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)