7b75752899
- Update to version 1.19 Too many changes to list, for details see https://github.com/samtools/samtools/releases/tag/1.19 - Update to version 1.18 Too many changes to list, for details see https://github.com/samtools/samtools/releases/tag/1.18 - Update to version 1.17 Too many changes to list, for details see https://github.com/samtools/samtools/releases/tag/1.17 OBS-URL: https://build.opensuse.org/request/show/1136377 OBS-URL: https://build.opensuse.org/package/show/science/samtools?expand=0&rev=17
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-------------------------------------------------------------------
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Wed Jan 3 01:46:12 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 1.19
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Too many changes to list, for details see
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https://github.com/samtools/samtools/releases/tag/1.19
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- Update to version 1.18
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Too many changes to list, for details see
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https://github.com/samtools/samtools/releases/tag/1.18
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- Update to version 1.17
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Too many changes to list, for details see
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https://github.com/samtools/samtools/releases/tag/1.17
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-------------------------------------------------------------------
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Thu Sep 15 00:59:03 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 1.16.1
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* Fixed a bug with the template-coordinate sort which caused
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incorrect ordering when using threads, or processing large
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files that don't fit completely in memory.
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* Fixed a crash that occurred when trying to use samtools merge
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in template-coordinate mode.
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- Update to version 1.16.0
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* New work and changes:
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- samtools reference command added. This subcommand extracts
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the embedded reference out of a CRAM file.
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- samtools import now adds grouped by query-name to the header
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- Made samtools view read error messages more generic. Former
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error message would claim that there was a "truncated file
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or corrupt BAM index file" with no real justification. Also
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reset errno in stream_view which could lead to confusing
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error messages.
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- Make samtools view -p also clear mqual, tlen and cigar.
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- Add bedcov option -c to report read count.
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- Add UMI/barcode handling to samtools markdup.
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- Add a new template coordinate sort order to samtools sort
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and samtools merge. This is useful when working with unique
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molecular identifiers (UMIs).
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- Rename mpileup --ignore-overlaps to
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--ignore-overlaps-removal or --disable-overlap-removal.
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- The dict command can now read BWA's .alt file and add AH:*
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tags indicating reference sequences that represent
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alternate loci.
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- The samtools index command can now accept multiple alignment
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filenames with the new -M option, and will index each of
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them separately.
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- Allow samtools fastq -T "*". This allows all tags from SAM
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records to be written to fastq headers.
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* Bug Fixes:
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- Re-enable --reference option for samtools depth. The
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reference is not used but this makes the command line
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usage compatible with older releases.
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- Fix regex coordinate bug in samtools markdup.
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- Fix divide by zero in plot-bamstats -m, on unmapped data.
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- Fix missing RG headers when using samtools merge -r.
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- Fix a possible unaligned access in samtools reference.
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* Documentation:
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- Add documentation on CRAM compression profiles and some
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of the newer options that appear in CRAM 3.1 and above.
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- Add sclen filter expression keyword documentation.
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- Extend FILTER EXPRESSION man page section to match the
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changes made in HTSlib.
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-------------------------------------------------------------------
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Wed Apr 20 20:13:07 UTC 2022 - Ferdinand Thiessen <rpm@fthiessen.de>
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- Update to version 1.15.1
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* Samtools mpileup VCF and BCF output (deprecated in release 1.9)
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has been removed. Please use bcftools mpileup instead.
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* Added --min-BQ and --min-MQ options to depth.
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* Improved automatic file type detection with view -u or
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view -1.
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* For markdup optical duplicate marking add regex options for
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custom coordinates.
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* New samtools consensus subcommand for generating consensus
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from SAM, BAM or CRAM files based on the contents of the
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alignment records.
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* New samtools view --fetch-pairs option.
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* New samtools head subcommand for conveniently displaying
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the headers of a SAM, BAM, or CRAM file.
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* Bug fixes
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- Update to version 1.14
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* The legacy samtools API has been removed:
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libbam.a, bam_endian.h, sam.h and most of bam.h
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* New samtools samples command to list the samples used in a
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SAM/BAM/CRAM file.
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* mpileup now supports base modifications via the SAM Mm/MM
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auxiliary tag. Please see the --output-mods option.
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* Added mpileup --output-BP-5 option to output the BP field in
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5' to 3' order instead of left to right.
