The interactive file manager requires Javascript. Please enable it or use sftp or scp.
You may still browse the files here.
Get an email when there's a new version of SAM tools
| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.md.txt | 2017-06-21 | 2.5 kB | |
| bcftools-1.5.tar.bz2 | 2017-06-21 | 3.0 MB | |
| htslib-1.5.tar.bz2 | 2017-06-21 | 1.1 MB | |
| samtools-1.5.tar.bz2 | 2017-06-21 | 4.2 MB | |
| Totals: 4 Items | 8.2 MB | 1 | |
------------------------------------------------------------------------------ htslib - changes v1.5 ------------------------------------------------------------------------------ * Added a new logging API: hts_log(), along with hts_log_error(), hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan for the implementation. (#499, #543, #551) * Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to alter the hFILE buffer size. * Fixed various bugs, including compilation issues samtools/bcftools#610, samtools/bcftools#611 and robustness to corrupted data #537, #538, #541, #546, #548, #549, #554. ------------------------------------------------------------------------------ samtools - changes v1.5 ------------------------------------------------------------------------------ * Samtools fastq now has a -i option to create a fastq file from an index tag, and a -T option (similar to -t) to add user specified aux tags to the fastq header line. * Samtools fastq can now create compressed fastq files, by giving the output filenames an extention of .gq, .bgz, or .bgzf * Samtools sort has a -t TAG option, that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged. (#675; thanks to Patrick Marks of 10xgenomics). ------------------------------------------------------------------------------ BCFtools - changes v1.5 ------------------------------------------------------------------------------ * Added autoconf support to bcftools. See `INSTALL` for more details. * `norm`: Make norm case insensitive (#601). Trim the reference allele (#602). * `mpileup`: fix for misreported indel depths for reads containing adjacent indels (3c1205c1). * `plot-vcfstats`: Open stats file in text mode, not binary (#618). * `fixref` plugin: Allow multiallelic sites in the `-i, --use-id reference`. Also flip genotypes, not just REF/ALT! * `merge`: fix gVCF merge bug when last record on a chromosome opened a gVCF block (#616) * New options added to the ROH plotting script. * `consensus`: Properly flush chain info (#606, thanks to @krooijers). * New `+prune` plugin for pruning sites by LD (R2) or maximum number of records within a window. * New N_MISSING, F_MISSING (number and fraction missing) filtering expressions. * Fix HMM initialization in `roh` when snapshots are used in multiple chromosome VCF. * Fix buffer overflow (#607) in `filter`.