samtools release 1.20:

* Added a `--max-depth` option to `bedcov`, for more control over
  the depth limit used when calculating the pileup.  Previously
  this limit was set at 64000; now it is set to over 2 billion, so
  effectively all bases will be counted. (PR #1970, fixes #1950. 
  Reported by ellisjj)

* Added `mpileup --output-extra RLEN` to display the unclipped read
  length. (PR #1971, feature request #1959.  Requested by Feng Tian)

* Improved checking of symbolic flag names (e.g. UNMAP) passed to
  samtools. (PR #1981, fixes #1977.  Reported by Ilya Shlyakhter)

* The `samtools consensus --min-depth` option now works for the
  Bayesian mode as well as the simple one. (PR #1989, feature
  request #1982.  Requested by Gautier Richard)

* It's now possible to use the `samtools fastq` `-d tag:val` option
  multiple times, allowing matches on more than one tag/value.  It
  also gets a `-D` option which allows the values to be listed in a
  file. (PR #1993, feature request #1958.  Requested by
  Tristan Lefebure)

* Added `samtools fixmate` `-M` option to sanity check base
  modification (`ML`, `MM`, `MN`) tags, and where necessary
  adjust modification data on hard-clipped records. (PR #1990)

* Made `mpileup` run faster. (PR #1995)

* `samtools import` now adds a `@PG` header to the files it makes. As
  with other sub-commands, this can be disabled by using `--no-PG`.
  (PR #2008.  Requested by Steven Leonard)

* The `samtools split` `-d` option to split by tag value now works
  on tags with integer values. (PR #2005, feature request #1956. 
  Requested by Alex Leonard)

* Adjusted `samtools sort -n` (by name) so that primary reads are
  always sorted before secondary / supplementary. (PR #2012, feature
  request #2010.  Requested by Stijn van Dongen)

* Added `samtools bedcov` `-H` option to print column headers in the
  output. (PR #2025.  Thanks to Dr. K. D. Murray)

Documentation:

* Added a note that BAQ is applied before filtering and overlap
  removal during mpileup processing. (PR #1988, fixes #1985. 
  Reported by Joseph Galasso)

* Added 3.1 to the list of supported CRAM versions in the samtools
  manual page. (PR #2009.  Thanks to Andrew Thrasher)

* Made assorted improvements to ampliconclip, flagstat and markdup
  manual pages. (PR #2014)

Bug Fixes:

* Security fix: Fixed double free that could occur if bed file
  indexing failed due to running out of memory.  This bug first
  appeared in version 1.19.1. (PR #2026)

* Corrected error message printed when faidx fails to load the fai
  index. (PR #1987.  Thanks to Nick Moore)

* Fixed bug introduced in release 1.4 that caused incorrect reference
  bases to be printed by `samtools mpileup -a -f ref.fa` in the
  zero-depth regions at the end of each reference. (PR #2019, fixes
  #2018.  Reported by Joe Georgeson)

* Fixed a samtools view usage crash on MinGW when given invalid
  options. (PR #2030, fixes #2029.  Reported by Divon Lan)

Non user-visible changes and build improvements:

* Added tests to ensure that CRAM compression is working properly.
  (PR #1969, part of fix for #1968.  Reported by Clockris)

samtools release 1.19.2:

Bug Fixes:

* Fixed a regression in 1.19.1 that broke BED filtering for inputs
  where the region start positions for the same reference were not
  sorted in ascending order. (PR #1975, fixes #1974.  Reported by
  Anže Starič)

samtools release 1.19.1:

Bug Fixes:

* Fixed a possible array bounds violation when looking up regions
  in a BED file (e.g. using `samtools view -L`).  This could lead
  to crashes or the return of incomplete results if the BED file
  contained a large number of entries all referencing low
  positions on a chromosome. (PR #1962, fixes #1961.  Reported by
  geertvandeweyer)

* Fixed a crash in samtools stats that occurred when trying to clean
  up after it was unable to open a CRAM reference file. (PR #1957,
  fixes crash reported in samtools/htslib#1723.  Reported by
  Alex Leonard)

Documentation:

* Fixed inverted logic in the `samtools consensus --show-del` manual
  page description. (PR #1955, fixes #1951.  Reported by
  Mikhail Schelkunov)

* Added a description of the MPC section to the `samtools stats`
  manual page. (PR #1963, fixes #1954.  Reported by litun-fkby)

samtools release 1.19:

New work and changes:

* Samtools coverage: add a new --plot-depth option to draw depth (of
  coverage) rather than the percentage of bases covered. (PR #1910. 
  Thanks to Pierre Lindenbaum)

* Samtools merge / sort: add a lexicographical name-sort option via
  the -N option.  The "natural" alpha-numeric sort is still available
  via -n. (PR #1900, fixes #1500.  Reported by Steve Huang)

* Samtools view: add -N ^NAME_FILE and -R ^RG_FILE options.  The
  standard -N and -R options only output reads matching a specified
  list of names or read-groups.  With a caret (^) prefix these may
  be negated to only output read not matching the specified files.
  (PR #1896, fixes #1895.  Suggested by Feng Tian)

* Cope with Htslib's change to no longer close stdout on hts_close.
  Htslib companion PR is samtools/htslib#1665. (PR #1909.  Thanks to
  John Marshall)

* Plot-bamstats: add a new plot of the read lengths ("RL") from
  samtools stats output. (PR #1922, fixes #1824.  Thanks to
  @erboone, suggested by Martin Pollard)

* Samtools split: support splitting files based on the contents of
  auxiliary tags.  Also adds a -M option to limit the number of files
  split can make, to avoid accidental resource over-allocation, and
  fixes some issues with --write-index. (PR #1222, PR #1933, fixes
  #1758.  Thanks to Valeriu Ohan, suggested by Scott Norton)

Bug Fixes:

* Samtools stats: empty barcode tags are now treated as having no
  barcode. (PR #1929, fixes #1926.  Reported by Jukka Matilainen)

* Samtools cat: add support for non-seekable streams.  The file
  format detection blocked pipes from working before, but now files
  may be non-seekable such as stdin or a pipe. (PR #1930, fixes
  #1731.  Reported by Julian Hess)

* Samtools mpileup -aa (absolutely all positions) now produces an
  output even when given an empty input file. (PR #1939.  Reported by
  Chang Y)

* Samtools markdup: speed up optical duplicate tagging on regions
  with very deep data. (PR #1952)

Documentation:

* Samtools mpileup: add more usage examples to the man page. (PR
  #1913, fixes #1801)

* Samtools fastq: explicitly document the order that filters apply.
  (PR #1907)

* Samtools merge: fix example output to use an uppercase RG PL field.
  (PR #1917.  Thanks to John Marshall.  Reported by Michael Macias)

* Add hclen SAM filter documentation. (PR #1902.  See also
  samtools/htslib#1660)

* Samtools consensus: remove the -5 option from documentation.  This
  option was renamed before the consensus subcommand was merged, but
  accidentally left in the man page. (PR #1924)

samtools release 1.18:

New work and changes:

