Release 1.4.1  (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Added options to fastq to create fastq files from BC (or other)
  tags.

* Samtools view has gained a -G <flags> option to exclude on all bits
  set.  For example to discard reads where neither end has been
  mapped use "-G 12".

* Samtools cat has a -b <fofn> option to ease concatenation of many
  files.

* Added misc/samtools_tab_completion for bash auto-completion of
  samtools sub-commands. (#560)

* Samtools tview now has J and K keys for verticale movement by 20
  lines. (#257)

* Various compilation / portability improvements.

* Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
(#667)

Release 1.4  (13 March 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Noteworthy changes in samtools:

* Fixed Issue #345 - out-by-one error in insert-size in samtools stats

* bam_split now add a @PG header to the bam file

* Added mate cigar tag support to fixmate

* Multi-threading is now supported for decoding BAM and CRAM (as well
  as the previously supported encoding).  Most commands that read BAM
  or CRAM have gained an -@ or --threads arguments, providing a
  significant speed bonus.  For commands that both read and write
  files the threads are shared between decoding and encoding tasks.

* Added -a option to samtools mpileup to show all locations, including
  sites with zero depth; repeating the option as -aa or -a -a additionally
  shows reference sequences without any reads mapped to them (#496).

* The mpileup text output no longer contains empty columns at zero coverage
  positions.  Previously it would output "...0\t\t..." in some circumstances
  (zero coverage due to being below a minumum base quality); this has been
  fixed to output as "...0\t*\t*..." with placeholder '*' characters as in
  other zero coverage circumstances (see PR #537).

* To stop it from creating too many temporary files, samtools sort
  will now not run unless its per-thread memory limit (-m) is set to
  at least 1 megabyte (#547).

* The misc/plot-bamstats script now has a -l / --log-y option to change
  various graphs to display their Y axis log-scaled.  Currently this
  affects the Insert Size graph (PR #589; thanks to Anton Kratz).

* Fixmate will now also add and update MC (mate CIGAR) tags.

Samtools release 1.3.1: bug fixes, notably sort temporary files

* The sort command creates any needed temporary files alongside the final
  output file (similarly to the pre-1.3 behaviour), and now aborts when
  it detects a collision with another sort invocation's temporary files.

  When the -T PREFIX option specified is a directory (or when sorting to
  standard output), a random component is now added to temporary filenames
  to try to avoid collisions (#432, #523, #529, #535, PR #530).

* All samtools commands now check for I/O errors more carefully, especially
  when writing output files (#111, #253, #470, PR #467).

* Build fixes for 32-bit systems; be sure to run configure on such systems
  to enable large file support and access to 2GiB+ files.

* The fasta/fastq/bam2fq command no longer ignores reads when the -s option
  is used (#532).

* The fastq -O option no longer crashes on reads that do not have an OQ tag
  field (#517).

* The merge and sort commands now handle (unusual) BAM files that have no
  textual @SQ headers (#548, #550).

* Sorting files containing @CO headers no longer duplicates the comment
  headers, which previously happened on large sorts for which temporary
  files were needed (#563).

* The rmdup and view -l commands no longer crash on @RG headers that do not
  have a LB field (#538).

* Fixed miscellaneous issues #128, #130, #131, #489, and #514.

Samtools release 1.3: many improvements, fixes, new commands

* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
  If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
  and/or -o FILE instead.  (#295, #349, #356, #418, PR #441; see also
  discussions in #171, #213.)

* The "bamshuf" command has been renamed to "collate" (hence the term
  bamshuf no longer appears in the documentation, though it still works
  on the command line for compatibility with existing scripts).

* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
  rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
  INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
  the existing DV, DP4, DPR annotations.

* The mpileup command now applies BAQ calculations at all base positions,
  regardless of which -l or -r options are used (previously with -l it was
  not applied to the first few tens of bases of each chromosome, leading
  to different mpileup results with -l vs. -r; #79, #125, #286, #407).

* Samtools now has a configure script which checks your build environment
  and facilitates choosing which HTSlib to build against.  See INSTALL
  for details.

* Samtools's Makefile now fully supports the standard convention of
  allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
  Previously it listened to $(LDLIBS) instead; if you were overriding
  that, you should now override LIBS rather than LDLIBS.

* A new addreplacerg command that adds or alters @RG headers and RG:Z
  record tags has been added.

* The rmdup command no longer immediately aborts (previously it always
  aborted with "bam_get_library() not yet implemented"), but remains
  not recommended for most use (#159, #252, #291, #393).

* Merging files with millions of headers now completes in a reasonable
  amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
  Chris Smowton, Martin Pollard, Rob Davies).

* Samtools index's optional index output path argument works again (#199).

* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
  alignments with POS far beyond the end of their reference sequences.

* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
  or bam_prob_realn_core() functions, note that these now take an additional
  ref_len parameter.  (The versions named without "_core" are unchanged.)

* The tview command's colour scheme has been altered to be more suitable
  for users with colour blindness (#457).

* Samtools depad command now handles CIGAR N operators and accepts
  CRAM files (#201, #404).

* Samtools stats now outputs separate "N" and "other" columns in the
  ACGT content per cycle section (#376).

* Added -a option to samtools depth to show all locations, including
  zero depth sites (#374).

* New samtools dict command, which creates a sequence dictionary
  (as used by Picard) from a FASTA reference file.

* Samtools stats --target-regions option works again.

* Added legacy API sam.h functions sam_index_load() and samfetch() providing
  bam_fetch()-style iteration over either BAM or CRAM files.  (In general
  we recommend recoding against the htslib API directly, but this addition
  may help existing libbam-using programs to be CRAM-enabled easily.)

* Fixed legacy API's samopen() to write headers only with "wh" when writing
  SAM files.  Plain "w" suppresses headers for SAM file output, but this
  was broken in 1.2.

* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
  this failed with "[bam_mating] cannot determine output format".

* Restored previous "samtools calmd -u" behaviour of writing compression
  level 0 BAM files.  Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
  BAM files, which cannot be read by most other tools.  (Samtools commands
  other than calmd were unaffected by this bug.)

* Restored bam_nt16_nt4_table[] to legacy API header bam.h.

* Fixed bugs #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
  #462, #475, and #495.

Bug fix release

Bug fix release

First HTSlib-based Samtools release

Final standalone non-htslib samtools release

Test release RC12

Test release RC11

Test release RC10

Test release RC9

Test release RC8

Test release RC7

Test release RC6

Test release RC5

Test release RC4

Test release RC3

Test release RC2

Test release RC1