[med-svn] [htslib] annotated tag 1.4.1 created (now 1e1d9ec)

[Andreas Tille]

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

tille pushed a change to annotated tag 1.4.1
in repository htslib.

        at  1e1d9ec   (tag)
   tagging  6c06833519551eb61d4e5b9aceb2383e21996930 (commit)
  replaces  1.4
 tagged by  jenniferliddle
        on  Mon May 8 11:10:35 2017 +0100

- Log -----------------------------------------------------------------
Noteworthy changes in release 1.4.1  (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is primarily a security bug fix update.

* Fixed SECURITY issue with buffer overruns with malicious data. (#514).

* S3 support for non Amazon AWS endpoints. (#506)

* Support for variant breakpoints in bcftools. (#516)

* Improved handling of BCF NaNs. (#485)

* Compilation / portability improvements. (#255, #423, #498, #488)

* Miscellaneous bug fixes (#482, #521, #522, #523, #524).

* Sanitise headers (#509)

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Anders Kaplan (7):
      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.
      Handling of float-type missing values in VCF files, part 2 of 3: bcf_get_info_values.
      Handling of float-type missing values in VCF files, part 3 of 3: bcf_get_format_values.
      Replaced memcpy with the more descriptive bcf_float_set_missing in vcf_parse.
      oops
      Reordered test cases so that the output file ends up the way it's supposed to.
      Made the changes slightly smaller through the use of bcf_float_set.

Isaac Turner (1):
      Use -lpthread instead of -pthread when only linking; Fixes clang warning

James Blachly (1):
      Add check for libsocket to autoconf (needed to compile on illumos/Solaris)

James Bonfield (13):
      Merge PR #255 into develop.
      Added tabix to the "make test" dependency.
      Tweak to tabix long opts to remove duplicate 'h'.
      Fixes to support a stricter C99 plus POSIX.1-2001 environment.
      Replaces the itf8* macro abominations with static inline functions.
      Tidy up non-standard C99 issues.
      Fixed kputd printing of NaN.
      Fix buffer overrun on corrupted data.
      Harden rANS decoding against malicious or random input.
      CRAM check for embedded references being too small for slice.
      Further rANS protections.
      Trivial SAM header sanitising.
      NEWS update. (#529)

Petr Danecek (3):
      Free file name strings upon successful faidx loading
      Make bcf_set_variant_type() aware of breakends
      Bug fix in VCF/BCF header parsing

Rob Davies (16):
      Merge check for libsocket (commit 3a31ddf from PR#488)
      Merge Merge NaN issue fix (PR#485)
      Merge C99 compliance improvements (PR#498)
      Ensure B aux tags have a comma after the type charater
      Ensure BGZF block length is longer than the block header
      Check number of symbols is sensible in Huffman codec stream
      Improve end of name detection in fai_read
      Improve fai_fetch() and faidx_fetch_seq()
      Prevent fai_retrieve() from reading one character too many
      Change isspace to isspace_c
      Ensure bcf_hdr_read() is reading vcf or bcf
      Limit query name to 251 bytes to prevent l_qname overflow
      Ensure bcf_hdr_t is destroyed when bcf_hdr_parse() fails
      Ensure bcf_hdr_parse_line() always finishes at the next newline or NUL
      Simplify bcf_hdr_parse()
      Improve sam_hdr_sanitise()

Shane McCarthy (1):
      add test-bcf-sr to .gitignore [minor]

jenniferliddle (2):
      Merge version number bump and NEWS file from master
      Release 1.4.1: summary

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