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* Added samtools view --rf option as an additional FLAG
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filtering method.
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* New samtools import -N option to use the second word on
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a FASTQ header line, matching the SRA/ENA FASTQ variant.
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* Improve view -x option to simplify specifying multiple tags,
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and added the reverse --keep-tag option to include rather
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than exclude.
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* Switched the processing order of view -x (tag filtering)
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and -e (expression) handling.
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* Added filter expression endpos keyword.
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* samtools view errors now appear after any SAM output,
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improving their visibility.
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* Improved samtools sort use of temporary files, both tidying
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up if it fails and recovery when facing pre-existing
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temporary files.
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* Filtering in samtools view now sets the UNMAP BAM flag
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when given the -p option.
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* Make CRAM references shared during samtools merge so
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merging many files has a lower memory usage.
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* Bug fixes
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- Update to version 1.13
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* Fixed samtools view FILE REGION, mpileup -r REGION,
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coverage -r REGION and other region queries
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* Added options to set and clear flags to samtools view
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* samtools view now has long option equivalents for most of its
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single-letter options
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* A new tool, samtools import, has been added.
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It reads one or more FASTQ files and converts them into unmapped
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SAM, BAM or CRAM.
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* Fixed samtools coverage error message when the target region name#
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is not present in the file header.
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* Made samtools coverage ASCII mode produce true ASCII output.
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* samtools coverage now allows setting the maximum depth,
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using the -d/--depth option.
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* samtools flags now accepts any number of command line arguments,
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allowing multiple SAM flag combinations to be converted at once.
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* samtools ampliconclip, ampliconstats and plot-ampliconstats now support
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inputs that list more than one reference.
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* samtools ampliconclip now accepts the --tolerance option,
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which allows the user to set the number of bases within which a region
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is matched.
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* Fixed negative depth values in ampliconstats output.
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* samtools addreplacerg now allows for updating (replacing) an
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existing @RG line in the output header, if a new @RG line is provided
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in the command line, via the -r argument.
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* Stopped samtools cat from outputting multiple CRAM EOF markers.
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* Three new counts have been added to samtools flagstat:
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primary, mapped primary and duplicate primary.
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* samtools merge now accepts a -o FILE option specifying the output file,
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similarly to most other subcommands.
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-------------------------------------------------------------------
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Wed Apr 28 15:57:19 UTC 2021 - Ferdinand Thiessen <rpm@fthiessen.de>
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- Update to version 1.12
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* The legacy samtools API (libbam.a, bam.h, sam.h, etc) is
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deprecated and will be removed entirely in a future SAMtools
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release. It is recommend coding against the HTSlib API directly.
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* I/O errors and record parsing errors during the reading of
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SAM/BAM/CRAM files are now always detected.
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* samtools --version now displays a summary of the compilation
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details and available features, including flags, used libraries
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and enabled plugins from HTSlib.
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* samtools stats now displays the number of supplementary reads
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in the SN section. Also, supplementary reads are no longer
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considered when splitting read pairs by orientation.
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* samtools stats now counts only the filtered alignments that
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overlap target regions, if any are specified.
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* samtools view now accepts option -N, which takes a file containing
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read names of interest. This allows the output of only the reads
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with names contained in the given file.
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* samtools view -d option now works without a tag associated value,
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which allows it to output all the reads with the given tag.
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* samtools view -d and -D options now accept integer and single
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character values associated with tags, not just strings.
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* samtools view now works with the filtering expressions introduced
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by HTSlib. The filtering expression is passed to the program using
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the specific option -e or the global long option --input-fmt-option.
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* samtools markdup now benefits from an increase in performance
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in the situation when a single read has tens or hundreds of
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thousands of duplicates.
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* A new FASTA/FASTQ sanitizer script (fasta-sanitize.pl) was
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added, which corrects the invalid characters in the reference
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names.
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* Fixed a bug in samtools cat, which prevented the command from
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running in multi-threaded mode.
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* Fixed a samtools merge segmentation fault when it failed to
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merge header @PG records.
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* Ampliconclip and ampliconstats now guard against the BED file
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containing more than one reference (chromosome) and fail when
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found. Adding proper support for multiple references will
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appear later.