* Add minimiser sort option to collate by an indexed fasta.  Expand
  the minimiser sort to arrange the minimiser values in the same
  order as they occur in the reference genome. This is acts as an
  extremely crude and simplistic read aligner that can be used to
  boost read compression. (PR#1818)

* Add a --duplicate-count option to markdup.  Adds the number of
  duplicates (including itself) to the original read in a 'dc' tag.
  (PR#1816. Thanks to wulj2)

* Make calmd handle unaligned data or empty files without throwing an
  error. This is to make pipelines work more smoothly.  A warning
  will still be issued. (PR#1841, fixes #1839.  Reported by
  Filipe G. Vieira)

* Consistent, more comprehensive flag filtering for fasta/fastq. 
  Added --rf/--incl[ude]-flags and long options for -F
  (--excl[ude]-flags and -f (--require-flags). (PR#1842.  Thanks
  to Devang Thakkar)

* Apply fastq --input-fmt-option settings.  Previously any options
  specified were not being applied to the input file. (PR#1855. 
  Thanks to John Marshall)

* Add fastq -d TAG[:VAL] check.  This mirrors view -d and will only
  output alignments that match TAG (and VAL if specified). (PR#1863,
  fixes #1854.  Requested by Rasmus Kirkegaard)

* Extend import --order TAG to --order TAG:length.  If length is
  specified, the tag format goes from integer to a 0-padded string
  format.  This is a workaround for BAM and CRAM that cannot encode
  an order tag of over 4 billion records. (PR#1850, fixes #1847. 
  Reported by Feng Tian)

* New -aa mode for consensus.  This works like the -aa option in
  depth and mpileup. The single 'a' reports all bases in contigs
  covered by alignments. Double 'aa' (or '-a -a') reports Ns even
  for the references with no alignments against them. (PR#1851,
  fixes #1849.  Requested by Tim Fennell)

* Add long option support to samtools index. (PR#1872, fixes #1869. 
  Reported by Jason Bacon)

* Be consistent with rounding of "average length" in samtools stats.
  (PR#1876, fixes #1867.  Reported by Jelinek-J)

* Add option to ampliconclip that marks reads as unmapped when they
  do not have enough aligned bases left after clipping.  Default is
  to unmap reads with zero aligned bases. (PR#1865, fixes #1856. 
  Requested by ces)

Bug Fixes:

* [From HTSLib] Fix a major bug when searching against a CRAM
  index where one container has start and end coordinates entirely
  contained within the previous container. This would occasionally
  miss data, and sometimes return much more than required.  The
  bug affected versions 1.11 to 1.17, although the change in 1.11
  was bug-fixing multi-threaded index queries. This bug did not
  affect index building.  There is no need to reindex your CRAM
  files. (PR#samtools/htslib#1574, PR#samtools/htslib#1640. Fixes
  #samtools/htslib#1569, #samtools/htslib#1639, #1808, #1819. 
  Reported by xuxif, Jens Reeder and Jared Simpson)

* Fix a sort -M bug (regression) when merging sub-blocks.  Data was
  valid but in a poor order for compression. (PR#1812)

* Fix bug in split output format.  Now SAM and CRAM format can chosen
  as well as BAM.  Also a documentation change, see below. (PR#1821)

* Add error checking to view -e filter expression code.  Invalid
  expressions were not returning an error code. (PR#1833, fixes
  #1829.  Reported by Steve Huang)

* Fix reheader CRAM output version.  Sets the correct CRAM output
  version for non-3.0 CRAMs. (PR#1868, fixes #1866.  Reported by
  John Marshall)

Documentation:

* Expand the default filtering information on the mpileup man page.
  (PR#1802, fixes #1801.  Reported by gevro)

* Add an explanation of the default behaviour of split files on
  generating a file for reads with missing or unrecognised RG
  tags.  Also a small bug fix, see above. (PR#1821, fixes #1817. 
  Reported by Steve Huang)

* In the INSTALL instructions, switched back to openssl for
  Alpine.  This matches the current Alpine Linux practice.
  (PR#1837, see htslib#1591.  Reported by John Marshall)

* Fix various typos caught by lintian parsers. (PR#1877.  Thanks to
  Étienne Mollier)

* Document consensus --qual-calibration option. (PR#1880, fixes
  #1879.  Reported by John Marshall)

* Updated the page about samtools duplicate marking with more detail
  at www.htslib.org/algorithms/duplicate.html

Non user-visible changes and build improvements:

* Removed a redundant line that caused a warning in gcc-13. (PR#1838)

samtools release 1.17:

New work and changes:

* New samtools reset subcommand.  Removes alignment information. 
  Alignment location, CIGAR, mate mapping and flags are updated.
  If the alignment was in reverse direction, sequence and its
  quality values are reversed and complemented and the reverse
  flag is reset.  Supplementary and secondary alignment data are
  discarded. (PR#1767, implements #1682. Requested by dkj)

* New samtools cram-size subcommand.  It writes out metrics about a
  CRAM file reporting aggregate sizes per block "Content ID" fields,
  the data-series contained within them, and the compression methods
  used. (PR#1777)

* Added a --sanitize option to fixmate and view.  This performs some
  sanity checks on the state of SAM record fields, fixing up common
  mistakes made by aligners. (PR#1698)

* Permit 1 thread with samtools view.  All other subcommands already
  allow this and it does provide a modest speed increase. (PR#1755,
  fixes #1743. Reported by Goran Vinterhalter)

* Add CRAM_OPT_REQUIRED_FIELDS option for view -c.  This is a big
  speed up for CRAM (maybe 5-fold), but it depends on which filtering
  options are being used. (PR#1776, fixes #1775. Reported by Chang Y)

* New filtering options in samtools depth.  The new --excl-flags
  option is a synonym for -G, with --incl-flags and --require-flags
  added to match view logic. (PR#1718, fixes #1702. Reported by
  Dario Beraldi)

* Speed up calmd's slow handling of non-position-sorted data by
  adding caching. This uses more memory but is only activated when
  needed. (PR#1723, fixes #1595. Reported by lxwgcool)

* Improve samtools consensus for platforms with instrument specific
  profiles, considerably helping for data with very different indel
  error models and providing base quality recalibration tables. On
  PacBio HiFi, ONT and  Ultima Genomics consensus qualities are also
  redistributed within homopolymers and the likelihood of nearby
  indel errors is raised. (PR#1721, PR#1733)

* Consensus --mark-ins option.  This permits he consensus output to
  include a markup indicating the next base is an insertion. This is
  necessary as we need a way of outputting both consensus and also
  how that consensus marries up with the reference coordinates.
  (PR#1746)

* Make faidx/fqidx output line length default to the input line
  length. (PR#1738, fixes #1734. Reported by John Marshall)

* Speed up optical duplicate checking where data has a lot of
  duplicates compared to non-duplicates. (PR#1779, fixes #1771.
  Reported by Poshi)

* For collate use TMPDIR environment variable, when looking for a
  temporary folder. (PR#1782, based on PR#1178 and fixes #1172. 
  Reported by Martin Pollard)

Bug Fixes:

* Fix stats breakage on long deletions when given a reference.
  (PR#1712, fixes #1707. Reported by John Didion)

