What's New

This page describes the additions (NEW), changes (CHG) and bug fixes (BUG) that have been made to Tablet in recent versions. For full details on all the changes between versions, please see the subversion change log.

New in 1.12.02.06

NEW: The majority of colours used for the various visualization components are now customizable.
NEW: Cigar insertions can now be shown with a permanent overlay. This is in place of the previous mouse-over highlight code.
NEW: Added a snapshot history feature which tracks previously visited points of interest within the current contig.
NEW: Searching for subsequences now also searches the reverse complement of a sequence.
NEW: It is now possible to copy features to the clipboard from the features track.
CHG: Removed the ability to search for subsequences within reads (searching within consensus/reference is still possible).
BUG: Fixed Ctrl+F shortcut opening up the Read Group tab instead of the Find panel.
BUG: Fixed keyboard shortcuts only working if their associated ribbon button was on the active tab.
BUG: Fixed incorrect page left/right functionality in contigs with negative coordinate space.
BUG: Fixed dialogs disappearing off-screen if the resolution or number of monitors had changed since the last run.

New in 1.11.11.01

NEW: All of the tables (in the control panel) can now have their contents copied to the clipboard via right-click menu options.
NEW: Two new colours are now available with the Read Type scheme. These represent first in pair (mate in different contig) and second in pair (mate in different contig).
NEW: The portion of reference sequence mapping to a feature can now be copied to the clipboard.
NEW: Added a new colour scheme that highlights read length.
NEW: Individual reads can now be outlined by right clicking on them.
NEW: Added the ability to toggle variant tagging/highlighting on or off for unknown, padded and N bases.
NEW: Restriction enzyme sites can now be added to the features tracks via automatic inclusion from REBASE.
NEW: Added the version of samtools used by Tablet to the About Tablet dialog box.
NEW: Tooltips for features (on the canvas and in the table) now support all their tags.
NEW: Significantly enhanced the read group support so that all tags (not just sample) are available.
NEW: Added right-click Colour-by options to the Reads Group table.
CHG: The Read Group table now displays all read groups (using IDs) along with their platform tag information.
CHG: The main selections for the active colour scheme have been moved to their own tab within the ribbon bar.
CHG: Tablet should now use less memory when a large number of features are loaded.
CHG: BAM files loaded without reference data now display their length in the title label of the ribbon.
CHG: Replaced the classic scheme with the variants scheme. The new colour scheme is designed to make it very easy to spot bases which differ from the consensus / reference.
BUG: Dragging GFF files into the interface when the 'warn if existing file open' option was active was showing the message box when it shouldn’t have.
BUG: Cancelling a BAM-window data load after dragging the BamBar slider resulted in the overlay not being removed from the canvas.
BUG: Fixed a problem with overlapping features on the GFF tracks not being drawn.
BUG: Due to a design flaw in Picard, validation stringency wasn’t being set correctly for objects that needed to parse the header.
BUG: Fixed a problem with reads which had more than one CIGAR insert at the same location losing all but the first insert at that location for the read.
BUG: Fixed a problem with long file paths causing problems with the combo boxes on OS X.
BUG: Searching for reads within BAM files wasn't checking if the read was unmapped or not.

New in 1.11.08.10

NEW: Added a new colour scheme for displaying Read Groups in SAM and BAM files.
NEW: Added a new control panel tab for viewing and editing Read Group colours.
NEW: GFF files now support drag and drop loading.
NEW: GFF files can now be specified on the command line (or via web start).
NEW: Reduced the initial detection time for BAM files, which should speed loading.
NEW: Added a tablet.xml preferences variable which governs the number of insert events a CIGAR-I feature has to relate to before it is included.
CHG: String values longer than 75 characters in the graphical tooltips are now be truncated.
CHG: All searches are now case insensitive.
CHG: The setting for using less-strict BAM validation checks is now on by default.
BUG: Toggling Show Bases wasn't causing the screen to refresh.
BUG: Fixed a crash that could occur when searching over consensus sequences.
BUG: The recent-file tooltips on Linux and OS X weren’t working with paths beginning with "/".
BUG: RegEx characters included in a BAM file’s name (eg ‘[]’) were stopping Tablet from locating the corresponding BAI file.

New in 1.11.05.03

NEW: Consensus sequence data is now cached to disk which should result in less memory being used with large contigs.
CHG: Improved the mechanism used to search for read names across non-BAM datasets (should be significantly faster).
CHG: Simplified the Search UI so that all secondary options are check boxes and search type is the only remaining combo box.
CHG: Changed Tablet's look and feel now that SCRI has become part of The James Hutton Institute.
BUG: The total read count shown in the contigs panel was suffering from integer overflow with more than 2 billion reads.
BUG: Fixed an "off by one" bug in the position attribute of the read printer output.
BUG: Read names with :1 /1 etc postfixes were being truncated by one character prior to the postfix.
BUG: Fixed various enabled/disabled UI issues.
BUG: The Find Panel was not allowing reselection (and highlighting) of its results.

