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)