This project is mirrored from https://:*****@github.com/Ensembl/Bio-DB-HTS.git.
Pull mirroring updated .
- 11 Jan, 2023 1 commit
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Shashank Budhanuru Ramaraju authored
Copyright update 2023
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- 05 Jan, 2023 1 commit
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Shashank Budhanuru Ramaraju authored
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- 14 Apr, 2022 1 commit
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sgiorgetti authored
master branch has become main
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- 09 Mar, 2022 1 commit
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Stefano Giorgetti authored
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- 07 Jan, 2022 1 commit
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Tamara El Naboulsi authored
Yearly copyright update - 2022
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- 06 Jan, 2022 1 commit
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Tamara El Naboulsi authored
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- 21 Sep, 2021 1 commit
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Tamara El Naboulsi authored
Remove perl 5.10 testing in travis
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- 10 Sep, 2021 1 commit
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Tamara El Naboulsi authored
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- 11 Jan, 2021 1 commit
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Magali Ruffier authored
Yearly copyright update
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- 06 Jan, 2021 1 commit
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nwillhoft authored
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- 31 Jul, 2020 1 commit
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Magali Ruffier authored
Delete DISCLAIMER
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- 18 Jul, 2020 1 commit
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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.
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- 21 Jan, 2020 1 commit
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Tiago Grego authored
Yearly copyright update
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- 17 Jan, 2020 1 commit
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Tiago Grego authored
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- 02 Jan, 2020 1 commit
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Tiago Grego authored
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- 10 Jul, 2019 2 commits
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Kieron Taylor authored
Build.PL: Improve pkgconfig integration
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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.
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- 09 Jul, 2019 1 commit
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Tiago Grego authored
Build.PL: allow explicit definition of hts_include and hts_lib
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- 26 Apr, 2019 3 commits
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Tiago Grego authored
Release 3.01.
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Alessandro Vullo authored
copyright update
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Tiago Grego authored
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- 23 Apr, 2019 2 commits
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Alessandro Vullo authored
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Alessandro Vullo authored
Documentation fixes
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- 11 Apr, 2019 2 commits
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John Marshall authored
These are described in HTSlib as of samtools/htslib@445b0d721eb391e8825b5f07b9ebf8f72ef93367.
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John Marshall authored
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- 22 Mar, 2019 1 commit
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Alessandro Vullo authored
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- 08 Mar, 2019 1 commit
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Alessandro Vullo authored
no sudo available. In those cases, the installation step would fail as it invokes the command with sudo. Consider all possible cases and for each one check whether the step has actually installed the expected to system-dependent location.
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- 22 Feb, 2019 6 commits
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Alessandro Vullo authored
Ignore .gzi index files and clean test output files
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John Marshall authored
The .gzi index is generated alongside the .fai index when you faidx-index a compressed .fa file. Ignore such files, and remove the one that is in the repository. Also clean up the test output files (based on the list in .gitignore) when "./Build clean" is used.
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Alessandro Vullo authored
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Alessandro Vullo authored
Reuse bcf_get_info/_format API buffers
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John Marshall authored
Similarly to the previous commit, track the buffers' maximum sizes and reuse them throughout vcfrow_get_info().
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- 21 Feb, 2019 1 commit
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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.
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- 08 Feb, 2019 6 commits
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
Ensembl travis build problem solved. Move on and fix that later on, e.g. separate bioperl-1.7.4 installation during ensembl-(rest,production) build.
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Alessandro Vullo authored
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