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master branch has become main

Yearly copyright update - 2022

Remove perl 5.10 testing in travis

Yearly copyright update

Delete DISCLAIMER

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.

Yearly copyright update

Build.PL: Improve pkgconfig integration

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.

Build.PL: allow explicit definition of hts_include and hts_lib

Release 3.01.

copyright update

Documentation fixes

These are described in HTSlib as of samtools/htslib@445b0d721eb391e8825b5f07b9ebf8f72ef93367.

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.

Ignore .gzi index files and clean test output files

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.

Reuse bcf_get_info/_format API buffers

Similarly to the previous commit, track the buffers' maximum sizes
and reuse them throughout vcfrow_get_info().

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.

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.