Skip to content

1.7
Compare
Choose a tag to compare
@daviesrob daviesrob released this 26 Jan 15:32
· 852 commits to develop since this release
1.7
This tag was signed with the committer’s verified signature.
daviesrob
GPG key ID: 1ECBE5BA15C64CCC
Learn about vigilant mode.
6d79411

  • 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