* In ampliconclip, stop hard clipping from wrongly removing entire
  reads. (PR#1722, fixes #1717. Reported by Kevin Xu)

* Fix bug in ampliconstats where references mentioned in the input
  file headers but not in the bed file would cause it to complain
  that the SAM headers were inconsistent. (PR#1727, fixes #1650.
  Reported by jPontix)

* Fixed SEGV in samtools collate when no filename given. (PR#1724)

* Changed the default UMI barcode regex in markdup.  The old
  regex was too restrictive.  This version will at least allow
  the default read name UMI as given in the Illumina example
  documentation. (PR#1737, fixes #1730. Reported by yloemie)

* Fix samtools consensus buffer overrun with MD:Z handling. (PR#1745,
  fixes #1744. Reported by trilisser)

* Fix a buffer read-overflow in mpileup and tview on sequences with
  seq "*". (PR#1747)

* Fix view -X command line parsing that was broken in 1.15. (PR#1772,
  fixes #1720.  Reported by Francisco Rodríguez-Algarra and
  Miguel Machado)

* Stop samtools view -d from reporting meaningless system errors when
  tag validation fails. (PR#1796)

Documentation:

* Add a description of the samtools tview display layout to the
  man page. Documents . vs , and upper vs lowercase. Adds a -s
  sample example, and documents the -w option. (PR#1765, fixes
  #1759. Reported by Lucas Ferreira da Silva)

* Clarify intention of samtools fasta/q in man page and soft vs hard
  clipping. (PR#1794, fixes #1792. Reported by Ryan Lorig-Roach)

* Minor fix to wording of mpileup --rf usage and man page. (PR#1795,
  fixes #1791. Reported by Luka Pavageau)

Non user-visible changes and build improvements:

* Use POSIX grep in testing as egrep and fgrep are considered
  obsolete. (PR#1726, thanks to David Seifert)

* Switch MacOS CI tests to an ARM-based image. (PR#1770)

samtools release 1.16.1:

Bug fixes:

 * Fixed a bug with the template-coordinate sort which caused
   incorrect ordering when using threads, or processing large
   files that don't fit completely in memory. (PR#1703, thanks to
   Nils Homer)

 * Fixed a crash that occurred when trying to use `samtools merge` in
   template-coordinate mode. (PR#1705, thanks to Nils Homer)

samtools release 1.16:

New work and changes:

 * samtools reference command added.  This subcommand extracts the
   embedded reference out of a CRAM file. (PR#1649, addresses #723. 
   Requested by Torsten Seemann)

  * samtools import now adds grouped by query-name to the header.
    (PR#1633, thanks to Nils Homer)

 * Made samtools view read error messages more generic.  Former
   error message would claim that there was a "truncated file or
   corrupt BAM index file" with no real justification.  Also
   reset errno in stream_view which could lead to confusing error
   messages. (PR#1645, addresses some of the issues in #1640. 
   Reported by Jian-Guo Zhou)

 * Make samtools view -p also clear mqual, tlen and cigar. (PR#1647,
   fixes #1606.  Reported by eboyden)

 * Add bedcov option -c to report read count. (PR#1644, fixes #1629. 
   Reported by Natchaphon Rajudom)

 * Add UMI/barcode handling to samtools markdup. (PR#1630, fixes
   #1358 and #1514.  Reported by Gert Hulselmans and Poshi)

 * Add a new template coordinate sort order to samtools sort and
   samtools merge.  This is useful when working with unique molecular
   identifiers (UMIs). (PR#1605, fixes #1591.  Thanks to Nils Homer)

 * Rename mpileup --ignore-overlaps to --ignore-overlaps-removal or
   --disable-overlap-removal.  The previous name was ambiguous and
   was often read as an option to enable removal of overlapping
   bases, while in reality this is on by default and the option
   turns off the ability to remove overlapping bases. (PR#1666,
   fixes #1663.  Reported by yangdingyangding)

 * The dict command can now read BWA's .alt file and add AH:* tags
   indicating reference sequences that represent alternate loci.
   (PR#1676.  Thanks to John Marshall)

 * The "samtools index" command can now accept multiple alignment
   filenames with the new -M option, and will index each of them
   separately. (Specifying the output index filename via out.index
   or the new -o option is currently only applicable when there is
   only one alignment file to be indexed.) (PR#1674.  Reported by
   Abigail Ramsøe and Nicola Romanò. Thanks to John Marshall)

 * Allow samtools fastq -T "*". This allows all tags from SAM records
   to be written to fastq headers. This is a counterpart to samtools
   import -T "*". (PR#1679.  Thanks to cjw85)

Bug Fixes:

 * Re-enable --reference option for samtools depth.  The reference is
   not used but this makes the command line usage compatible with
   older releases. (PR#1646, fixes #1643.  Reported by Randy Harr)

 * Fix regex coordinate bug in samtools markdup. (PR#1657, fixes
   #1642.  Reported by Randy Harr)

 * Fix divide by zero in plot-bamstats -m, on unmapped data.
   (PR#1678, fixes #1675.  Thanks to Shane McCarthy)

 * Fix missing RG headers when using samtools merge -r. (PR#1683,
   addresses htslib#1479.  Reported by Alex Leonard)

 * Fix a possible unaligned access in samtools reference. (PR#1696)

Documentation:

 * Add documentation on CRAM compression profiles and some of the
   newer options that appear in CRAM 3.1 and above. (PR#1659, fixes
   #1656.  Reported by Matthias De Smet)

 * Add "sclen" filter expression keyword documentation. (PR#1661, see
   also htslib#1441)

 * Extend FILTER EXPRESSION man page section to match the changes
   made in HTSlib. (PR#1687, samtools/htslib#1478)

Non user-visible changes and build improvements:

 * Ensure generated test files are ignored (by git) and cleaned (by
   make testclean) (PR#1692, Thanks to John Marshall)

samtools release 1.15.1:

Bug fixes:

 * A bug which prevented the samtools view --region-file (and the
   equivalent -M -L <file>) options from working in version 1.15 has
   been fixed. (#1617)

 * Fixed a crash triggered by using the samtools view -c/--count and
   --unmap options together.  The --unmap option is now ignored in
   counting mode. (#1619)

Documentation:

 * The consensus command was missing from the main samtools.1 manual
   page. It has now been added. (#1603)

 * Corrected instructions for reproducing the samtools stats "raw
   total sequences" count using samtools view -c. (#1620; reported by
   @krukanna)

 * Improved manual page formatting.  (#1625; thanks to John Marshall)

Non user-visible changes and build improvements:

 * Unnecessary #include lines have been removed from bam_plcmd.c.
   (#1607; thanks to John Marshall)

samtools release 1.15:

Notice:

 * Samtools mpileup VCF and BCF output (deprecated in release 1.9)
   has been removed.  Please use bcftools mpileup instead.

