SAM tools Files

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htslib - changes v1.6
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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.

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samtools - changes v1.6
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* Added new markdup sub-command and '-m' option for fixmate.  Used together,
  they allow duplicates to be marked and optionally removed.  This
  fixes a number of problems with the old 'rmdup' sub-command, for
  example samtools issue #497.  'rmdup' is kept for backwards compatibility
  but 'markdup' should be used in preference.

* Sort is now much better at keeping within the requested memory limit.  It
  should also be slightly faster and need fewer temporary files when the file
  to be sorted does not fit in memory.  (#593; thanks to Nathan Weeks.)

* Sort no longer rewrites the header when merging from files.  It can also
  now merge from memory, so fewer temporary files need to be written and
  it is better at sorting in parallel when everything fits in memory.

* Both sort and merge now resolve ties when merging based on the position
  in the input file(s).  This makes them fully stable for all ordering
  options.  (Previously position sort was stable, but name and by tag
  sorts were not).

* New --output-qname option for mpileup.

* Support for building on Windows using msys2/mingw64 or cygwin has
  been improved.

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BCFtools - changes v1.6
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* New `sort` command.

* New options added to the `consensus` command. Note that the `-i, --iupac`
  option has been renamed to `-I, --iupac`, in favor of the standard 
  `-i, --include`.

* Filtering expressions (`-i/-e`): support for `GT=<type>` expressions and
  for lists and ranges (#639) - see the man page for details.

* `csq`: relax some GFF3 parsing restrictions to enable using Ensembl
  GFF3 files for plants (#667)

* `stats`: add further documentation to output stats files (#316) and
  include haploid counts in per-sample output (#671).

* `plot-vcfstats`: further fixes for Python3 (@nsoranzo, #645, #666).

* `query` bugfix (#632)

* `+setGT` plugin: new option to set genotypes based on a two-tailed binomial
  distribution test. Also, allow combining `-i/-e` with `-t q`.

* `mpileup`: fix typo (#636)

* `convert --gvcf2vcf` bugfix (#641)

* `+mendelian`: recognize some mendelian inconsistencies that were
  being missed (@oronnavon, #660), also add support for multiallelic
  sites and sex chromosomes.