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@daviesrob daviesrob released this 26 Jan 15:32
· 1318 commits to master since this release
1.7
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daviesrob
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  • BAM: HTSlib now supports BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).

  • BCF/VCF:

    • Removed the need for long double in pileup calculations.
    • Sped up the synced reader in some situations.
    • Bug fixing: removed memory leak in bcf_copy.

  • CRAM:

    • Added support for HTS_IDX_START in cram iterators.
    • Easier to build when lzma header files are absent.
    • Bug fixing: a region query with REQUIRED_FIELDS option to disable sequence retrieval now gives correct results.
    • Bug fixing: stop queries to regions starting after the last read on a chromosome from incorrectly reporting errors (#651, #653; reported by Imran Haque and @egafni via pysam).

  • Multi-region iterator: The new structure takes a list of regions and iterates over all, deduplicating reads in the process, and producing a full list of file offset intervals. This is usually much faster than repeatedly using the old single-region iterator on a series of regions.

  • Curl improvements:

    • Add Bearer token support via HTS_AUTH_LOCATION env (#600).
    • Use CURL_CA_BUNDLE environment variable to override the CA (#622; thanks to Garret Kelly & David Alexander).
    • Speed up (removal of excessive waiting) for both http(s) and ftp.
    • Avoid repeatedly reconnecting by removal of unnecessary seeks.
    • Bug fixing: double free when libcurl_open fails.

  • BGZF block caching, if enabled, now performs far better (#629; reported by Ram Yalamanchili).

  • Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas Hickman).

  • Tidied up the drand48 support (intended for systems that do not provide this function).

The htslib-1.7.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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