New work and changes:

 * Added "--min-BQ" and "--min-MQ" options to "depth". These
   match the equivalent long options found in "samtools mpileup"
   and gives a consistent way of specifying the base and mapping
   quality filters. (#1584; fixes #1580. Reported by Chang Y) 

 * Improved automatic file type detection with "view -u" or "view
   -1".  Setting either of these options would default to BAM format
   regardless of the usual automatic file type selection based on the
   file name.  The defaults are now only used when the file name does
   not indicate otherwise. (#1582)

 * For "markdup" optical duplicate marking add regex options for
   custom coordinates.  For the case of non standard read names
   (QNAME), add options to read the coordinates and, optionally,
   another part of the string to test for optical duplication.
   (#1558)

 * New "samtools consensus" subcommand for generating consensus from
   SAM, BAM or CRAM files based on the contents of the alignment
   records.  The consensus is written as FASTA, FASTQ or as a pileup
   oriented format.  The default FASTA/FASTQ output includes one base
   per non-gap consensus, with insertions with respect to the aligned
   reference being included and deletions removed. This could be used
   to compute a new reference from sequence assemblies to realign
   against. (#1557)

 * New "samtools view --fetch-pairs" option.  This options retrieves
   pairs even when the mate is outside of the requested region. 
   Using this option enables the multi-region iterator and a region
   to search must be specified.  The input file must be an indexed
   regular file. (#1542)

 * Building on #1530 below, add a tview reflist for Goto. (#1539,
   thanks to Adam Blanchet)

 * Completion of references added to tview Goto. (#1530; thanks to
   Adam Blanchet)

 * New "samtools head" subcommand for conveniently displaying the
   headers of a SAM, BAM, or CRAM file. Without options, this is
   equivalent to `samtools view --header-only --no-PG` but more
   succinct and memorable. (#1517; thanks to John Marshall)

Bug Fixes:

 * Free memory when stats fails to read the header of a file. (#1592;
   thanks to Mathias Schmitt)

 * Fixed empty field on unsupported aux tags in "mpileup
   --output-extra". Replaces the empty fields on unsupported aux
   tags with a '*'. (#1553; fixes #1544. Thanks to Adam Blanchet)

 * In mpileup, the --output-BP-5 and --output-BP are no longer
   mutually exclusive.  This fixes the problem of output columns
   being switched. (#1540; fixes 1534.  Reported by Konstantin Riege)

 * Fix for hardclip bug in ampliconclip.  Odd length sequences
   resulted in random characters appearing in sequence. (#1538;
   fixes #1527. Reported by Ivana Mihalek)

   Documentation:

 * Improved mpileup documentation. (#1566; fixes #1564.  Reported by
   Chang Y) 

 * Fixed "samtools depth -J" documentation, which was reversed.
   (#1552; fixes #1549.  Reported by Stephan Hutter)

 * Numerous minor man page fixes. (#1528, #1536, #1579, #1590. 
   Thanks to John Marshall for some of these)

Non user-visible changes and build improvements:

 * Replace CentOS test build with Rocky Linux.  The CentOS Docker
   images that our test build depended on has stopped working. 
   Switched to Rocky Linux as the nearest available equivalent.
   (#1589)

 * Fix missing autotools on Appveyor.  Newer versions of msys2
   removed autotools from their base-devel package.  This is
   putting them back. (#1575) 

 * Fixed bug detected by clang-13 with -Wformat-security. (#1553)

 * Switch to using splaysort in bam_lpileup.  Improves speed and
   efficiency in "tview". (#1548; thanks to Adam Blanchet)

samtools release 1.14:

Notice:

 * Samtools mpileup VCF and BCF output (deprecated in release 1.9)
   will be removed in the next release.  Please use bcftools mpileup
   instead.

New work and changes:

 * The legacy samtools API (libbam.a, bam_endian.h, sam.h and
   most of bam.h) has been removed.  We recommend coding against
   the HTSlib API directly. The legacy API had not been actively
   maintained since 2015. (#1483)

 * New "samtools samples" command to list the samples used in a
   SAM/BAM/CRAM file. (#1432; thanks to Pierre Lindenbaum)

 * "mpileup" now supports base modifications via the SAM Mm/MM
   auxiliary tag.  Please see the "--output-mods" option. (#1311)

 * Added "mpileup --output-BP-5" option to output the BP field in 5'
   to 3' order instead of left to right. (#1484; fixes #1481)

 * Added "samtools view --rf" option as an additional FLAG filtering
   method.  This keeps records only if (FLAG & N) != 0. (#1508; fixes
   #1470)

 * New "samtools import -N" option to use the second word on a FASTQ
   header line, matching the SRA/ENA FASTQ variant. (#1485)

 * Improve "view -x" option to simplify specifying multiple tags,
   and added the reverse "--keep-tag" option to include rather than
   exclude. (#516)

 * Switched the processing order of "view" -x (tag filtering) and
   -e (expression) handling.  Expressions now happen first so we
   can filter on tags which are about to be deleted.  This is now
   consistent with the "view -d" behaviour too. (#1480; fixes
   #1476. Reported by William Rowell)

 * Added filter expression "endpos" keyword. (#1464.  Thanks to
   John Marshall)

 * "samtools view" errors now appear after any SAM output, improving
   their visibility. (#1490.  Thanks to John Marshall)

 * Improved "samtools sort" use of temporary files, both tidying up
   if it fails and recovery when facing pre-existing temporary files.
   (#1510; fixes #1035, #1503.  Reported by Vivek Rai and
   Maarten Kooyman)

 * Filtering in "samtools markdup" now sets the UNMAP BAM flag when
   given the "-p" option. (#1512; fixes #1469)

 * Make CRAM references shared during "samtools merge" so merging
   many files has a lower memory usage. (#471)

Bug fixes:

 * Prevent "samtools depth" from closing stdout when outputting to
   terminal, avoiding a bad interaction with PySam. (#1465.  Thanks
   to John Marshall)

 * In-place "samtools reheader" now works on CRAMs produced using a
   higher than default compression level. (#1479)

 * Fix setting of the dt tag in "markdup".  Optical duplicates
   were being marked too early, negating the tagging and counting
   elsewhere. (#1487; fixes #1486.  Reported by Kevin Lewis)

 * Reinstate the "samtools stats -I" option to filter by sample.
   (#1496; fixes #1489.  Reported by Matthias Bernt)

 * Fix "samtools fastq" handling of dual index tags on single-ended
   input. (#1474)

 * Improve "samtools coverage" documentation. (#1521; fixes #1504.
   Reported by Peter Menzel)

Non user-visible changes and build improvements:

 * Replace Curses mvprintw() with va_list-based equivalent. (#1509.
   Thanks to John Marshall and Andreas Tille)

 * Fixed some clang-13 warning messages. (#1506)

 * Improve quoting of options in "samtools import" tests. (#1466.
   Thanks to John Marshall)

 * Fixed a faulty test which caused test harness failures on NetBSD.
   (#1520)

samtools release 1.13:

 * Fixed samtools view FILE REGION, mpileup -r REGION, coverage -r
   REGION and other region queries: fixed bug introduced in 1.12,
   which led to region queries producing very few reads for some
   queries (especially for larger target regions) when unmapped reads
   were present. Thanks to `@vinimfava` (#1451), `@JingGuo1997` (#1457)
   and Ramprasad Neethiraj (#1460) for reporting the respective
   issues.