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-------------------------------------------------------------------
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Fri Mar 19 09:18:00 UTC 2021 - Wang Jun <jgwang@suse.com>
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- Update to version 1.11
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* New samtools ampliconclip sub-command for removing primers from
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amplicon-based sequencing experiments, including the current
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COVID-19 projects. The primers are listed in a BED file and can be
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either soft-clipped or hard-clipped. (#1219)
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* New samtools ampliconstats sub-command to produce a textual summary
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of primer and amplicon usage, in a similar style to "samtools
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stats". The misc/plot-ampliconstats script can generate PNG
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images based on this text report. (#1227)
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* Samtools fixmate, addreplacerg, markdup, ampliconclip and sort now
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accept a -u option to enable uncompressed output, which is useful when
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sending data over a pipe to another process. Other subcommands which
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already support this option for the same purpose are calmd, collate,
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merge, view and depad. (#1265)
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* samtools stats has a new GCT section, where it reports ACGT content
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percentages, similar to GCC but taking into account the read orientation.
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(#1274)
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* Samtools split now supports splitting by tag content with the -d
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option (#1211)
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* samtools merge now accepts a BED file as a command line argument (-L) and
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does the merging only with reads overlapping the specified regions (#1156)
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* Samtools sort now has a minhash collation (-M) to group unmapped
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reads with similar sequence together. This can sometimes
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significantly reduce the file size. (#1093)
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* Samtools bedcov now has -g and -G options to filter-in and
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filter-out based on the FLAG field. Also the new -d option adds
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an extra column per file counting the number of bases with a depth
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greater than or equal to a given threshold. (#1214)
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* Fixed samtools bedcov -j option (discard deletions and ref-skips)
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with multiple input files (#1212)
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* samtools bedcov will now accept BED files with columns separated by
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spaces as well as tabs (#1246; #1188 reported by Mary Carmack)
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* samtools depth can now include deletions (D) when computing the base
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coverage depth, if the user adds the -J option to the command
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line (#1163).
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* samtools depth will count only the bases of one read, for the overlapping
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section of a read pair, if the -s option is used in the command line
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(#1241, thanks to Teng Li).
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* samtools depth will now write zeros for the entire reference length,
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when "samtools depth -aa" is run on a file with no alignments. (#1252;
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#1249 reported by Paul Donovan)
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* Stopped depth from closing stdout, which triggered test fails
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in pysam (#1208, thanks to John Marshall).
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* samtools view now accepts remote URIs for FASTA and FAI files.
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Furthermore, the reference and index file can be provided in a single
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argument, such as
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samtools view -T ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai a.cram
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(#1176; samtools/htslib#933 reported by @uitde007)
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* samtools faidx gets new options --fai-idx and --gzi-idx to allow
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specification of the locations of the .fai and (if needed) .gzi index
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files. (#1283)
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* The samtools fasta/fastq '-T' option can now add SAM array (type 'B') tags
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to the output header lines. (#1301)
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* samtools mpileup can now display MAPQ either as ASCII characters (with
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-s/--output-MQ; column now restored to its documented order as in 1.9 and
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previous versions) or comma-separated numbers (with --output-extra MAPQ;
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in SAM column order alongside other selected --output-extra columns).
