NAME
    Bio::HTS - XS module providing an interface to htslib

DESCRIPTION
    The beginnings of an XS wrapper around the many useful methods in
    htslib. All the other perl modules use the old samtools or aren't on
    cpan.

    So far only Tabix is supported.

    Contributions welcome on github:
    <http://www.github.com/congenica/perl_htslib>

  Installation
    To install you will need a compiled copy of htslib (I wrote the code
    against htslib1.2.1, so use that)

    If you have done make install in htslib and htslib.so is installed
    system wide then I think it should just work.

    If you want to link to a htslib installed somewhere else you will need
    to add the install directory to your LD_LIBRARY_PATH environment
    variable BEFORE running cpanm -- the Build.PL script will search through
    all folders in LD_LIBRARY_PATH looking for libhts.so and a htslib
    subfolder containing .h files. Any perl script you run that uses
    Bio::HTS will need htslib in LD_LIBRARY_PATH.

    If it has installed but is not working, checking the linking of the .so
    file like so:

        ldd lib/arch/auto/Bio/HTS/HTS.so

        linux-vdso.so.1 =>  (0x00007fff34fff000)
        libhts.so.1     => not found
        libc.so.6       => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe398205000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fe3987e4000)

    libhts.so.1 is listed as not found, so the module will die when it is
    loaded. It is fixed by setting the LD_LIBRARY_PATH:

        export LD_LIBRARY_PATH=~/htslib-1.2.1

        ldd lib/arch/auto/Bio/HTS/HTS.so

        linux-vdso.so.1 =>  (0x00007fff34fff000)
        libhts.so.1 => /users/alex/htslib-1.2.1/libhts.so.1 (0x00007ff666ea6000)
        ...

LICENSE
    Licensed under the terms of the GNU AFFERO GENERAL PUBLIC LICENSE (AGPL)

COPYRIGHT
    Copyright 2015 Congenica Ltd.

AUTHOR
    Alex Hodgkins

