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