Information & Computational Sciences

New in Tablet

By on 10/09/2010 in News with 0 Comments

Tablet has just been updated to version

NEW: Added support for paired-end data from SAM or BAM input files.
NEW: Added graphical support for paired-end data via special paired-end packed
     and stacked views.
NEW: The information tooltip over reads now displays differently based on normal
     or paired-end reads.
NEW: Mouse-over on any paired-end read will also show information on its mate.
NEW: Added a new colour scheme - Read Type - that paints reads based on type:
     unpaired, 1st in pair, 2nd in pair, or orphaned.
NEW: Added right-click mouse options to jump to a read's mate (within same BAM
     window, different window, or different contig).
NEW: Right-clicking on two paired reads' link lines gives options to jump to the
     reads at either end.
NEW: BAM files can now be loaded without the need to specify a reference file.
NEW: The Contigs Table now contains custom rendering based on what data is
     available (important for BAM).
NEW: GFF features can now be rendered alongside the alignment.
NEW: GFF features are rendered in a distinct colour per type.
NEW: Added custom rendering of features if type "SNP" is detected.
NEW: Added a "Select Tracks" option and dialog to control selection of the
     visible feature (types) and their order.
NEW: Added a summary message at the end of importing features that gives
     information on the numbers imported.
NEW: Added installer file type association for ace, afg, sam, and bam (for OS X
NEW: Made the (current) 500 results limit on searches into a user-configurable
     amount (tablet.xml: guiSearchLimit).
NEW: Added a few more entries to the FAQ.
NEW: Details on all reads on screen, or all reads crossing the column position
     under the mouse can now be exported to a file (by right-clicking).
NEW: CIGAR insertion events are now plotted on screen using the features tracks.
NEW: Individual CIGAR insertions can be drawn over a read by selecting the
     insertion on the features track.
NEW: Enabled proper number format cell rendering on the various display tables.
NEW: Selecting a read from the Find Reads table will now also highlight it on
     the overview.
NEW: Added mouse drag navigation to all reference tracking visual elements
     (consensus, coverage, scale, etc).
NEW: Tablet now warns if the reference length expected by a BAM file differs
     from that of the actual reference imported by the user.
NEW: Moved the default location for saving prefs information from ~/.tablet.xml
     to ~/.scri-bioinf/tablet.xml (with old files being automatically moved over
     if found).
NEW: Updated the GFF reader to cope with files containing ##FASTA directives.
CHG: Pack style selection is now performed via a drop down menu rather than
     separate ribbon buttons.
CHG: Major changes to the way files are handled, detected and loaded.
CHG: Only one open/close operation is needed per file now to detect its type
     (rather than one open/close per possible type).
CHG: Changed the highlight colours used by the overview window to try and make
     them work a bit better with all the colour schemes.
BUG: Fixed unformatted large numbers in OverviewCanvas.
BUG: Feature types (SNP, INDEL, etc) were still being added even if the feature
     they belonged to was rejected during the import.
BUG: The find results wouldn't scroll to the selected contig in the contigs list
     when highlighting it.

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