samtools: updated to 1.9

Release 1.9:

* Samtools mpileup VCF and BCF output is now deprecated.  It is still
  functional, but will warn.  Please use bcftools mpileup instead.

* Samtools mpileup now handles the '-d' max_depth option differently.  There
  is no longer an enforced minimum, and '-d 0' is interpreted as limitless
  (no maximum - warning this may be slow).  The default per-file depth is
  now 8000, which matches the value mpileup used to use when processing
  a single sample.  To get the previous default behaviour use the higher
  of 8000 divided by the number of samples across all input files, or 250.

* Samtools stats new features:

  - The '--remove-overlaps' option discounts overlapping portions of
    templates when computing coverage and mapped base counting.

  - When a target file is in use, the number of bases inside the
    target is printed and the percentage of target bases with coverage
    above a given threshold specified by the '--cov-threshold' option.

  - Split base composition and length statistics by first and last reads.

* Samtools faidx new features:

  - Now takes long options.

  - Now warns about zero-length and truncated sequences due to the
    requested range being beyond the end of the sequence.

  - Gets a new option (--continue) that allows it to carry on
    when a requested sequence was not in the index.

  - It is now possible to supply the list of regions to output in a text
    file using the new '--region-file' option.

  - New '-i' option to make faidx return the reverse complement of
    the regions requested.

  - faidx now works on FASTQ (returning FASTA) and added a new
    fqidx command to index and return FASTQ.

* Samtools collate now has a fast option '-f' that only operates on
  primary pairs, dropping secondary and supplementary.  It tries to write
  pairs to the final output file as soon as both reads have been found.

* Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
  reference skips (N) when computing coverage.

* Small speed up to samtools coordinate sort, by converting it to use
  radix sort.

* Samtools idxstats now works on SAM and CRAM files, however this
  isn't fast due to some information lacking from indices.

* Compression levels may now be specified with the level=N
  output-fmt-option.  E.g. with -O bam,level=3.

* Various documentation improvements.

* Bug-fixes:

  - Improved error reporting in several places.

  - Various test improvements.

  - Fixed failures in the multi-region iterator (view -M) when regions
    provided via BED files include overlaps

  - Samtools stats now counts '=' and 'X' CIGAR operators when
    counting mapped bases.

  - Samtools stats has fixes for insert size filtering (-m, -i).

  - Samtools stats -F now longer negates an earlier -d option.

  - Fix samtools stats crash when using a target region.

  - Samtools sort now keeps to a single thread when the -@ option is absent.
    Previously it would spawn a writer thread, which could cause the CPU
    usage to go slightly over 100%.

  - Fixed samtools phase '-A' option which was incorrectly defined to take
    a parameter.

  - Fixed compilation problems when using C_INCLUDE_PATH.

  - Fixed --version when built from a Git repository.

  - Use noenhanced mode for title in plot-bamstats.  Prevents unwanted
    interpretation of characters like underscore in gnuplot version 5.

  - blast2sam.pl now reports perfect match hits (no indels or mismatches).

  - Fixed bug in fasta and fastq subcommands where stdout would not be flushed
    correctly if the -0 option was used.

  - Fixed invalid memory access in mpileup and depth on alignment records
    where the sequence is absent.

(adam)