longrefs/index.vcf
=====================================
@@ -213,4 +213,4 @@
1 10010000107 . G <*> 0 . DP=1;I16=0,1,0,0,33,1089,0,0,29,841,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL 0,3,29
1 10010000108 . C <*> 0 . DP=1;I16=0,1,0,0,32,1024,0,0,29,841,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL 0,3,29
1 10010000109 . A <*> 0 . DP=1;I16=0,1,0,0,35,1225,0,0,29,841,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL 0,3,29
-1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000 PL 0,1,45
+1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000;QS=1,0 PL 0,1,45
=====================================
test/test.pl
=====================================
@@ -660,18 +660,19 @@ sub test_view
testv $opts, "./test_view $tv_args -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110";
testv $opts, "./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam";
- # VCF round trip
- unlink("longrefs/index.tmp.vcf.gz.csi"); # To stop vcf_hdr_read from reading a stale index
- testv $opts, "./test_view $tv_args -z -p longrefs/index.tmp.vcf.gz -x longrefs/index.tmp.vcf.gz.csi.otf -m 14 longrefs/index.vcf";
- testv $opts, "./test_view $tv_args -p longrefs/index.tmp.vcf_ longrefs/index.tmp.vcf.gz";
- testv $opts, "cmp longrefs/index.vcf longrefs/index.tmp.vcf_";
-
- # Build index and compare with on-the-fly one made earlier.
- test_compare $opts, "$$opts{path}/test_index -c longrefs/index.tmp.vcf.gz", "longrefs/index.tmp.vcf.gz.csi.otf", "longrefs/index.tmp.vcf.gz.csi", gz=>1;
-
- # test_view can't do indexed look-ups on vcf, but we can use tabix
- test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000100-10010000105 > longrefs/index.tmp.tabix1.vcf", "longrefs/index.expected1.vcf", "longrefs/index.tmp.tabix1.vcf", fix_newlines => 1;
- test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000120-10010000130 > longrefs/index.tmp.tabix2.vcf", "longrefs/index.expected2.vcf", "longrefs/index.tmp.tabix2.vcf", fix_newlines => 1;
+ # 64-bit positions are currently not compiled in by default for VCF
+ # # VCF round trip
+ # unlink("longrefs/index.tmp.vcf.gz.csi"); # To stop vcf_hdr_read from reading a stale index
+ # testv $opts, "./test_view $tv_args -z -p longrefs/index.tmp.vcf.gz -x longrefs/index.tmp.vcf.gz.csi.otf -m 14 longrefs/index.vcf";
+ # testv $opts, "./test_view $tv_args -p longrefs/index.tmp.vcf_ longrefs/index.tmp.vcf.gz";
+ # testv $opts, "cmp longrefs/index.vcf longrefs/index.tmp.vcf_";
+ #
+ # # Build index and compare with on-the-fly one made earlier.
+ # test_compare $opts, "$$opts{path}/test_index -c longrefs/index.tmp.vcf.gz", "longrefs/index.tmp.vcf.gz.csi.otf", "longrefs/index.tmp.vcf.gz.csi", gz=>1;
+ #
+ # # test_view can't do indexed look-ups on vcf, but we can use tabix
+ # test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000100-10010000105 > longrefs/index.tmp.tabix1.vcf", "longrefs/index.expected1.vcf", "longrefs/index.tmp.tabix1.vcf", fix_newlines => 1;
+ # test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000120-10010000130 > longrefs/index.tmp.tabix2.vcf", "longrefs/index.expected2.vcf", "longrefs/index.tmp.tabix2.vcf", fix_newlines => 1;
if ($test_view_failures == 0) {
passed($opts, "large position tests");
=====================================
vcf.c
=====================================
@@ -59,10 +59,26 @@ HTSLIB_EXPORT
uint32_t bcf_float_vector_end = 0x7F800002;
HTSLIB_EXPORT
-uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 3, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
static bcf_idinfo_t bcf_idinfo_def = { .info = { 15, 15, 15 }, .hrec = { NULL, NULL, NULL}, .id = -1 };
+/*
+ Partial support for 64-bit POS and Number=1 INFO tags.
