NEWS

Noteworthy changes in release a.b
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Noteworthy changes in release 1.8 (3rd April 2018)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* 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)

Noteworthy changes in release 1.7 (26th January 2018)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* 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).