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htslib

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    More general CRAM multi-threading fixes (not related to multi-slice).
    James Bonfield authored and Rob Davies committed 
    These were spotted by gcc -fsanitize=thread.

1. Decoding: fd->no_ref is set while decoding the compression header
and used in subsequent slice decodes, but we may then decode the next
container compression header before the previous slices have finished
decoding.

2. Decoding: avoid race when limiting data via required_fields.

fd->decode_md is now copied to s->decode_md, so the slice can disable
this itself if required (such as when the user asked for MD tag to be
filled out while also asking not to return any auxiliary blocks).

Although technically fixing a threading violation, the practical
implementations means this is just a tidyup rather than any real
behavior changes.

3. Encoding: Cram_encode_aux needed an extra guard surrounding the
fd->tags_used field.  This is used to hold tag types seen so far in
the file, within any container or block, so we can keep track of the
compression methods that work best for a any specific tag type.
    1c4acb41
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    user avatar 1c4acb41
    History
    Name Last commit Last update
    cram
    htslib
    m4
    os
    test
    .appveyor.yml
    .gitattributes
    .gitignore
    .travis.yml
    INSTALL
    LICENSE
    Makefile
    NEWS
    README
    README.md
    bcf_sr_sort.c
    bcf_sr_sort.h
    bgzf.c
    bgzip.c
    config.mk.in
    configure.ac
    errmod.c
    faidx.5
    faidx.c
    hfile.c
    hfile_gcs.c
    hfile_internal.h
    hfile_libcurl.c
    hfile_net.c
    hfile_s3.c
    hts.c
    hts_internal.h
    hts_os.c
    htsfile.1
    htsfile.c
    htslib.mk
    htslib.pc.in
    htslib_vars.mk
    kfunc.c
    knetfile.c
    kstring.c
    md5.c
    multipart.c
    plugin.c
    probaln.c
    realn.c
    regidx.c
    sam.5
    sam.c
    synced_bcf_reader.c
    tabix.1
    tabix.c
    tbx.c
    textutils.c
    textutils_internal.h
    thread_pool.c
    thread_pool_internal.h
    vcf.5
    vcf.c
    vcf_sweep.c
    vcfutils.c
    version.sh
    README.md

    HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

    HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

    This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and the bgzip compression utility.

    Building HTSlib

    See INSTALL for complete details. Release tarballs contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:

    autoheader     # If using configure, generate the header template...
autoconf       # ...and configure script (or use autoreconf to do both)
./configure    # Optional, needed for choosing optional functionality
make
make install