This project is mirrored from https://github.com/Ensembl/Bio-DB-HTS.git. Pull mirroring updated .
  1. 21 Sep, 2021 1 commit
  2. 10 Sep, 2021 1 commit
  3. 11 Jan, 2021 1 commit
  4. 06 Jan, 2021 1 commit
  5. 31 Jul, 2020 1 commit
  6. 18 Jul, 2020 1 commit
    • Marek Szuba's avatar
      Delete DISCLAIMER · 75a2de15
      Marek Szuba authored
      This file talks about the old licence and a somewhat questionable one (it contains an indemnity clause) as well. Simply remove it so that it is clear Bio::DB::HTS is now licensed wholly under Apache-2.0.
      75a2de15
  7. 21 Jan, 2020 1 commit
  8. 17 Jan, 2020 1 commit
  9. 02 Jan, 2020 1 commit
  10. 10 Jul, 2019 2 commits
    • Kieron Taylor's avatar
      Merge pull request #74 from mkszuba/build-pkgconfig · 83c93272
      Kieron Taylor authored
      Build.PL: Improve pkgconfig integration
      83c93272
    • Marek Szuba's avatar
      Build.PL: Improve pkgconfig integration · fc8861a6
      Marek Szuba authored
      The old way of using pkgconfig in Build.PL has got a few shortcomings:
       - instead of retrieving both libdir and includedir, it only retrieves
         the former and transforms it into what it expects includedir to be
         (assuming in the process that libdir is .../lib and not e.g.
         .../lib64) - i.e. does the same as for all other ways of specifying
         location of htslib;
       - it directly accesses variables in htslib.pc instead of using --cflags
         and --libs, which is the recommended way;
       - it works by running the pkg-config executable so extending this would
         likely require processing the output of this command;
       - it still checks for the presence of hts.h and libhts.a/so, even
         though pkgconfig is supposed to return valid locations.
      
      This commit adds an alternative implementation of pkgconfig-based
      detection of htslib which retrieves both includedir and libdir, uses
      --cflags and --libs instead of accessing variables directly, and which
      avoids custom implementation of the handling of pkg-config output by
      using an existing Perl module designed for that purpose. It also extends
      set_include_and_compiler_flags() to handle the scenario of $hts_include
      and $hts_lib being empty, which is the case when --cflags/--libs are
      used and htslib has been installed to a standard prefix such as /usr.
      
      In order to retain backward compatibility, for the time being the new
      implementation is only invoked after all earlier attempts of locating
      htslib - including the old way of invoking pkg-config - have failed.
      Will leave it to the maintainers to decide whether to move this
      implementation up in the queue and/or retire any old detection modes.
      
      Note that this adds an optional build-time dependency on
      ExtUtils::PkgConfig.
      fc8861a6
  11. 09 Jul, 2019 1 commit
  12. 26 Apr, 2019 3 commits
  13. 23 Apr, 2019 2 commits
  14. 11 Apr, 2019 2 commits
  15. 22 Mar, 2019 1 commit
  16. 08 Mar, 2019 1 commit
  17. 22 Feb, 2019 6 commits
  18. 21 Feb, 2019 1 commit
    • John Marshall's avatar
      Reuse bcf_get_format_float/_char/_int32() buffers · 7ab8f572
      John Marshall authored
      These functions work by reallocating &buf/&max_buf (if necessary) each
      time they're called, and returning the number of buffer items used.
      Previous code called them with NULL/0 the first time but <dangling-ptr>/0
      on subsequent calls, as after each call the pointer was freed but not set
      to NULL.
      
      Fix the way the API is used by tracking the buffers' maximum sizes and
      reusing them throughout vcfrow_get_format().
      
      Fixes #76 and fixes #82.
      7ab8f572
  19. 08 Feb, 2019 7 commits
  20. 07 Feb, 2019 5 commits