samtools/samtools 1.11

on GitHub

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 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)