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NEWS
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Release 1.16.1 (2nd September 2022)
-----------------------------------
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)
Release 1.16 (18th August 2022)
-------------------------------
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)
Release 1.15.1 (7th April 2022)
-------------------------------
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)
Release 1.15 (21st February 2022)
---------------------------------
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)
Release 1.14 (22nd October 2021)
--------------------------------
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)
Release 1.13 (7th July 2021)
----------------------------
* 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)
Release 1.12 (17th March 2021)
------------------------------
* 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)
Release 1.11 (22nd September 2020)
----------------------------------
* 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)
Release 1.10 (6th December 2019)
--------------------------------
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)
Release 1.9 (18th July 2018)
----------------------------
* 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: