Mercurial > repos > youngkim > ezbamqc
comparison ezBAMQC/src/htslib/NEWS @ 0:dfa3745e5fd8
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| author | youngkim |
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| date | Thu, 24 Mar 2016 17:12:52 -0400 |
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| -1:000000000000 | 0:dfa3745e5fd8 |
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| 1 Noteworthy changes in release 1.2.1 (3 February 2015) | |
| 2 | |
| 3 * Reinstated hts_file_type() and FT_* macros, which were available until 1.1 | |
| 4 but briefly removed in 1.2. This function is deprecated and will be removed | |
| 5 in a future release -- you should use hts_detect_format() etc instead | |
| 6 | |
| 7 | |
| 8 Noteworthy changes in release 1.2 (2 February 2015) | |
| 9 | |
| 10 * HTSlib now has a configure script which checks your build environment | |
| 11 and allows for selection of optional extras. See INSTALL for details | |
| 12 | |
| 13 * By default, reference sequences are fetched from the EBI CRAM Reference | |
| 14 Registry and cached in your $HOME cache directory. This behaviour can | |
| 15 be controlled by setting REF_PATH and REF_CACHE enviroment variables | |
| 16 (see the samtools(1) man page for details) | |
| 17 | |
| 18 * Numerous CRAM improvements: | |
| 19 - Support for CRAM v3.0, an upcoming revision to CRAM supporting | |
| 20 better compression and per-container checksums | |
| 21 - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks) | |
| 22 - Non-standard values for PNEXT and TLEN fields are now preserved | |
| 23 - hts_set_fai_filename() now provides a reference file when encoding | |
| 24 - Generated read names are now numbered from 1, rather than being | |
| 25 labelled 'slice:record-in-slice' | |
| 26 - Multi-threading and speed improvements | |
| 27 | |
| 28 * New htsfile command for identifying file formats, and corresponding | |
| 29 file format detection APIs | |
| 30 | |
| 31 * New tabix --regions FILE, --targets FILE options for filtering via BED files | |
| 32 | |
| 33 * Optional iRODS file access, disabled by default. Configure with --with-irods | |
| 34 to enable accessing iRODS data objects directly via 'irods:DATAOBJ' | |
| 35 | |
| 36 * All occurences of 2^29 in the source have been eliminated, so indexing | |
| 37 and querying against reference sequences larger than 512Mbp works (when | |
| 38 using CSI indices) | |
| 39 | |
| 40 * Support for plain GZIP compression in various places | |
| 41 | |
| 42 * VCF header editing speed improvements | |
| 43 | |
| 44 * Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table) | |
| 45 | |
| 46 * Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1. | |
| 47 Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually | |
| 48 faidx_fetch_nseq() will be deprecated and removed [#156] | |
| 49 | |
| 50 * Fixed bugs #141, #152, #155, #158, #159, and various memory leaks |