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@daviesrob daviesrob released this 28 Sep 16:52
· 1486 commits to develop since this release
1.6
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  • Fixed bug where iterators on CRAM files did not propagate error return values to the caller correctly. Thanks go to Chris Saunders.

  • Overhauled Windows builds. Building with msys2/mingw64 now works correctly and passes all tests.

  • More improvements to logging output (thanks again to Anders Kaplan).

  • Return codes from sam_read1() when reading cram have been made consistent with those returned when reading sam/bam. Thanks to Chris Saunders (#575).

  • BGZF CRC32 checksums are now always verified.

  • It's now possible to set nthreads = 1 for cram files.

  • hfile_libcurl has been modified to make it thread-safe. It's also better at handling web servers that do not honour byte range requests when attempting to seek - it now sets errno to ESPIPE and keeps the existing connection open so callers can revert to streaming mode it they want to.

  • hfile_s3 now recalculates access tokens if they have become stale. This fixes a reported problem where authentication failed after a file had been in use for more than 15 minutes.

  • Fixed bug where remote index fetches would fail to notice errors when writing files.

  • bam_read1() now checks that the query sequence length derived from the CIGAR alignment matches the sequence length in the BAM record.

The htslib-1.6.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.

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