 * Added options to set and clear flags to samtools view.  Along with
   the existing remove aux tags this gives the ability to remove mark
   duplicate changes (part of #1358) (#1441)

 * samtools view now has long option equivalents for most of its
   single-letter options. Thanks to John Marshall. (#1442)

 * A new tool, samtools import, has been added.  It reads one or
   more FASTQ files and converts them into unmapped SAM, BAM or
   CRAM. (#1323)

 * Fixed samtools coverage error message when the target region name
   is not present in the file header. Thanks to `@Lyn16` for reporting
   it. (#1462; fixes #1461)

 * Made samtools coverage ASCII mode produce true ASCII output. 
   Previously it would produce UTF-8 characters. (#1423; fixes #1419)

 * samtools coverage now allows setting the maximum depth, using the
   -d/--depth option. Also, the default maximum depth has been set to
   1000000. (#1415; fixes #1395)

 * Complete rewrite of samtools depth.  This means it is now
   considerably faster and does not need a depth limit to avoid
   high memory usage.  Results should mostly be the same as the
   old command with the potential exception of overlap removal.
   (#1428; fixes #889, helps ameliorate #1411)

 * samtools flags now accepts any number of command line arguments,
   allowing multiple SAM flag combinations to be converted at once. 
   Thanks to John Marshall. (#1401, fixes #749)

 * samtools ampliconclip, ampliconstats and plot-ampliconstats now
   support inputs that list more than one reference. (#1410 and
   #1417; fixes #1396 and #1418)

 * samtools ampliconclip now accepts the --tolerance option, which
   allows the user to set the number of bases within which a region
   is matched.  The default is 5. (#1456)

 * Updated the documentation on samtools ampliconclip to be clearer
   about what it does.  From a suggestion by Nathan S Watson-Haigh.
   (#1448)

 * Fixed negative depth values in ampliconstats output. (#1400)

 * samtools addreplacerg now allows for updating (replacing) an
   existing `@RG` line in the output header, if a new `@RG` line is
   provided in the command line, via the -r argument. The update
   still requires the user's approval, which can be given with the
   new -w option.  Thanks to Chuang Yu. (#1404)

 * Stopped samtools cat from outputting multiple CRAM EOF markers.
   (#1422)

 * Three new counts have been added to samtools flagstat: primary,
   mapped primary and duplicate primary. (#1431; fixes #1382)

 * samtools merge now accepts a `-o FILE` option specifying the
   output file, similarly to most other subcommands. The existing
   way of specifying it (as the first non-option argument, alongside
   the input file arguments) remains supported. Thanks to David
   McGaughey and John Marshall. (#1434)

 * The way samtools merge checks for existing files has been changed
   so that it does not hang when used on a named pipe. (#1438; fixes
   #1437)

 * Updated documentation on mpileup to highlight the fact that the
   filtering options on FLAGs work with ANY rules. (#1447; fixes
   #1435)

 * samtools can now be configured to use a copy of HTSlib that has
   been set up with separate build and source trees.  When this is
   the case, the `--with-htslib` configure option should be given
   the location of the HTSlib build tree.  (Note that samtools
   itself does not yet support out-of-tree builds).  Thanks to John
   Marshall. (#1427; companion change to samtools/htslib#1277)

samtools release 1.12:

 * The legacy samtools API (libbam.a, bam.h, sam.h, etc) has not
   been actively maintained since 2015. It is deprecated and will
   be removed entirely in a future SAMtools release. We recommend
   coding against the HTSlib API directly.

 * I/O errors and record parsing errors during the reading of
   SAM/BAM/CRAM files are now always detected. Thanks to
   John Marshall (#1379; fixed #101)

 * New make targets have been added: check-all, test-all,
   distclean-all, mostlyclean-all, testclean-all, which allow
   SAMtools installations to call corresponding Makefile targets
   from embedded HTSlib installations.

 * samtools --version now displays a summary of the compilation
   details and available features, including flags, used libraries
   and enabled plugins from HTSlib. As an alias, `samtools version`
   can also be used. (#1371)

 * samtools stats now displays the number of supplementary reads in
   the SN section. Also, supplementary reads are no longer considered
   when splitting read pairs by orientation (inward, outward, other).
   (#1363)

 * samtools stats now counts only the filtered alignments that
   overlap target regions, if any are specified. (#1363)

 * samtools view now accepts option -N, which takes a file containing
   read names of interest. This allows the output of only the reads
   with names contained in the given file. Thanks to Daniel Cameron.
   (#1324)

 * samtools view -d option now works without a tag associated
   value, which allows it to output all the reads with the given
   tag. (#1339; fixed #1317)

 * samtools view -d and -D options now accept integer and single
   character values associated with tags, not just strings. Thanks
   to `@dariome` and Keiran Raine for the suggestions. (#1357,
   #1392)

 * samtools view now works with the filtering expressions
   introduced by HTSlib. The filtering expression is passed to
   the program using the specific option -e or the global long
   option --input-fmt-option. E.g.
     samtools view -e 'qname =~ "#49$" && mrefid != refid && refid != -1 && mrefid != -1' align.bam
   looks for records with query-name ending in `#49` that have
   their mate aligned in a different chromosome. More details
   can be found in the FILTER EXPRESSIONS section of the main man
   page. (#1346)

 * samtools markdup now benefits from an increase in performance in
   the situation when a single read has tens or hundreds of thousands
   of duplicates. Thanks to `@denriquez` for reporting the issue.
   (#1345; fixed #1325)

 * The documentation for samtools ampliconstats has been added to the
   samtools man page. (#1351)

 * A new FASTA/FASTQ sanitizer script (`fasta-sanitize.pl`) was
   added, which corrects the invalid characters in the reference
   names. (#1314) Thanks to John Marshall for the installation fix.
   (#1353)

 * The CI scripts have been updated to recurse the HTSlib submodules
   when cloning HTSlib, to accommodate for the CRAM codecs, which now
   reside in the htscodecs submodule. (#1359)

 * The CI integrations now include Cirrus-CI rather than Travis.
   (#1335; #1365)

 * Updated the Windows image used by Appveyor to 'Visual Studio
   2019'. (#1333; fixed #1332)

 * Fixed a bug in samtools cat, which prevented the command from
   running in multi-threaded mode. Thanks to Alex Leonard for
   reporting the issue. (#1337; fixed #1336)

 * A couple of invalid CIGAR strings have been corrected in the test
   data. (#1343)

 * The documentation for `samtools depth -s` has been improved.
   Thanks to `@wulj2`. (#1355)

 * Fixed a `samtools merge` segmentation fault when it failed to
   merge header `@PG` records. Thanks to John Marshall.  (#1394;
   reported by Kemin Zhou in #1393)

 * Ampliconclip and ampliconstats now guard against the BED file
   containing more than one reference (chromosome) and fail when
   found.  Adding proper support for multiple references will appear
   later.  (#1398)

samtools release 1.11:

 * New samtools ampliconclip sub-command for removing primers from
   amplicon-based sequencing experiments, including the current
   COVID-19 projects.  The primers are listed in a BED file and can
   be either soft-clipped or hard-clipped. (#1219)

