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@valeriuo valeriuo released this Sep 22, 2020 · 9 commits to develop since this release

Download the source code here: samtools-1.11.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

  • 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 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/ 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)

Assets 3

@daviesrob daviesrob released this Dec 6, 2019 · 115 commits to develop since this release

The samtools-1.10.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

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)
    1. 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/ Python script, as it takes consensus-pileup as input, which was removed from samtools in release 0.1.17 in 2011. (#1125)

Assets 3

@daviesrob daviesrob released this Jul 18, 2018 · 336 commits to develop since this release

The samtools-1.9.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

  • 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)

    • 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.

Assets 3

@daviesrob daviesrob released this Apr 3, 2018 · 396 commits to develop since this release

  • 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)

The samtools-1.8.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

Assets 3

@daviesrob daviesrob released this Jan 26, 2018 · 413 commits to develop since this release

  • 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.

The samtools-1.7.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

Assets 3

@daviesrob daviesrob released this Sep 28, 2017 · 438 commits to develop since this release

  • 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 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.

The samtools-1.6.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

Assets 3

@valeriuo valeriuo released this Jun 21, 2017 · 456 commits to develop since this release

  • Samtools fastq now has a -i option to create a fastq file from an index tag, and a -T option (similar to -t) to add user specified aux tags to the fastq header line.

  • Samtools fastq can now create compressed fastq files, by giving the output filenames an extention of .gq, .bgz, or .bgzf

  • Samtools sort has a -t TAG option, that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged. (#675; thanks to Patrick Marks of 10xgenomics).

The samtools-1.5.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files.

Assets 3

@jenniferliddle jenniferliddle released this May 8, 2017 · 462 commits to master since this release

This is primarily a security bug fix update.

  • Added options to fastq to create fastq files from BC (or other)

  • Samtools view has gained a -G option to exclude on all bits
    set. For example to discard reads where neither end has been
    mapped use "-G 12".

  • Samtools cat has a -b option to ease concatenation of many

  • Added misc/samtools_tab_completion for bash auto-completion of
    samtools sub-commands. (#560)

  • Samtools tview now has J and K keys for verticale movement by 20
    lines. (#257)

  • Various compilation / portability improvements.

  • Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.

The samtools-1.4.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files.

Assets 4

@jenniferliddle jenniferliddle released this Mar 13, 2017 · 486 commits to master since this release

Release 1.4 (13 March 2017)

Noteworthy changes in samtools:
* Fixed Issue #345 - out-by-one error in insert-size in samtools stats

* bam_split now add a @PG header to the bam file
* Added mate cigar tag support to fixmate
* Multi-threading is now supported for decoding BAM and CRAM (as well
  as the previously supported encoding).  Most commands that read BAM
  or CRAM have gained an -@ or --threads arguments, providing a
  significant speed bonus.  For commands that both read and write
  files the threads are shared between decoding and encoding tasks.

* Added -a option to samtools mpileup to show all locations, including
  sites with zero depth; repeating the option as -aa or -a -a additionally
  shows reference sequences without any reads mapped to them (#496).

* The mpileup text output no longer contains empty columns at zero coverage
  positions.  Previously it would output "...0\t\t..." in some circumstances
  (zero coverage due to being below a minumum base quality); this has been
  fixed to output as "...0\t*\t*..." with placeholder '*' characters as in
  other zero coverage circumstances (see PR #537).

* To stop it from creating too many temporary files, samtools sort
  will now not run unless its per-thread memory limit (-m) is set to
  at least 1 megabyte (#547).

* The misc/plot-bamstats script now has a -l / --log-y option to change
  various graphs to display their Y axis log-scaled.  Currently this
  affects the Insert Size graph (PR #589; thanks to Anton Kratz).

* Fixmate will now also add and update MC (mate CIGAR) tags.


_The **[foo-1.x].tar.bz2** download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files._
Assets 4

@jmarshall jmarshall released this Apr 22, 2016 · 561 commits to develop since this release

  • The sort command creates any needed temporary files alongside the final output file (similarly to the pre-1.3 behaviour), and now aborts when it detects a collision with another sort invocation's temporary files.

    When the -T PREFIX option specified is a directory (or when sorting to standard output), a random component is now added to temporary filenames to try to avoid collisions (#432, #523, #529, #535, PR #530).

  • All samtools commands now check for I/O errors more carefully, especially when writing output files (#111, #253, #470, PR #467).

  • Build fixes for 32-bit systems; be sure to run configure on such systems to enable large file support and access to 2GiB+ files.

  • The fasta/fastq/bam2fq command no longer ignores reads when the -s option is used (#532).

  • The fastq -O option no longer crashes on reads that do not have an OQ tag field (#517).

  • The merge and sort commands now handle (unusual) BAM files that have no textual @SQ headers (#548, #550).

  • Sorting files containing @CO headers no longer duplicates the comment headers, which previously happened on large sorts for which temporary files were needed (#563).

  • The rmdup and view -l commands no longer crash on @RG headers that do not have a LB field (#538).

  • Fixed miscellaneous issues #128, #130, #131, #489, and #514.

The samtools-1.3.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

Assets 3
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