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When both -s/--output-MQ and -O/--output-BP are used, samtools 1.10 printed
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the extra columns in the opposite order. This changes the format produced
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by 1.10's --output-extra MAPQ. (#1281, thanks to John Marshall; reported
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by Christoffer Flensburg)
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* samtools tview now accepts a -w option to set the output width in
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text mode (-d T). (#1280)
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* The dict command can now add AN tags containing alternative names with
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"chr" prefixes added to or removed from each sequence name as appropriate
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and listing both "M" and "MT" alternatives for mitochondria. (#1164,
|
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thanks to John Marshall)
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* The samtools import command, labelled as obsolete in May 2009 and
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removed from all help and documentation later that year, has
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finally been removed. Use samtools view instead. (#1185)
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* Replaced the remaining usage of the Samtools 0.1 legacy API with
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htslib calls. (#1187, thanks to John Marshall)
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* Documentation / help improvements (#1154; #1168; #1191; #1199;
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#1204; #1313):
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- Fixed a few man-page table layout issues
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- Added <file>##idx##<index> filename documentation
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- Fixed usage statement for samtools addreplacerg
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- Miscellaneous spelling and grammar fixes
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- Note fixmate/markdup name collated rather than name sorted input
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- Note that fastq and fasta inputs should also be name collated
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- Reshuffled order of main man-page and added -@ to more sub-pages
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- The misc/seq_cache_populate.pl script now gives REF_CACHE guidance
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* Additional documentation improvements, thanks to John Marshall (#1181;
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#1224; #1248; #1262; #1300)
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- Emphasise that samtools index requires a position-sorted file
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- Document 2^29 chromosome length limit in BAI indexes
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- Numerous typing, spelling and formatting fixes
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* Improved the message printed when samtools view fails to read its
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input (#1296)
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* Added build support for the OpenIndiana OS (#1165, thanks to John Marshall)
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* Fixed failing tests on OpenBSD (#1151, thanks to John Marshall)
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* The samtools sort tests now use less memory so the test suite works better
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on small virtual machines. (#1159)
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* Improved markdup's calculation of insert sizes (#1161)
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Also improved tests (#1150) and made it run faster when not checking
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for optical duplicates or adding 'do' tags (#1308)
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* Fixed samtools coverage minor inconsistency vs idxstats (#1205; #1203
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reported by @calliza)
|
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* Fixed samtools coverage quality thresholding options which were the
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wrong way round compared to mpileup (-q is the mapping quality threshold
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and -Q is base quality). (#1279; #1278 reported by @kaspernie)
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* Fixed bug where `samtools fastq -i` would add two copies of the barcode
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in the fastq header if both reads in a pair had a "BC:Z" tag (#1309;
|
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#1307 reported by @mattsoup)
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* Samtools calmd no longer errors with a SEQ of "*" (#1230; #1229
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reported by Bob Harris)
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* Samtools tview now honours $COLUMNS, fixing some CI tests (#1171; #1162
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reported by @cljacobs)
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* Fixed a samtools depad overflow condition (#1200)
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* Improved curses detection in configure script (#1170, #577, #940)
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* Fixed samtools stats integer overflows and added support for long
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references (#1174; #1173)
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* Fixed a 1-byte undersized memory allocation in samtools merge. (#1302)
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-------------------------------------------------------------------
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Wed Feb 5 15:01:48 UTC 2020 - Todd R <toddrme2178@gmail.com>
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+ Changes affecting the whole of samtools, or multiple sub-commands:
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* Samtools now uses the new HTSlib header API. As this adds more checks
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for invalid headers, it is possible that some illegal files will now
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be rejected when they would have been allowed by earlier versions.
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Examples of problems that will now be rejected include @SQ lines with
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no SN: tag, and @RG or @PG lines with no ID: tag.
|
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* samtools sub-commands will now add '@PG' header lines to output sam/bam/cram
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files. To disable this, use the '--no-PG' option.
|
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* samtools now supports alignment records with reference positions greater
|
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than 2 gigabases. This allows samtools to process alignments for
|
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species which have large chromosomes, like axolotl and lungfish. Note that
|
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due to file format limitations, data with large reference positions
|
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must use the SAM format.
|
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* Improved the efficiency of reading and writing SAM format data by 2 fold
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(single thread). This is further improved by the ability to use multiple
|
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threads, as previously done with BAM and CRAM.
|
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* samtools can now write BGZF-compressed SAM format. To enable this,
|
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either save files with a '.sam.gz' suffix, or use '--output-fmt sam.gz'.
|
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* samtools can now index BGZF-compressed SAM files.
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* The region parsing code has been improved to handle colons in reference
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names. Strings can be disambiguated by the use of braces, so for
|
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example when reference sequences called "chr1" and "chr1:100-200"
|
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are both present, the regions "{chr1}:100-200" and "{chr1:100-200}"
|
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unambiguously indicate which reference is being used.
|
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* samtools flags, flagstats, idxstats and stats now have aliases
|
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flag, flagstat, idxstat and stat.
|
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* A new global '--write-index' option has been added. This allows output
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sam.gz/bam/cram files to be indexed while they are being written out.