 * New samtools ampliconstats sub-command to produce a textual
   summary of primer and amplicon usage, in a similar style to
   "samtools stats". The misc/plot-ampliconstats script can
   generate PNG images based on this text report. (#1227)

 * Samtools fixmate, addreplacerg, markdup, ampliconclip and sort
   now accept a -u option to enable uncompressed output, which is
   useful when sending data over a pipe to another process.  Other
   subcommands which already support this option for the same
   purpose are calmd, collate, merge, view and depad. (#1265)

 * samtools stats has a new GCT section, where it reports ACGT
   content percentages, similar to GCC but taking into account the
   read orientation. (#1274)

 * Samtools split now supports splitting by tag content with the -d
   option (#1211)

 * samtools merge now accepts a BED file as a command line argument
   (-L) and does the merging only with reads overlapping the
   specified regions (#1156)

 * Samtools sort now has a minhash collation (-M) to group
   unmapped reads with similar sequence together.  This can
   sometimes significantly reduce the file size. (#1093)

 * Samtools bedcov now has -g and -G options to filter-in and
   filter-out based on the FLAG field.  Also the new -d option
   adds an extra column per file counting the number of bases
   with a depth greater than or equal to a given threshold.
   (#1214)

 * Fixed samtools bedcov -j option (discard deletions and ref-skips)
   with multiple input files (#1212)

 * samtools bedcov will now accept BED files with columns separated
   by spaces as well as tabs (#1246; #1188 reported by Mary Carmack)

 * samtools depth can now include deletions (D) when computing the
   base coverage depth, if the user adds the -J option to the command
   line (#1163).

 * samtools depth will count only the bases of one read, for the
   overlapping section of a read pair, if the -s option is used in
   the command line (#1241, thanks to Teng Li).

 * samtools depth will now write zeros for the entire reference
   length, when "samtools depth -aa" is run on a file with no
   alignments. (#1252; #1249 reported by Paul Donovan)

 * Stopped depth from closing stdout, which triggered test fails in
   pysam (#1208, thanks to John Marshall).

 * samtools view now accepts remote URIs for FASTA and FAI files.
   Furthermore, the reference and index file can be provided in a
   single argument, such as samtools view -T
   ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai a.cram
   (#1176; samtools/htslib#933 reported by @uitde007)

 * samtools faidx gets new options --fai-idx and --gzi-idx to allow
   specification of the locations of the .fai and (if needed) .gzi
   index files. (#1283)

 * The samtools fasta/fastq '-T' option can now add SAM array (type
   'B') tags to the output header lines. (#1301)

 * samtools mpileup can now display MAPQ either as ASCII characters
   (with -s/--output-MQ; column now restored to its documented order
   as in 1.9 and previous versions) or comma-separated numbers (with
   --output-extra MAPQ; in SAM column order alongside other selected
   --output-extra columns).

 When both -s/--output-MQ and -O/--output-BP are used, samtools 1.10
printed the extra columns in the opposite order.  This changes the
format produced by 1.10's --output-extra MAPQ. (#1281, thanks to John
Marshall; reported by Christoffer Flensburg)

 * samtools tview now accepts a -w option to set the output width in
   text mode (-d T). (#1280)

 * The dict command can now add AN tags containing alternative names
   with "chr" prefixes added to or removed from each sequence name
   as appropriate and listing both "M" and "MT" alternatives for
   mitochondria. (#1164, thanks to John Marshall)

 * The samtools import command, labelled as obsolete in May 2009
   and removed from all help and documentation later that year,
   has finally been removed.  Use samtools view instead. (#1185)

 * Replaced the remaining usage of the Samtools 0.1 legacy API with
   htslib calls. (#1187, thanks to John Marshall)

 * Documentation / help improvements (#1154; #1168; #1191; #1199;
   #1204; #1313):

   - Fixed a few man-page table layout issues

   - Added <file>##idx##<index> filename documentation

   - Fixed usage statement for samtools addreplacerg

   - Miscellaneous spelling and grammar fixes

   - Note fixmate/markdup name collated rather than name sorted input

   - Note that fastq and fasta inputs should also be name collated

   - Reshuffled order of main man-page and added -@ to more sub-pages

   - The misc/seq_cache_populate.pl script now gives REF_CACHE
     guidance

 * Additional documentation improvements, thanks to John Marshall
   (#1181; #1224; #1248; #1262; #1300)

   - Emphasise that samtools index requires a position-sorted file

   - Document 2^29 chromosome length limit in BAI indexes

   - Numerous typing, spelling and formatting fixes

 * Improved the message printed when samtools view fails to read its
   input (#1296)

 * Added build support for the OpenIndiana OS (#1165, thanks to John
   Marshall)

 * Fixed failing tests on OpenBSD (#1151, thanks to John Marshall)

 * The samtools sort tests now use less memory so the test suite
   works better on small virtual machines. (#1159)

 * Improved markdup's calculation of insert sizes (#1161) Also
   improved tests (#1150) and made it run faster when not checking
   for optical duplicates or adding 'do' tags (#1308)

 * Fixed samtools coverage minor inconsistency vs idxstats (#1205;
   #1203 reported by @calliza)

 * Fixed samtools coverage quality thresholding options which
   were the wrong way round compared to mpileup (-q is the
   mapping quality threshold and -Q is base quality). (#1279;
   #1278 reported by @kaspernie)

 * Fixed bug where `samtools fastq -i` would add two copies of the
   barcode in the fastq header if both reads in a pair had a "BC:Z"
   tag (#1309; #1307 reported by @mattsoup)

 * Samtools calmd no longer errors with a SEQ of "*" (#1230; #1229
   reported by Bob Harris)

 * Samtools tview now honours $COLUMNS, fixing some CI tests (#1171;
   #1162 reported by @cljacobs)

 * Fixed a samtools depad overflow condition (#1200)

 * Improved curses detection in configure script (#1170, #577, #940)

 * Fixed samtools stats integer overflows and added support for long
   references (#1174; #1173)

 * Fixed a 1-byte undersized memory allocation in samtools merge.
   (#1302)

samtools release 1.10:

Changes affecting the whole of samtools, or multiple sub-commands:

 * Samtools now uses the new HTSlib header API.  As this adds more
   checks for invalid headers, it is possible that some illegal files
   will now be rejected when they would have been allowed by earlier
   versions. (#998)

   Examples of problems that will now be rejected include @SQ lines
   with no SN: tag, and @RG or @PG lines with no ID: tag.

 * samtools sub-commands will now add '@PG' header lines to output
   sam/bam/cram files.  To disable this, use the '--no-PG' option.
   (#1087; #1097)

 * samtools now supports alignment records with reference positions
   greater than 2 gigabases.  This allows samtools to process
   alignments for species which have large chromosomes, like axolotl
   and lungfish.  Note that due to file format limitations, data
   with large reference positions must use the SAM format. (#1107;
   #1117)

 * Improved the efficiency of reading and writing SAM format data by
   2 fold (single thread). This is further improved by the ability to
   use multiple threads, as previously done with BAM and CRAM.

 * samtools can now write BGZF-compressed SAM format.  To enable
   this, either save files with a '.sam.gz' suffix, or use
   '--output-fmt sam.gz'.

