SAM tools Files

The 1.2.1 release of HTSlib and the 1.2 releases of Samtools and BCFtools provide substantial 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 (The 1.2 HTSlib release was immediately superseded by 1.2.1 when a compatibilty issue with previous HTSlib releases was identified.)

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 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 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.)