New upstream version 1.9

============

Building HTSlib requires a few programs and libraries to be present.

See the "System Specific Details" below for guidance on how to install

these.

At least the following are required:

    GNU make

from the library.  Note that some Linux distributions put include files in

a development ('-dev' or '-devel') package separate from the main library.

    libz       (required)

    zlib       (required)

    libbz2     (required, unless configured with --disable-bz2)

    liblzma    (required, unless configured with --disable-lzma)

    libcurl    (optional, but strongly recommended)

    make DESTDIR=/tmp/staging prefix=/opt

would install into bin, lib, etc subdirectories under /tmp/staging/opt.

System Specific Details

=======================

Installing the prerequisites is system dependent and there is more

than one correct way of satisfying these, including downloading them

from source, compiling and installing them yourself.

For people with super-user access, we provide an example set of commands

below for installing the dependencies on a variety of operating system

distributions.  Note these are not specific recommendations on distribution,

compiler or SSL implementation.  It is assumed you already have the core set

of packages for the given distribution - the lists may be incomplete if

this is not the case.

Debian / Ubuntu

---------------

sudo apt-get update  # Ensure the package list is up to date

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev

Note: libcurl4-openssl-dev can be used as an alternative to libcurl4-gnutls-dev.

RedHat / CentOS

---------------

sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel

Alpine Linux

------------

sudo apk update  # Ensure the package list is up to date

sudo apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev

OpenSUSE

--------

sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel

The MIT/Expat License

Copyright (C) 2012-2014 Genome Research Ltd.

Copyright (C) 2012-2018 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

The Modified-BSD License

Copyright (C) 2012-2014 Genome Research Ltd.

Copyright (C) 2012-2018 Genome Research Ltd.

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:

cram_os_h = cram/os.h $(htslib_hts_endian_h)

cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)

cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)

cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h $(htslib_khash_h)

cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h cram/mFILE.h $(htslib_khash_h)

cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h

bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h)

hfile_internal_h = hfile_internal.h $(htslib_hfile_h) $(textutils_internal_h)

hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)

textutils_internal_h = textutils_internal.h $(htslib_kstring_h)

	$(CC) -shared $(LDFLAGS) -o $@ $< hts.dll.a $(LIBS)

bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) cram/pooled_alloc.h $(htslib_khash_h)

errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h)

bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) cram/pooled_alloc.h $(htslib_khash_h)

errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h) $(htslib_hts_os_h)

kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)

knetfile.o knetfile.pico: knetfile.c config.h $(htslib_hts_log_h) $(htslib_knetfile_h)

hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)

hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)

hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)

hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)

hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)

hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)

hts.o hts.pico: hts.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(hfile_internal_h) $(htslib_hfile_h) version.h $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h)

hts.o hts.pico: hts.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_hts_endian_h) version.h $(hts_internal_h) $(hfile_internal_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h)

hts_os.o hts_os.pico: hts_os.c config.h os/rand.c

vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h)

sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_hts_endian_h)

tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(hts_internal_h) $(htslib_khash_h)

tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_hts_endian_h) $(hts_internal_h) $(htslib_khash_h)

faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) $(hts_internal_h)

bcf_sr_sort.o bcf_sr_sort.pico: bcf_sr_sort.c config.h bcf_sr_sort.h $(htslib_kseq_h) $(htslib_khash_str2int_h)

synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) $(htslib_thread_pool_h)

bcf_sr_sort.o bcf_sr_sort.pico: bcf_sr_sort.c config.h $(bcf_sr_sort_h) $(htslib_khash_str2int_h)

synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) $(htslib_thread_pool_h) $(bcf_sr_sort_h)

vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)

vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)

kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)

cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)

cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)

cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)

cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h

cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h $(cram_os_h) $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)

cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.h

cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h $(cram_os_h) $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) $(htslib_hts_log_h)

cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)

cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h

cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h

cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(htslib_hts_log_h) $(cram_sam_header_h) cram/string_alloc.h

cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h

thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h)