 * samtools can now index BGZF-compressed SAM files.

 * The region parsing code has been improved to handle colons in
   reference names.  Strings can be disambiguated by the use of
   braces, so for example when reference sequences called "chr1" and
   "chr1:100-200" are both present, the regions "{chr1}:100-200" and
   "{chr1:100-200}" unambiguously indicate which reference is being
   used. (#864)

 * samtools flags, flagstats, idxstats and stats now have aliases
   flag, flagstat, idxstat and stat. (#934)

 * A new global '--write-index' option has been added.  This allows
   output sam.gz/bam/cram files to be indexed while they are being
   written out. This should work with addreplacerg, depad, markdup,
   merge, sort, split, and view. (#1062)

 * A global '--verbosity' option has been added to enable/disable
   debugging output. (#1124, thanks to John Marshall)

 * It is now possible to have data and index files stored in
   different locations.  There are two ways to tell samtools
   where to find the index:

   1. Samtools bedcov, depth, merge, mpileup, stats, tview, and
      view accept a new option (-X).  When this is used, each input
      sam/bam/cram listed on the command line should have a
      corresponding index file.

      Note that all the data files should be listed first, followed
      by all the index files. (#978, thanks to Mingfei Shao)

   2. A delimiter '##idx##' can be appended to the data file name
      followed by the index file name.  This can be used both for
      input files and outputs when indexing on-the-fly.

 * HTSlib (and therefore SAMtools) now uses version 4 signatures by
   default for its s3:// plug-in.  It can also write to S3 buckets,
   as long as version 4 signatures are in use.  See HTSlib's NEWS
   file and htslib-s3-plugin manual page for more information.

 * HTSlib (and therefore SAMtools) no longer considers a
   zero-length file to be a valid SAM file.  This has been
   changed so that pipelines such as `somecmd | samtools ...`
   with `somecmd` aborting before outputting anything will now
   propagate the error to the second command.

 * The samtools manual page has been split up into one for each
   sub-command.  The main samtools.1 manual page now lists the
   sub-commands and describes the common global options. (#894)

 * The meaning of decode_md, store_md and store_nm in the fmt-option
   section of the samtools.1 man page has been clarified. (#898,
   thanks to Evan Benn)

 * Fixed numerous memory leaks. (#892)

 * Fixed incorrect macro definition on Windows. (#950)

 * bedcov, phase, misc/ace2sam and misc/wgsim now check for
   failure to open files.  (#1013, thanks to Julie Blommaert and
   John Marshall)

Changes affecting specific sub-commands:

 * A new "coverage" sub-command has been added.  This prints a
   tabular format of the average coverage and percent coverage for
   each reference sequence, as well as number of aligned reads,
   average mapping quality and base quality.  It can also (with the
   '-m' option) plot a histogram of coverage across the genome.
   (#992, thanks to Florian Breitwieser)

 * samtools calmd:

   - Reference bases in MD: tags are now converted to upper case.
     (#981, #988)

 * samtools depth:

   - Add new options to write a header to the output (-H) and to
     direct the output to a file (-o).  (#937, thanks to Pierre
     Lindenbaum)

   - New options '-g' and '-G' can be used to filter reads. (#953)

   - Fix memory leak when failing to set CRAM options. (#985, thanks
     to Florian Breitwieser)

   - Fix bug when using region filters where the '-a' option did not
     work for regions with no coverage. (#1113; #1112 reported by
     Paweł Sztromwasser)

 * samtools fasta and fastq:

   - '-1 FILE -2 FILE' with the same filename now works properly.
     (#1042)

   - '-o FILE' is added as a synonym for '-1 FILE -2 FILE'. (#1042)

   - The '-F' option now defaults to 0x900 (SECONDARY,SUPPLEMENTARY).
     Previously secondary and supplementary records were filtered
     internally in a way that could not be turned off. (#1042; #939
     reported by @finswimmer)

   - Allow reading from a pipe without an explicit '-' on the command
     line. (#1042; #874 reported by John Marshall)

   - Turn on multi-threading for bgzf compressed output files. (#908)

   - Fixed bug where the samtools fastq -i would output incorrect
     information in the Casava tags for dual-index reads.  It
     also now prints the tags for dual indices in the same way as
     bcl2fastq, using a '+' sign between the two parts of the
     index. (#1059; #1047 reported by Denis Loginov)

 * samtools flagstat:

   - Samtools flagstat can now optionally write its output in JSON
     format or as a tab-separated values file. (#1106, thanks to
     Vivek Rai).

 * samtools markdup:

   - It can optionally tag optical duplicates (reads following
     Illumina naming conventions only).  The is enabled with the
     '-d' option, which sets the distance for duplicates to be
     considered as optical. (#1091; #1103; #1121; #1128; #1134)

   - The report stats (-s) option now outputs counts for optical and
     non-primary (supplementary / secondary) duplicates.  It also
     reports the Picard "estimate library size" statistic.  A new
     '-f' option can be used to save the statistics in a given file.
     (#1091)

   - The rules for calling duplicates can be changed using the new
     --mode option.  This mainly changes the position associated with
     each read in a pair.  '--mode t' (the default) is the existing
     behaviour where the position used is that of the outermost
     template base associated with the read. Alternatively '--mode s'
     always uses the first unclipped sequence base.  In practice,
     this only makes a difference for read pairs where the two reads
     are aligned in the same direction. (#1091)

   - A new '-c' option can be used to clear any existing duplicate
     tags. (#1091)

   - A new '--include-fails' option makes markdup include QC-failed
     reads. (#1091)

   - Fixed buffer overflow in temporary file writer when writing a
     mixture of long and short alignment records. (#911; #909)

 * samtools mpileup:

   - mpileup can now process alignments including CIGAR P (pad)
     operators correctly.  They will now also produce the correct
     output for alignments where insertions are immediately followed
     by deletions, or deletions by insertions.  Note that due to
     limitations in HTSlib, they are still unable to output sequences
     that have been inserted before the first aligned base of a read.
     (#847; #842 reported by Tiffany Delhomme. See also htslib issue
     #59 and pull request #699).

