Staden Package 2.0.0b11-2016 released

The asymptoptic approach of version 2.0 is now one step closer. Alas we still haven't had time to give the documentation a work over, hence still labelling this release as Beta.

The primary changes are to Gap5, mainly involving stability and bug fixing although several new features have arrived too. Release notes follow.

April 2016 - 2.0.0b11

Gap5 Updates

  • Find Haplotypes function for use within the contig editor. This
    replaces the old Sort By Sequence mode as well as generating lists
    of read IDs per haplotype. It also creates a master "haplotypes"
    list of lists.

  • Disassemble Readings now handles list of lists (in addition to
    normal lists of readings), for use with the haplotype output.

  • Improvements to Shuffle Pads. It can now use cutoff/soft-clip
    data to detect concordant soft-clips (regions where all the
    soft-clip data agrees with one another). It auto-detects likely
    adapter sequences to avoid extending these.
    It also now detects short tandem repeats and handles these more
    carefully. An STR overlapping a heterozygous indel can be clipped
    back if the read doesn't span the entire STR, in order to not cause
    bias in the copy numbers.

  • The Realign Selection option now brings up a user interface if invoked
    from the main menu, but not when right clicked via the popup menu
    (unless Control key is held down while right-clicking).

  • Export Contigs has an additional depadded option to use original
    reference sequence coordinates. Note this isn't 100% robust as it
    depends on which edits have happened, in particular joining and
    breaking contigs.

  • Export SAM, BAM and CRAM should now be much faster in excessively
    deep regions with soft-clips.

  • The quality values can now be overriden when importing FASTQ or the
    default quality changed when importing FASTA.

  • Gap5_cmd has gained Contig Extend and Contig Trim commands.

  • Gap5_cmd auto_join now honours the -min_overlap and -max_overlap

  • Improved the consensus discrepancy score by taking into account a
    per-base difference rather than joining all together.

  • Check Assembly text results are now more verbose, for easier
    comparison between databases.

  • The current selected reading list in the Contig Editor now shows the
    number of items in that list.

  • Highlight Disagreements for cutoff data now defaults to displaying
    foreground coloured differences.

  • The consensus algorithm has been tweaked to cope with different
    overcall and undercall likelihoods. This is tied to sequencing
    technology, for which the default can be adjusted in the Options
    menu. This uses the @RG "PL"atform heading in BAM files. The List
    Libraries window permits editing of this field after import.

  • Small tweaks to Find Internal Joins block alignments.

  • Save Consensus can now optionally emit ambiguity codes for
    heterozygous positions.

  • Added back Mask/Mark consensus filtering modes to Find Internal

  • Read name indexing should uses less temporary disk space in

  • The multi-column reading list viewer now has Template Status and
    Library Name columns for display/sorting.

  • The Template Display now has hot-keys for configurations. Use
    Shift-Function-Key to remember the current settings and Function-Key
    to switch to that setting. The File -> Save Settings option will
    write these to your ~/.gap5rc.

Gap5 Fixes

  • Fixed a bug where using the contig selector / contig list to fill
    out a dialogue box without then doing anything else at all could
    cause the name to be considered invalid.

  • Removed used of some unintialised data in Shuffle Pads.

  • Validate_clip_regions could process annotation record numbers that
    have been removed already.
  • Functions setting sequence clip points could potentially set clips
    beyond the sequence ends.

  • Fixed a bin corruption caused by updates to read pairs spanning two
    contigs, eg with one editor open on each end. (See r3996 for the
    long description.)

  • Auto-scrolling int he template display now takes into account the
    contig start location.

  • Many bug fixes to Shuffle Pads, but there is also a lot of new code
    in there too (hopefully without new bugs!).

  • Tg_index -g mode was erroneously adding columns of pads in some
    cases. Also fixed an issue with tg_index -a -g not working in some

  • Fixed rounding issues when zooming the template display quality

  • Some more (rather obscure) gap5 database corruptions have been

  • Improved robustness in the presence of database corruptions. While
    not foolproof, the program shouldn't crash as often.

  • Import Reads no longer clears the "readings" list.

  • Corrected the (reversed) insertion / deletion percentages in List
    Base Confidence.

  • Quality value "*" in BAM is no longer treated as quality -1.

  • Fixed a potential buffer overrun in querying individual items in the
    contig selector.

  • Overhauled the base insertion and deletion code in the Contig
    Editor, fixing several problems (in particular with Undo).

  • Various fixes to keep the contig start / end coordinates correct,
    removing bin errors.

  • Fixed issues with annotation positions after using the editor
    commands to move sequences. Similarly consensus tags at the ends of
    contigs should be more robust when inserting and removing consensus

  • SAM/BAM export should now correct the mate-pair flags and positions.

  • Fixed exporting CRAM in padded mode. It was outputting a depadded
    consensus, causing CRAM to work excessively hard in encoding reference

  • Added back fsync to main .g5d file. This should resolve some
    database corruptions caused by running gap5 on a cluster, saving the
    gap5 database (but not closing gap5) and then manually copying the
    database from a different cluster node.


  • The contig editor should now work better with newer X11 window managers.

  • Fixed a bug in showing the reading frame translations. It
    overflowed the buffer by 1 byte (a ~2002 bug).


Posted by James Bonfield 2016-04-25

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