	test/hfile

	test/test_bgzf test/bgziptest.txt

	cd test/tabix && ./test-tabix.sh tabix.tst

	REF_PATH=: test/sam test/ce.fa test/faidx.fa

	REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq

	test/test-regidx

	cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}

test/test-bcf-translate: test/test-bcf-translate.o libhts.a

	$(CC) $(LDFLAGS) -o $@ test/test-bcf-translate.o libhts.a -lz $(LIBS) -lpthread

test/hts_endian.o: test/hts_endian.c $(htslib_hts_endian_h)

test/hts_endian.o: test/hts_endian.c config.h $(htslib_hts_endian_h)

test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)

test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)

test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)

test/test_bgzf.o: test/test_bgzf.c $(htslib_bgzf_h) $(htslib_hfile_h)

test/test-realn.o: test/test_realn.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h)

test/test_bgzf.o: test/test_bgzf.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hfile_internal_h)

test/test-realn.o: test/test_realn.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h)

test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h) $(hts_internal_h)

test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)

test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)

test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)

test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_vcf_sweep_h) bcf_sr_sort.h

test/test-bcf-translate.o: test/test-bcf-translate.c config.h

test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_synced_bcf_reader_h)

test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)

test/thrash_threads1: test/thrash_threads1.o libhts.a

Noteworthy changes in release 1.9 (18th July 2018)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* If `./configure` fails, `make` will stop working until either configure

  is re-run successfully, or `make distclean` is used.  This makes

  configuration failures more obvious.  (#711, thanks to John Marshall)

* The default SAM version has been changed to 1.6.  This is in line with the

  latest version specification and indicates that HTSlib supports the

  CG tag used to store long CIGAR data in BAM format.

* bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner)

* Faidx can now index fastq files as well as fasta.  The fastq index adds

  an extra column to the `.fai` index which gives the offset to the quality

  values.  New interfaces have been added to `htslib/faidx.h` to read the

  fastq index and retrieve the quality values.  It is possible to open

  a fastq index as if fasta (only sequences will be returned), but not

  the other way round. (#701)

* New API interfaces to add or update integer, float and array aux tags. (#694)

* Add `level=<number>` option to `hts_set_opt()` to allow the compression

  level to be set.  Setting `level=0` enables uncompressed output. (#715)

* Improved bgzip error reporting.

* Better error reporting when CRAM reference files can't be opened. (#706)

* Fixes to make tests work properly on Windows/MinGW - mainly to handle

  line ending differences. (#716)

* Efficiency improvements:

  - Small speed-up for CRAM indexing.

  - Reduce the number of unnecessary wake-ups in the thread pool. (#703)

  - Avoid some memory copies when writing data, notably for uncompressed

    BGZF output. (#703)

* Bug fixes:

  - Fix multi-region iterator bugs on CRAM files. (#684)

  - Fixed multi-region iterator bug that caused some reads to be skipped

    incorrectly when reading BAM files. (#687)

  - Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691,

    reported by @freeseek)

  - Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary

    when removing samples. (#692, reported by @freeseek)

  - Fixed bug where the VCF record ref length was calculated incorrectly

    if an INFO END tag was present. (71b00a)

  - Fixed warnings found when compiling with gcc 8.1.0. (#700)

  - sam_hdr_read() and sam_hdr_write() will now return an error code

    if passed a NULL file pointer, instead of crashing.

  - Fixed possible negative array look-up in sam_parse1() that somehow

    escaped previous fuzz testing. (#731, reported by @fCorleone)

  - Fixed bug where cram range queries could incorrectly report an error

    when using multiple threads. (#734, reported by Brent Pedersen)

  - Fixed very rare rANS normalisation bug that could cause an assertion

    failure when writing CRAM files.  (#739, reported by @carsonhh)

Noteworthy changes in release 1.8 (3rd April 2018)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    THE SOFTWARE.

*/

#include <config.h>

#include <strings.h>

#include "bcf_sr_sort.h"

    memset(srt,0,sizeof(sr_sort_t));

    return srt;

}

void bcf_sr_sort_reset(sr_sort_t *srt)

{

    srt->chr = NULL;

}

void bcf_sr_sort_destroy(sr_sort_t *srt)

{

    free(srt->active);