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This should work with addreplacerg, depad, markdup, merge, sort, split,
|
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and view.
|
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* A global '--verbosity' option has been added to enable/disable
|
|
debugging output.
|
|
* It is now possible to have data and index files stored in different
|
|
locations.
|
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* HTSlib (and therefore SAMtools) now uses version 4 signatures by default
|
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for its s3:// plug-in. It can also write to S3 buckets, as long as
|
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version 4 signatures are in use. See HTSlib's NEWS file and
|
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htslib-s3-plugin manual page for more information.
|
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* 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
|
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anything will now propagate the error to the second command.
|
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* 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.
|
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* The meaning of decode_md, store_md and store_nm in the fmt-option section
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of the samtools.1 man page has been clarified.
|
|
* Fixed numerous memory leaks.
|
|
* Fixed incorrect macro definition on Windows.
|
|
* bedcov, phase, misc/ace2sam and misc/wgsim now check for failure to open
|
|
files.
|
|
+ Changes affecting specific sub-commands:
|
|
* A new "coverage" sub-command has been added. This prints a tabular format
|
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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.
|
|
* samtools calmd:
|
|
> Reference bases in MD: tags are now converted to upper case.
|
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* samtools depth:
|
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> Add new options to write a header to the output (-H) and to direct
|
|
the output to a file (-o).
|
|
> New options '-g' and '-G' can be used to filter reads.
|
|
> Fix memory leak when failing to set CRAM options.
|
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> Fix bug when using region filters where the '-a' option did not
|
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work for regions with no coverage.
|
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* samtools fasta and fastq:
|
|
> '-1 FILE -2 FILE' with the same filename now works properly.
|
|
> '-o FILE' is added as a synonym for '-1 FILE -2 FILE'.
|
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> The '-F' option now defaults to 0x900 (SECONDARY,SUPPLEMENTARY).
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Previously secondary and supplementary records were filtered internally
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in a way that could not be turned off.
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> Allow reading from a pipe without an explicit '-' on the command line.
|
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> Turn on multi-threading for bgzf compressed output files.
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> Fixed bug where the samtools fastq -i would output incorrect information
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in the Casava tags for dual-index reads. It also now prints the tags
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for dual indices in the same way as bcl2fastq, using a '+' sign between
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the two parts of the index.
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* samtools flagstat:
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> Samtools flagstat can now optionally write its output in JSON format or
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as a tab-separated values file..
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* samtools markdup:
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> It can optionally tag optical duplicates (reads following Illumina
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naming conventions only). The is enabled with the '-d' option,
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which sets the distance for duplicates to be considered as optical.
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> The report stats (-s) option now outputs counts for optical and
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non-primary (supplementary / secondary) duplicates. It also reports
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the Picard "estimate library size" statistic. A new '-f' option
|
|
can be used to save the statistics in a given file.
|
|
> 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.
|
|
> A new '-c' option can be used to clear any existing duplicate tags.
|
|
> A new '--include-fails' option makes markdup include QC-failed reads.
|
|
> Fixed buffer overflow in temporary file writer when writing a mixture
|
|
of long and short alignment records.
|
|
* 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..
|
|
> 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.
|
|
> New option '--output-extra' can be used to add columns for user
|
|
selected alignment fields or aux tags.
|
|
> Fixed double-counting of overlapping bases in alignment records with
|
|
deletions or reference skips longer than twice the insert size.
|
|
> Improved manual page with documentation about what each output column
|
|
means.
|
|
* samtools quickcheck:
|
|
> Add unmapped (-u) option, which disables the check for @SQ lines in
|
|
the header.
|
|
* 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.
|
|
> Make it clear in help message that reheader --in-place only works on
|
|
CRAM files.
|
|
> Refuse to in-place reheader BAM files, instead of unexpectedly writing
|
|
a BAM file to stdout.
|
|
* 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.
|
|
> Fixed bug where samtools split would crash if it read a SAM header that
|
|
contained an @RG line with no ID tag.
|
|
* 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.
|
|
> New stats FTC and LTC showing total number of nucleotides for first and
|
|
last fragments.
|
|
> The rules for classifying reads as "first" or "last" fragment have been
|
|
tightened up.
|
|
> Fixed bug where stats could over-estimate coverage when using the
|
|
target-regions option or when a region was specified on the command-line..
|
|
> 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.
|
|
> Better catching and reporting of out of memory conditions.
|
|
> Improved manual page.
|
|
* 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.
|
|
> The "go to position" text entry box has been made wider.