+ Notes:
+ - the support for 64-bit values is motivated by POS and INFO/END for large genomes
+ - the use of 64-bit values does not conform to the specification
+ - cannot output 64-bit BCF and if it does, it is not compatible with anything
+ - experimental, use at your risk
+*/
+#ifdef VCF_ALLOW_INT64
+ #define BCF_MAX_BT_INT64 (0x7fffffffffffffff) /* INT64_MAX, for internal use only */
+ #define BCF_MIN_BT_INT64 -9223372036854775800LL /* INT64_MIN + 8, for internal use only */
+#endif
+
+#define BCF_IS_64BIT (1<<30)
+
+
static const char *dump_char(char *buffer, char c)
{
switch (c) {
@@ -1251,6 +1267,14 @@ static int bcf_dec_typed_int1_safe(uint8_t *p, uint8_t *end, uint8_t **q,
if (end - p < 4) return -1;
*q = p + 4;
*val = le_to_i32(p);
+#ifdef VCF_ALLOW_INT64
+ } else if (t == BCF_BT_INT64) {
+ // This case should never happen because there should be no 64-bit BCFs
+ // at all, definitely not coming from htslib
+ if (end - p < 8) return -1;
+ *q = p + 8;
+ *val = le_to_i64(p);
+#endif
} else {
return -1;
}
@@ -1290,6 +1314,9 @@ static int bcf_record_check(const bcf_hdr_t *hdr, bcf1_t *rec) {
uint32_t i, reports;
const uint32_t is_integer = ((1 << BCF_BT_INT8) |
(1 << BCF_BT_INT16) |
+#ifdef VCF_ALLOW_INT64
+ (1 << BCF_BT_INT64) |
+#endif
(1 << BCF_BT_INT32));
const uint32_t is_valid_type = (is_integer |
(1 << BCF_BT_NULL) |
@@ -1728,6 +1755,12 @@ int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v)
}
bcf1_sync(v); // check if the BCF record was modified
+ if ( v->unpacked & BCF_IS_64BIT )
+ {
+ hts_log_error("Data contains 64-bit values not representable in BCF. Please use VCF instead");
+ return -1;
+ }
+
BGZF *fp = hfp->fp.bgzf;
union {
uint32_t i;
@@ -2040,6 +2073,7 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
return 0; // FIXME: check for errs in this function
}
+#ifdef VCF_ALLOW_INT64
static int bcf_enc_long1(kstring_t *s, int64_t x) {
uint32_t e = 0;
if (x <= BCF_MAX_BT_INT32 && x >= BCF_MIN_BT_INT32)
@@ -2057,6 +2091,7 @@ static int bcf_enc_long1(kstring_t *s, int64_t x) {
}
return e == 0 ? 0 : -1;
}
+#endif
static inline int serialize_float_array(kstring_t *s, size_t n, const float *a) {
uint8_t *p;
@@ -2169,6 +2204,7 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p
{
if ( !bcf_hdr_nsamples(h) ) return 0;
+ static int extreme_int_warned = 0;
char *r, *t;
int j, l, m, g;
khint_t k;
@@ -2362,7 +2398,23 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p
int32_t *x = (int32_t*)(z->buf + z->size * m);
for (l = 0;; ++t) {
if (*t == '.') x[l++] = bcf_int32_missing, ++t; // ++t to skip "."
- else x[l++] = strtol(t, &t, 10);
+ else
+ {
+ errno = 0;
+ char *te;
+ long int tmp_val = strtol(t, &te, 10);
+ if ( te==t || errno!=0 || tmp_val<BCF_MIN_BT_INT32 || tmp_val>BCF_MAX_BT_INT32 )
+ {
+ if ( !extreme_int_warned )
+ {
+ hts_log_warning("Extreme FORMAT/%s value encountered and set to missing at %s:%"PRIhts_pos,h->id[BCF_DT_ID][fmt[j-1].key].key,bcf_seqname(h,v), v->pos+1);
+ extreme_int_warned = 1;
+ }
+ tmp_val = bcf_int32_missing;
+ }
+ x[l++] = tmp_val;
+ t = te;
+ }
if (*t != ',') break;
}
if ( !l ) x[l++] = bcf_int32_missing;
@@ -2469,6 +2521,7 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p
int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
{
+ static int extreme_int_warned = 0, negative_rlen_warned = 0;
int i = 0;
char *p, *q, *r, *t;
kstring_t *str;
@@ -2526,6 +2579,8 @@ int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
} else {
v->pos -= 1;
}
+ if (v->pos >= INT32_MAX)
+ v->unpacked |= BCF_IS_64BIT;
