New 1.2 versions of Samtools and BCFtools and a 1.2.1 version of HTSlib have been released. These provide improvements in CRAM support and variant calling, as well as a number of bug fixes and speed improvements. (The 1.2 HTSlib release was immediately superseded by 1.2.1 when a compatibilty issue with previous HTSlib releases was identified.)
These releases can be found at <http://www.htslib.org/>. Development and source code of these projects are linked from that web site and can be found in various Git repositories under <https://github.com/samtools>. Release archives are now being made available at both GitHub and SourceForge. Installing the tools will also install manual pages for them. Once installed, you should be able to use "man samtools" etc at your command line to find details of new commands and functionality. Manual pages and other documentation are also available online at <http://www.htslib.org/doc/>. John Noteworthy changes in BCFtools: * new consensus command * new annotate plugins: fixploidy, vcf2sex, tag2tag * more features in convert command, amongst others new --hapsample function (thanks to Warren Kretzschmar) * support for complements in bcftools annotate --remove * support for -i/-e filtering expressions in isec * improved error reporting * call command changes: - the default prior increased from -P1e-3 to -P1.1e-3, some clear calls were missed with default settings previously - support for the new symbolic allele <*> - support for -f GQ - bug fixes, such as: proper trimming of DPR tag with -c; the -A switch does not add back records removed by -v and the behaviour has been made consistent with -c and -m * many bug fixes and improvements, such as - bug in filtering, FMT & INFO vs INFO & FMT - fixes in bcftools merge - filter update AN/AC with -S - isec outputs matching records for both VCFs in the Venn mode - annotate considers alleles when working with Number=A,R tags - new --set-id feature for annotate - convert can be used similarly to view Noteworthy changes in Samtools: * Flagstat now works on SAM, BAM, or CRAM files (rather than BAM only) * Stats calculates mismatches per cycle for unclipped length * Merge can now merge SAM input files * CRAM reference files are now cached by default (see HTSlib below and samtools(1) man page) * Tested against Intel-optimised zlib (https://github.com/jtkukunas/zlib; see README for details) * Fixed bugs #302, #309, #318, and #327 Noteworthy changes in HTSlib: * HTSlib now has a configure script which checks your build environment and allows for selection of optional extras. See INSTALL for details * By default, reference sequences are fetched from the EBI CRAM Reference Registry and cached in your $HOME cache directory. This behaviour can be controlled by setting REF_PATH and REF_CACHE enviroment variables (see the samtools(1) man page for details) * Numerous CRAM improvements: - Support for CRAM v3.0, an upcoming revision to CRAM supporting better compression and per-container checksums - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks) - Non-standard values for PNEXT and TLEN fields are now preserved - hts_set_fai_filename() now provides a reference file when encoding - Generated read names are now numbered from 1, rather than being labelled slice:record-in-slice - Multi-threading and speed improvements * New htsfile command for identifying file formats, and corresponding file format detection APIs * New tabix --regions FILE, --targets FILE options for filtering via BED files * Optional iRODS file access, disabled by default. Configure with --with-irods to enable accessing iRODS data objects directly via irods:DATAOBJ * All occurences of 2^29 in the source have been eliminated, so indexing and querying against reference sequences larger than 512Mbp works (when using CSI indices) * Support for plain GZIP compression in various places * VCF header editing speed improvements * Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table[]) * Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1. Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually faidx_fetch_nseq() will be deprecated and removed [#156] * Reinstated hts_file_type() and FT_* macros, which were available until 1.1 but briefly removed in 1.2. This function is deprecated and will be removed in a future release -- you should use hts_detect_format() etc instead * Fixed bugs #141, #152, #155, #158, #159, and various memory leaks (Numbers in the form #NNN refer to corresponding issue numbers in the relevant GitHub repository.) -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
