7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/NEWS src/htslib/NEWS deleted file mode 100644 index 45246d547c2..00000000000 --- src/htslib/NEWS +++ /dev/null @@ -1,74 +0,0 @@ -Noteworthy changes in release 1.3 (15 December 2015) - -* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP - and FTP, when HTSlib is configured to use libcurl for network file access - rather than the included basic knetfile networking. - -* HTSlib can be built to use remote access hFILE backends (such as iRODS - and libcurl) via a plugin mechanism. This allows other backends to be - easily added and facilitates building tools that use HTSlib, as they - don't need to be linked with the backends' various required libraries. - -* fai_build() and samtools faidx now accept initial whitespace in ">" - headers (e.g., "> chr1 description" is taken to refer to "chr1"). - -* tabix --only-header works again (was broken in 1.2.x; #249). - -* HTSlib's configure script and Makefile now fully support the standard - convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden - as needed. Previously the Makefile listened to $(LDLIBS) instead; if you - were overriding that, you should now override LIBS rather than LDLIBS. - -* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296. - - -Noteworthy changes in release 1.2.1 (3 February 2015) - -* 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 - - -Noteworthy changes in release 1.2 (2 February 2015) - -* 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] - -* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks