Log Message:
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.