[med-svn] [htslib] branch debian/unstable updated (d6cab91 -> e8b1b66)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch debian/unstable
in repository htslib.

      from  d6cab91   add the cram_to_bam function to the public interface of htslib because it is used by code in Sambamba
       new  e880f57   Use -lpthread instead of -pthread when only linking; Fixes clang warning
      adds  879855b   Merge version number bump and NEWS file from master
       new  e2a1f18   Merge PR #255 into develop.
       new  e2a5578   Added tabix to the "make test" dependency.
       new  10bc1a7   Tweak to tabix long opts to remove duplicate 'h'.
       new  10081c4   add test-bcf-sr to .gitignore [minor]
       new  9986f5d   Fixed kputd printing of NaN.
       new  3a31ddf   Add check for libsocket to autoconf (needed to compile on illumos/Solaris)
       new  052a16e   Merge check for libsocket (commit 3a31ddf from PR#488)
       new  e7203ae   Fixed a bug in bcf_fmt_array with garbage allele frequencies. The special value 0x7f800001 (NaN), used to indicate a missing value, was changed to 0x7fc00001 (also NaN) when the function le_to_float returned.
       new  150334c   Handling of float-type missing values in VCF files, part 2 of 3: bcf_get_info_values.
       new  dd0c31d   Handling of float-type missing values in VCF files, part 3 of 3: bcf_get_format_values.
       new  cf469f6   Replaced memcpy with the more descriptive bcf_float_set_missing in vcf_parse.
       new  55e6404   oops
       new  b7bb8c7   Reordered test cases so that the output file ends up the way it's supposed to.
       new  9db2e71   Made the changes slightly smaller through the use of bcf_float_set.
       new  487f367   Merge Merge NaN issue fix (PR#485)
       new  a17fc73   Fixes to support a stricter C99 plus POSIX.1-2001 environment.
       new  65267c7   Replaces the itf8* macro abominations with static inline functions.
       new  b30fc6a   Tidy up non-standard C99 issues.
       new  ff8f83a   Merge C99 compliance improvements (PR#498)
       new  af89ccb   Free file name strings upon successful faidx loading
       new  9317ca6   Ensure B aux tags have a comma after the type charater
       new  1acad45   Fix buffer overrun on corrupted data.
       new  1e1bf97   Harden rANS decoding against malicious or random input.
       new  b1b2816   CRAM check for embedded references being too small for slice.
       new  2270547   Further rANS protections.
       new  0f60c35   Ensure BGZF block length is longer than the block header
       new  42bfe70   Check number of symbols is sensible in Huffman codec stream
       new  6a50863   Make bcf_set_variant_type() aware of breakends
       new  bb15901   Improve end of name detection in fai_read
       new  cd26782   Improve fai_fetch() and faidx_fetch_seq()
       new  74cd222   Prevent fai_retrieve() from reading one character too many
       new  8e1be4a   Change isspace to isspace_c
       new  ae4f3df   Ensure bcf_hdr_read() is reading vcf or bcf
       new  079c7b8   Limit query name to 251 bytes to prevent l_qname overflow
       new  8e96d8a   Bug fix in VCF/BCF header parsing
       new  affe5c0   Ensure bcf_hdr_t is destroyed when bcf_hdr_parse() fails
       new  94accfc   Ensure bcf_hdr_parse_line() always finishes at the next newline or NUL
       new  b8c6f7d   Simplify bcf_hdr_parse()
       new  72a7c2a   Trivial SAM header sanitising.
       new  0639ea1   Improve sam_hdr_sanitise()
       new  89ea70a   NEWS update. (#529)
       new  6c06833   Release 1.4.1: summary
       new  e8b1b66   Merge tag '1.4.1' into debian/unstable

The 44 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore           |   1 +
 Makefile             |  48 +++++----
 NEWS                 |  22 +++-
 bcf_sr_sort.c        |   2 +
 bgzf.c               |  11 +-
 bgzip.c              |   1 -
 configure.ac         |   5 +
 cram/cram_codecs.c   |  23 +++-
 cram/cram_decode.c   |   4 +
 cram/cram_io.c       | 290 +++++++++------------------------------------------
 cram/cram_io.h       | 209 ++++++++++++++++++++++++++++++++-----
 cram/cram_samtools.c |   2 +
 cram/rANS_byte.h     |   4 +-
 cram/rANS_static.c   |  47 +++++++--
 faidx.c              | 133 +++++++++++++++--------
 hfile.c              |   2 +-
 hts.c                |   8 +-
 htsfile.1            |   2 +-
 htslib/vcf.h         |  10 +-
 kstring.c            |   2 +-
 regidx.c             |   1 +
 sam.c                |  97 ++++++++++++++++-
 synced_bcf_reader.c  |   3 +-
 tabix.1              |   2 +-
 tabix.c              |   2 +-
 test/test-vcf-api.c  | 119 ++++++++++++++++++++-
 thread_pool.c        |   3 -
 vcf.c                | 228 +++++++++++++++++++++++++---------------
 28 files changed, 829 insertions(+), 452 deletions(-)

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