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)