|
|
> Fixed samtools tview -s option which was not filtering reads correctly.
|
|
It now only shows reads from the requested sample or read group.
|
|
* samtools view:
|
|
> New options '-d' and '-D' to only output alignments which have a tag
|
|
with a given type and value.
|
|
* misc/plot-bamstats script:
|
|
> Fixed merge (-m) option.
|
|
> Made the quality heatmap work with gnuplot version 5.2.7 and later.
|
|
> Fixed --do-ref-stats bug where fasta header lines would be counted
|
|
as part of the sequence when the --targets option was used.
|
|
* 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.
|
|
|
|
-------------------------------------------------------------------
|
|
Thu Sep 6 08:41:09 UTC 2018 - flyos@mailoo.org
|
|
|
|
- Update to 1.9
|
|
* 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:
|
|
- Improved error reporting in several places. (#827, #834, #877, cd7197)
|
|
- Various test improvements.
|
|
- Fixed failures in the multi-region iterator (view -M) when regions
|
|
provided via BED files include overlaps (#819, reported by Dave Larson).
|
|
- Samtools stats now counts '=' and 'X' CIGAR operators when
|
|
counting mapped bases. (#855)
|
|
- Samtools stats has fixes for insert size filtering (-m, -i). (#845; #697
|
|
reported by Soumitra Pal)
|
|
- Samtools stats -F now longer negates an earlier -d option. (#830)
|
|
- Fix samtools stats crash when using a target region. (#875, reported by
|
|
John Marshall)
|
|
- Samtools sort now keeps to a single thread when the -@ option is absent.
|
|
Previously it would spawn a writer thread, which could cause the CPU
|
|
usage to go slightly over 100%. (#833, reported by Matthias Bernt)
|
|
- Fixed samtools phase '-A' option which was incorrectly defined to take
|
|
a parameter. (#850; #846 reported by Dianne Velasco)
|
|
- Fixed compilation problems when using C_INCLUDE_PATH. (#870; #817 reported
|
|
by Robert Boissy)
|
|
- Fixed --version when built from a Git repository. (#844, thanks to John
|
|
Marshall)
|
|
- Use noenhanced mode for title in plot-bamstats. Prevents unwanted
|
|
interpretation of characters like underscore in gnuplot version 5. (#829,
|
|
thanks to M. Zapukhlyak)
|
|
- blast2sam.pl now reports perfect match hits (no indels or mismatches).
|
|
(#873, thanks to Nils Homer)
|
|
- Fixed bug in fasta and fastq subcommands where stdout would not be flushed
|
|
correctly if the -0 option was used.
|
|
- Fixed invalid memory access in mpileup and depth on alignment records
|
|
where the sequence is absent.
|
|
|
|
-------------------------------------------------------------------
|
|
Thu Jul 12 09:02:17 UTC 2018 - flyos@mailoo.org
|
|
|
|
- Cleaned spec file using spec-cleaner
|
|
- Update to 1.8
|
|
* samtools calmd now has a quiet mode. This can be enabled by passing `-Q` to
|
|
calmd. (Thanks to Colin Davenport)
|
|
* In samtools depth `-d 0` will effectively remove the depth limit. (#764)
|
|
* Improvements made to samtools collate's interface and documentation. It is
|
|
now possible to specify an output file name using `-o`, instead of deriving
|
|
it from the prefix used for temporary files. The prefix itself is now
|
|
optional if `-o` or `-O` (to stdout) is used. (#780)
|
|
* Bug-fixes:
|
|
- Make samtools addreplacerg choose output format by file extension. (#767;
|
|
reported by Argy Megalios)
|
|
- Merge tests now work on ungzipped data, allowing tests to be run against
|
|
different deflate libraries.
|
|
- samtools markdup error messages about missing tags have been updated with
|
|
the suggestion that samtools fixmate is run beforehand. (#765; reported by
|
|
Yudong Cai)
|
|
- Enables the `--reference` option for samtools fastq. Now works like other
|
|
programs when a reference sequence is needed for CRAM files. (#791,
|
|
reported by Milana Kaljevic)
|
|
* HTSlib, and so samtools, now support BAMs which include CIGARs with more
|
|
than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).
|
|
* samtools quickcheck will now write a warning to stderr if it finds
|
|
any problems. These messages can be suppressed with a new `-q` option.
