@jmarshall jmarshall released this Dec 15, 2015 · 681 commits to develop since this release

Assets 3
  • 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.

The htslib-1.3.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.