SAM tools Files

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htslib - changes v1.7
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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).

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samtools - changes v1.7
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* HTSlib, and so samtools, now support BAMs which include CIGARs with more
  than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).

* samtools quickcheck will now write a warning to stderr if it finds
  any problems.  These messages can be suppressed with a new `-q` option.

* samtools markdup can now mark supplementary alignments of reads where
  the primary alignment is found to be a duplicate.  Supplementary marking
  can be turned on by passing the `-S` option to markdup.  When this
  option is enabled, all the alignment data will be written to a temporary
  file so that supplementary alignments that occur before a duplicated
  primary can be correctly marked in the final output.  The location
  of this temporary file can be influenced using the new `-T` option.

* samtools view now supports HTSlib's new multi-region iterator.
  This can be enabled by passing the `-M` option to view.  When using
  this option:

  - The BED filter (`-L` option) will use the index to skip through the file
  - Reads from overlapping regions will only be output once

* samtools bedcov will now ignore BED comment and header lines (#571; thanks
  to Daniel Baker).

* samtools collate now updates the @HD SO: and GO: tags, and sort will
  remove a GO: tag if present.  (#757; reported by Imran Haque).

* Bug-fixes:

 - maq2sam now checks for input files that end early.  (#751; patch supplied
   by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.)

 - Fixed incorrect check when looking up header tags that could lead
   to a crash in samtools stats. (#208; thanks to Dave Larson.)

 - Fixed bug in samtools fastq `-O` option where it would fail if
   the OQ tag in the input file had an unexpected type. (#758;
   reported by Taejeong Bae)

 - The MD5 calculations in samtools dict and md5fa did not handle
   non-alphabetic characters in the same way as the CRAM MD5 function.
   They have now been updated to match. (#704; reported by Chris Norman).

 - Fix possible infinite loop in samtools targetcut.

 - Building bam_tview_curses should no longer fail if a curses header file
   cannot be found.

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bcftools - changes v1.7
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* `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields
  and missing values. New GT=ref,alt,mis etc keywords, check the
  documentation for details.

* `query`: Only matching expression are printed when both the -f and -i/-e
  expressions contain genotype fields. Note that this changes the original
  behaviour. Previously all samples were output when one matching sample was
  found. This functionality can be achieved by pre-filtering with view and
  then streaming to query. Compare
        bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
  and
        bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

* `annotate`: New -k, --keep-sites option

* `consensus`: Fix --iupac-codes output

* `csq`: Homs always considered phased and other fixes

* `norm`: Make `-c none` work and remove `query -c`

* `roh`: Fix errors in the RG output

* `stats`: Allow IUPAC ambiguity codes in the reference file; report the
  number of missing genotypes

* `+fill-tags`: Add ExcHet annotation

* `+setGt`: Fix bug in binom.test calculation, previously it worked only
  for nAlt<nRef!

* `+split`: New plugin to split a multi-sample file into single-sample
  files in one go

* Improve python3 compatibility in plotting scripts