|
|
* samtools markdup can now mark supplementary alignments of reads where
|
|
the primary alignment is found to be a duplicate. Supplementary marking
|
|
can be turned on by passing the `-S` option to markdup. When this
|
|
option is enabled, all the alignment data will be written to a temporary
|
|
file so that supplementary alignments that occur before a duplicated
|
|
primary can be correctly marked in the final output. The location
|
|
of this temporary file can be influenced using the new `-T` option.
|
|
* samtools view now supports HTSlib's new multi-region iterator.
|
|
This can be enabled by passing the `-M` option to view. When using
|
|
this option:
|
|
- The BED filter (`-L` option) will use the index to skip through the file
|
|
- Reads from overlapping regions will only be output once
|
|
* samtools bedcov will now ignore BED comment and header lines (#571; thanks
|
|
to Daniel Baker).
|
|
* samtools collate now updates the @HD SO: and GO: tags, and sort will
|
|
remove a GO: tag if present. (#757; reported by Imran Haque).
|
|
* Bug-fixes:
|
|
- maq2sam now checks for input files that end early. (#751; patch supplied
|
|
by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.)
|
|
- Fixed incorrect check when looking up header tags that could lead
|
|
to a crash in samtools stats. (#208; thanks to Dave Larson.)
|
|
- Fixed bug in samtools fastq `-O` option where it would fail if
|
|
the OQ tag in the input file had an unexpected type. (#758;
|
|
reported by Taejeong Bae)
|
|
- The MD5 calculations in samtools dict and md5fa did not handle
|
|
non-alphabetic characters in the same way as the CRAM MD5 function.
|
|
They have now been updated to match. (#704; reported by Chris Norman).
|
|
- Fix possible infinite loop in samtools targetcut.
|
|
- Building bam_tview_curses should no longer fail if a curses header file
|
|
cannot be found.
|
|
* Added new markdup sub-command and '-m' option for fixmate. Used together,
|
|
they allow duplicates to be marked and optionally removed. This
|
|
fixes a number of problems with the old 'rmdup' sub-command, for
|
|
example samtools issue #497. 'rmdup' is kept for backwards compatibility
|
|
but 'markdup' should be used in preference.
|
|
* Sort is now much better at keeping within the requested memory limit. It
|
|
should also be slightly faster and need fewer temporary files when the file
|
|
to be sorted does not fit in memory. (#593; thanks to Nathan Weeks.)
|
|
* Sort no longer rewrites the header when merging from files. It can also
|
|
now merge from memory, so fewer temporary files need to be written and
|
|
it is better at sorting in parallel when everything fits in memory.
|
|
* Both sort and merge now resolve ties when merging based on the position
|
|
in the input file(s). This makes them fully stable for all ordering
|
|
options. (Previously position sort was stable, but name and by tag
|
|
sorts were not).
|
|
* New --output-qname option for mpileup.
|
|
* Support for building on Windows using msys2/mingw64 or cygwin has
|
|
been improved.
|
|
|
|
-------------------------------------------------------------------
|
|
Mon Jul 10 21:26:49 UTC 2017 - flyos@mailoo.org
|
|
|
|
- Update to 1.5
|
|
- Fixed some runtime dependencies (perl and python)
|
|
|
|
-------------------------------------------------------------------
|
|
Wed May 4 17:08:15 UTC 2016 - flyos@mailoo.org
|
|
|
|
- Fixed Perl dependency
|
|
|
|
-------------------------------------------------------------------
|
|
Sat Apr 30 16:40:04 UTC 2016 - flyos@mailoo.org
|
|
|
|
- Update to 1.3.1
|
|
|
|
-------------------------------------------------------------------
|
|
Sat Apr 30 16:25:54 UTC 2016 - flyos@mailoo.org
|
|
|
|
- Cleaner spec file
|
|
|
|
|
|
-------------------------------------------------------------------
|
|
Thu Apr 21 15:12:02 UTC 2016 - flyos@mailoo.org
|
|
|
|
- Changed "./configure" and "make install" for "%configure" and
|
|
"%make_install".
|
|
|
|
-------------------------------------------------------------------
|
|
Wed Apr 20 18:48:19 UTC 2016 - flyos@mailoo.org
|
|
|
|
Initial release.-
|
|
|