3.01 * HTSlib 1.9 compatibility * CentOS 7 compatible installation, courtesy of John Marshall * BioPerl version agnostic installation process * bugfix #75: reset versioning to avoid confusing perl runtime * bugfix #81: install in sudo-less environments, e.g. docker containers PR#83 - https://github.com/Ensembl/Bio-DB-HTS/pull/83, courtesy of John Marshall * bugfix #76, #82 - memory leaks due to improper use of bcf_get_format_float/_char/_int32() buffers PR#84 - https://github.com/Ensembl/Bio-DB-HTS/pull/84, courtesy of John Marshall * Ignore .gzi index files and clean test output files PR#87 - https://github.com/Ensembl/Bio-DB-HTS/pull/87, courtesy of John Marshall * Documentation fixes 2.11 * VCF/BCF interface enhancements: - retrieve header formatted text - fetch all info/format fields in a row - query arbitrary regions over tabix indexed VCF or CSI indexed BCF files PR#68 - https://github.com/Ensembl/Bio-DB-HTS/pull/68 courtesy of John Marshall * Refcount-based fix for index memory releasing problem PR#71 - https://github.com/Ensembl/Bio-DB-HTS/pull/71 courtesy of Rob Aganrab * fix minor POD issues 2.10 * Tabix changes: header represented as empty string when none is available; querying over an unrecognised seq region returns undefined, not an iterator * Bugfix: read SAM header when iterating over alignments, see issue #54 * Bugfix: could not handle sorting when building index for CRAM files PR#64 - https://github.com/Ensembl/Bio-DB-HTS/pull/64, courtesy of John Marshall * Implement filter for features of type coverage * Minor warning, memory leak and typo fixes PR#58 - https://github.com/Ensembl/Bio-DB-HTS/pull/58, courtesy of Keiran Raine * Minimal support for BAM with csi index (no index generation) 2.9 PR#50 - https://github.com/Ensembl/Bio-DB-HTS/pull/50 * Guarantee resource deallocation by adding DESTROY methods to replace close methods * add Bio::DB::HTS::VCF::HeaderPtr and Bio::DB::HTS::VCF::RowPtr packages 2.8 * Use the htslib his_remote function to determine which files are remote * Add output filename to wget functon in install script, courtesy of Zhicheng Liu * Use htslib v1.5 by default in install script * Use filetest access to allow POSIX ACLs, courtesy of Can Wood * Copyright updates * Update TravisCI Perl test versions 2.7 * change BioPerl version required in Build.PL to be 1.6.1 2.6 * tabix index files downloaded by default to system tmp directory * bugfix - Specify correct end when calling coverage if none specified * Create a way to Tabix query against chr containing ':', courtesy of Keiran Raine 2.5 * added CRAM/BAM writing, courtesy of Dietmar Rieder * CRAM read test reference embedded in CRAM file to allow test to pass when CRAM reference archive is unavailable 2.4 * github repo move to https://github.com/Ensembl/Bio-DB-HTS * -Wformat=no removed from build options * check results of archive fetches 2.3 * cram tests moved to the scripts directory to allow install when CRAM reference archive is unavailable 2.2 * Zip file downloads during install * HTSlib version set to 1.3.1 or specified parameter during install * https for remote file prefix check added, courtesy of Zhicheng-Liu 2.1 * add missing test file to manifest 2.0 * BCF addition * Kseq addition: courtesy of Andrew Yates and Chris Fields * Tabix bugfixes: see GitHub issue #17 * licence updated 1.13 * removed file existence Tabix check as it prevents remote access * Tabix bugfix * Build git clone commands use branch and depth options 1.12 * Build procedure static option added, courtesy of David Jones * TravisCI tests added * build_options script added to demonstrate build options * cpanfile updates 1.11 * FAIDX memory leak fix, courtesy Andy Yates & Keiran Raine * INSTALL.pl to local directory, courtesy Keiran Raine * documentation updates 1.10 * Tabix header_array subroutine added * Tabix DEMOLISH routines renamed close for consistency 1.09 * Tabix header subroutine, test added * README clarifications * prompt removed from install script 1.08 * Added missing test files 1.07 * Build.PL updated, courtesy of James Gilbert. * TABIX bindings added, courtesy of Alex Hodgkins, Congenica Ltd. 1.06 * htslib directory parameter added for perl Build.PL * faidx include directory bug fix added 1.05 * CRAM tests added * cpanfile added 1.04 * FAIDX added 1.03 * license field corrected in Build.PL * Version numbers added to PM files * Alien::HTSlib module referred to 1.02 * Version numbers added to PM files 1.01 * Package renaming 1.00 * First full release of htslib port from Bio::DB::Sam