   - In samtools mpileup, a deletion or pad on the reverse strand is
     now marked with a different character ('#') than the one used on
     a forward strand ('*'), if the '--reverse-del' option is used.
     (#1070)

   - New option '--output-extra' can be used to add columns for user
     selected alignment fields or aux tags. (#1073)

   - Fixed double-counting of overlapping bases in alignment records
     with deletions or reference skips longer than twice the insert
     size. (#989; #987 reported by @dariomel)

   - Improved manual page with documentation about what each output
     column means. (#1055, thanks to John Marshall)

 * samtools quickcheck:

   - Add unmapped (-u) option, which disables the check for @SQ lines
     in the header. (#920, thanks to Shane McCarthy)

 * samtools reheader:

   - A new option '-c' allows the input header to be passed to a
     given command.  Samtools then takes the output of this command
     and uses it as the replacement header. (#1007)

   - Make it clear in help message that reheader --in-place only
     works on CRAM files. (#921, thanks to Julian Gehring)

   - Refuse to in-place reheader BAM files, instead of unexpectedly
     writing a BAM file to stdout. (#935)

 * samtools split:

   - In samtools split, the '-u' option no longer accepts an extra
     file name from which a replacement header was read.  The two
     file names were separated using a colon, which caused problems
     on Windows and prevented the use of URLs.  A new '-h' option has
     been added to allow the replacement header file to be specified
     in its own option. (#961)

   - Fixed bug where samtools split would crash if it read a SAM
     header that contained an @RG line with no ID tag. (#954,
     reported by @blue-bird1)

 * samtools stats:

   - stats will now compute base compositions for BC, CR, OX and RX
     tags, and quality histograms for QT, CY, BZ and QX tags. (#904)

   - New stats FTC and LTC showing total number of nucleotides for
     first and last fragments. (#946)

   - The rules for classifying reads as "first" or "last" fragment
     have been tightened up. (#949)

   - Fixed bug where stats could over-estimate coverage when using
     the target-regions option or when a region was specified on the
     command-line. (#1027; #1025, reported by Miguel Machado; #1029,
     reported by Jody Phelan).

   - Fixed error in stats GCD percentile depth calculation when the
     depth to be reported fell between two bins.  It would report the
     depth entirely from the lower bin instead of taking a weighted
     average of the two. (#1048)

   - Better catching and reporting of out of memory conditions.
     (#984; #982, reported by Jukka Matilainen)

   - Improved manual page. (#927)

 * samtools tview:

   - tview can now display alignments including CIGAR P operators, D
     followed by I and I followed by D correctly.  See mpileup above
     for more information. (#847; #734, reported by Ryan Lorig-Roach)

   - The "go to position" text entry box has been made wider. (#968,
     thanks to John Marshall)

   - Fixed samtools tview -s option which was not filtering reads
     correctly. It now only shows reads from the requested sample or
     read group. (#1089)

 * samtools view:

   - New options '-d' and '-D' to only output alignments which
     have a tag with a given type and value. (#1001, thanks to
     Gert Hulselmans)

 * misc/plot-bamstats script:

   - Fixed merge (-m) option. (#923, #924 both thanks to Marcus D
     Sherman)

   - Made the quality heatmap work with gnuplot version 5.2.7 and
     later. (#1068; #1065 reported by Martin Mokrejš)

   - Fixed --do-ref-stats bug where fasta header lines would be
     counted as part of the sequence when the --targets option was
     used. (#1120, thanks to Neil Goodgame)

 * Removed the misc/varfilter.py Python script, as it takes
   consensus-pileup as input, which was removed from samtools in
   release 0.1.17 in 2011. (#1125)

samtools release 1.9:

 * Samtools mpileup VCF and BCF output is now deprecated.  It is
   still functional, but will warn.  Please use bcftools mpileup
   instead. (#884)

 * 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. (#859)

 * Samtools stats new features:

   - The '--remove-overlaps' option discounts overlapping portions
     of templates when computing coverage and mapped base counting.
     (#855)



   - 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. (#855)

   - Split base composition and length statistics by first and last
     reads. (#814, #816)

 * Samtools faidx new features:

   - Now takes long options. (#509, thanks to Pierre Lindenbaum)

   - Now warns about zero-length and truncated sequences due to the
     requested range being beyond the end of the sequence. (#834)



   - Gets a new option (--continue) that allows it to carry on when a
     requested sequence was not in the index. (#834)

   - It is now possible to supply the list of regions to output in a
     text file using the new '--region-file' option. (#840)

   - New '-i' option to make faidx return the reverse complement of
     the regions requested. (#878)

   - faidx now works on FASTQ (returning FASTA) and added a new fqidx
     command to index and return FASTQ. (#852)

 * 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. (#818)

 * Samtools bedcov gets a new '-j' option to make it ignore deletions
   (D) and reference skips (N) when computing coverage. (#843)

 * Small speed up to samtools coordinate sort, by converting it to
   use radix sort. (#835, thanks to Zhuravleva Aleksandra)

 * Samtools idxstats now works on SAM and CRAM files, however this
   isn't fast due to some information lacking from indices. (#832)

 * 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. (#827, #834, #877,
     cd7197)

   - Various test improvements.

   - Fixed failures in the multi-region iterator (view -M) when
     regions provided via BED files include overlaps (#819,
     reported by Dave Larson).

   - Samtools stats now counts '=' and 'X' CIGAR operators when
     counting mapped bases. (#855)

   - Samtools stats has fixes for insert size filtering (-m, -i).
     (#845; #697 reported by Soumitra Pal)

   - Samtools stats -F now longer negates an earlier -d option.
     (#830)

   - Fix samtools stats crash when using a target region. (#875,
     reported by John Marshall)

   - 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%. (#833, reported by
     Matthias Bernt)

   - Fixed samtools phase '-A' option which was incorrectly defined
     to take a parameter. (#850; #846 reported by Dianne Velasco)

   - Fixed compilation problems when using C_INCLUDE_PATH. (#870;
     #817 reported by Robert Boissy)

   - Fixed --version when built from a Git repository. (#844, thanks
     to John Marshall)

   - Use noenhanced mode for title in plot-bamstats.  Prevents
     unwanted interpretation of characters like underscore in
     gnuplot version 5. (#829, thanks to M. Zapukhlyak)

   - blast2sam.pl now reports perfect match hits (no indels or
     mismatches). (#873, thanks to Nils Homer)

   - 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.

samtools release 1.8:

 * samtools calmd now has a quiet mode.  This can be enabled by
   passing `-Q` to calmd. (Thanks to Colin Davenport)

 * In samtools depth `-d 0` will effectively remove the depth limit.
   (#764)

 * Improvements made to samtools collate's interface and
   documentation.  It is now possible to specify an output file
   name using `-o`, instead of deriving it from the prefix used
   for temporary files.  The prefix itself is now optional if
   `-o` or `-O` (to stdout) is used. (#780)

 * Bug-fixes:

   - Make samtools addreplacerg choose output format by file
     extension. (#767; reported by Argy Megalios)

   - Merge tests now work on ungzipped data, allowing tests to be run
     against different deflate libraries.

   - samtools markdup error messages about missing tags have been
     updated with the suggestion that samtools fixmate is run
     beforehand. (#765; reported by Yudong Cai)

   - Enables the `--reference` option for samtools fastq.  Now works
     like other programs when a reference sequence is needed for CRAM
     files. (#791, reported by Milana Kaljevic)

Samtools release 1.7: markdup supplementaries, multi-region iterator

* 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.

Release 1.6: New markdup command; sort improvements

* 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.

Release 1.5 [Solstice Release] (21st June 2017)
--------------------

* Samtools fastq now has a -i option to create a fastq file from an index
  tag, and a -T option (similar to -t) to add user specified aux tags to
  the fastq header line.

* Samtools fastq can now create compressed fastq files, by giving the
  output filenames an extention of .gq, .bgz, or .bgzf

* Samtools sort has a -t TAG option, that allows records to be sorted by
  the value of the specified aux tag, then by position or name.  Merge
  gets a similar option, allowing files sorted this way to be merged.
  (#675; thanks to Patrick Marks of 10xgenomics).