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@daviesrob daviesrob released this 03 Apr 16:04
· 1381 commits to develop since this release
1.8
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  • The URL to get sequences from the EBI reference server has been changed to https://. This is because the EBI no longer serve sequences via plain HTTP - requests to the http:// endpoint just get redirected. HTSlib needs to be linked against libcurl to download https:// URLs, so CRAM users who want to get references from the EBI will need to run configure and ensure libcurl support is enabled using the --enable-libcurl option.

  • Added libdeflate as a build option for alternative faster compression and decompression. Results vary by CPU but compression should be twice as fast and decompression faster.

  • It is now possible to set the compression level in bgzip. (#675; thanks to Nathan Weeks).

  • bgzip now gets its own manual page.

  • CRAM encoding now stored MD and NM tags verbatim where the reference contains 'N' characters, to work around ambiguities in the SAM specification (samtools #717/762). Also added "store_md" and "store_nm" cram-options for forcing these tags to be stored at all locations. This is best when combined with a subsequent decode_md=0 option while reading CRAM.

  • Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of references with -T ref.fa. (#654; reported by Chris Saunders)

  • CRAM multi-threading bugs fixed: don't try to call flush on reading; processing of multiple range queries; problems with multi-slice containers.

  • Fixed crashes caused when decoding some cramtools produced CRAM files.

  • Fixed a couple of minor rANS issues with handling invalid data.

  • Fixed bug where probaln_glocal() tried to allocate far more memory than needed when the query sequence was much longer than the reference. This caused crashes in samtools and bcftools mpileup when used on data with very long reads. (#572, problem reported by Felix Bemm via minimap2).

  • sam_prop_realn() now returns -1 (the same value as for unmapped reads) on reads that do not include at least one 'M', 'X' or '=' CIGAR operator, and no longer adds BQ or ZQ tags. BAQ adjustments are only made to bases covered by these operators so there is no point in trying to align reads that do not have them. (#572)

The htslib-1.8.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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