} else if (i == 2) { // ID
if (strcmp(p, ".")) bcf_enc_vchar(str, q - p, p);
else bcf_enc_size(str, 0, BCF_BT_CHAR);
@@ -2672,31 +2727,77 @@ int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
val_a = z;
}
if ((y>>4&0xf) == BCF_HT_INT) {
- // Allow first value only to be 64 bit
- // (for large END value)
- int64_t v64 = strtoll(val, &te, 10);
- if ( te==val ) { // conversion failed
- val_a[0] = bcf_int32_missing;
- v64 = bcf_int64_missing;
- } else {
- val_a[0] = v64 >= BCF_MIN_BT_INT32 && v64 <= BCF_MAX_BT_INT32 ? v64 : bcf_int32_missing;
+ i = 0, t = val;
+ int64_t val1;
+#ifdef VCF_ALLOW_INT64
+ int is_int64 = 0;
+ if ( n_val==1 )
+ {
+ errno = 0;
+ long long int tmp_val = strtoll(val, &te, 10);
+ if ( te==val ) tmp_val = bcf_int32_missing;
+ else if ( te==val || errno!=0 || tmp_val<BCF_MIN_BT_INT64 || tmp_val>BCF_MAX_BT_INT64 )
+ {
+ if ( !extreme_int_warned )
+ {
+ hts_log_warning("Extreme INFO/%s value encountered and set to missing at %s:%"PRIhts_pos,key,bcf_seqname(h,v), v->pos+1);
+ extreme_int_warned = 1;
+ }
+ tmp_val = bcf_int32_missing;
+ }
+ else
+ is_int64 = 1;
+ val1 = tmp_val;
+ t = te;
+ i = 1; // this is just to avoid adding another nested block...
}
- for (t = te; *t && *t != ','; t++);
- if (*t == ',') ++t;
- for (i = 1; i < n_val; ++i, ++t)
+#endif
+ for (; i < n_val; ++i, ++t)
{
- val_a[i] = strtol(t, &te, 10);
- if ( te==t ) // conversion failed
- val_a[i] = bcf_int32_missing;
+ errno = 0;
+ long int tmp_val = strtol(t, &te, 10);
+ if ( te==t ) tmp_val = bcf_int32_missing;
+ else if ( errno!=0 || tmp_val<BCF_MIN_BT_INT32 || tmp_val>BCF_MAX_BT_INT32 )
+ {
+ if ( !extreme_int_warned )
+ {
+ hts_log_warning("Extreme INFO/%s value encountered and set to missing at %s:%"PRIhts_pos,key,bcf_seqname(h,v), v->pos+1);
+ extreme_int_warned = 1;
+ }
+ tmp_val = bcf_int32_missing;
+ }
+ val_a[i] = tmp_val;
for (t = te; *t && *t != ','; t++);
}
if (n_val == 1) {
- bcf_enc_long1(str, v64);
+#ifdef VCF_ALLOW_INT64
+ if ( is_int64 )
+ {
+ v->unpacked |= BCF_IS_64BIT;
+ bcf_enc_long1(str, val1);
+ }
+ else
+ bcf_enc_int1(str, (int32_t)val1);
+#else
+ val1 = val_a[0];
+ bcf_enc_int1(str, (int32_t)val1);
+#endif
} else {
bcf_enc_vint(str, n_val, val_a, -1);
}
- if (strcmp(key, "END") == 0)
- v->rlen = v64 - v->pos;
+ if (n_val==1 && strcmp(key, "END") == 0)
+ {
+ if ( val1 <= v->pos )
+ {
+ if ( !negative_rlen_warned )
+ {
+ hts_log_warning("INFO/END=%"PRIhts_pos" is smaller than POS at %s:%"PRIhts_pos,val1,bcf_seqname(h,v),v->pos+1);
+ negative_rlen_warned = 1;
+ }
+ }
+ else
+ v->rlen = val1 - v->pos;
+ }
} else if ((y>>4&0xf) == BCF_HT_REAL) {
float *val_f = (float *)val_a;
for (i = 0, t = val; i < n_val; ++i, ++t)
@@ -3835,6 +3936,7 @@ int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const v
else
bcf_enc_vchar(&str, strlen((char*)values), (char*)values);
}
+#ifdef VCF_ALLOW_INT64
else if ( type==BCF_HT_LONG )
{
if (n != 1) {
@@ -3843,6 +3945,7 @@ int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const v
}
bcf_enc_long1(&str, *(int64_t *) values);
}
+#endif
else
{
hts_log_error("The type %d not implemented yet", type);
=====================================
version.sh
=====================================
@@ -24,7 +24,7 @@
# DEALINGS IN THE SOFTWARE.
# Master version, for use in tarballs or non-git source copies
-VERSION=1.10
+VERSION=1.10.1
# 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/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191217/744c5e18/attachment-0001.html>
More information about the debian-med-commit
mailing list