New in 1.11.03.14

BUG: OS X only. Added a temporary workaround for BAM files not being detected with the latest (1.6.0_24) version of Java due to changes in gzip handling.

New in 1.11.02.18

NEW: BAM files are now displayed with read count summaries, even before a contig has been viewed, so long as the index file was generated with samtools 0.1.8 or higher.
NEW: Tablet now uses the samtools executable for some tasks. The Options Dialog allows for an alternative path to be set if the version distributed with Tablet doesn't run.
NEW: The table column headers are now included in the output from the contig table's copy-to-clipboard option.
NEW: Tablet now accepts a "view" command-line argument that allows you to specify a contig and position to jump to after loading (view:contigName:position).
NEW: The Jump To Base Dialog now supports navigating to positions in contigs outwith the current contig.
NEW: The search code can now ignore pads and 'N's when looking for matches.
NEW: Added a new option to allow copying just part of a consensus/reference sequence to the clipboard.
CHG: SAM files containing paired-read data must now be sorted before Tablet will accept them.
BUG: Fixed array-out-of-bounds exceptions with SAM files containing paired-data.
BUG: The wrong start position for a read was sometimes shown in search results with BAM files.
BUG: The wrong name and position was being displayed for out-of-contig mates.

New in 1.11.01.25

NEW: Various improvements to the pair-matching code should result in much faster loading of paired-end data.
NEW: Drawing paired-reads that include "link lines" is now faster.
NEW: Added new right-click options to the main canvas that provides several export-to-disk options for reads.
NEW: Added a "Visible Reads" tab, that displays a dynamically changing table of all on-screen reads as you navigate around a contig.
NEW: Added CTRL/CMD mousewheel zooming to the main canvas.
CHG: Altered the SAM parsing code to better handle files which have been produced by tools which haven't adhered to the SAM specification.
CHG: Rearranged some of existing options on the main canvas's right-click menu.
CHG: Changed to a different SQLite binary for use on OS X that allows it to work on all systems again.
BUG: Fixed some installer problems that were causing issues on Ubuntu Linux.

New in 1.10.10.06

BUG: OS X only. Temporary fix for loading problems on OS X 10.5.8 due to issues with the SQLite driver. Performance will be lower than normal. 10.6.x seems unaffected.

New in 1.10.09.20

NEW: Added the ability to search for sequence strings within the consensus / reference.
BUG: Added fixes for issues where reads in SAM files weren't being paired properly.
BUG: Fixed a problem with read names that ended :1 or :2 not getting paired.

New in 1.10.09.10

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 only).
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.

New in 1.10.05.21

BUG: Fixed a critical bug that was resulting in some contigs hiding reads when in packed mode.

New in 1.10.05.18

NEW: Implemented a new, hopefully more robust, method of determining the version number for update purposes.
NEW: Added an option to set Picard's SAMFileReader validation stringency to lenient to suppress SamValidation errors.
NEW: Added a parse-time option force DNA ambiguity codes to be read as N.
CHG: Changed the protein translator to treat any base with an N as ok (codon will translate to X) rather than having it skip the base.
BUG: Fixed a problem copying any of the reverse strand protein translations to the clipboard.
BUG: Fixed problems relating to Tablet not re-initialising its BAM reader after encountering SamValidation error.

New in 1.10.05.06

NEW: Added a new colouring scheme based on read direction/orientation.
NEW: The overview displays can now be "subsetted", forcing them to show only an overview of whatever region you define for them.
NEW: Variant highlighting (in red) can now be turned on or off for the overviews or popups.
NEW: Added the ability to search for sequence substrings within reads.
NEW: Added a new graphical layer that performs "read shadowing", highlighting any reads under the a given column or mouse position.
NEW: Example files (linked to on the web) can now be opened directly from within Tablet.
NEW: The nucleotide text for each base can now be shown or hidden.
NEW: Added (optional) support for trimming reads in ACE files based on the QA tags.
CHG: Redesigned and added additional options to the control ribbon.
CHG: The ACE parser now ignores base quality information, making it more compatible with badly formatted files.
BUG: The SAM parser now looks for all possible header tags to determine if a file is SAM or not.
BUG: Fixed various issues with searching for reads.
BUG: Fixed some miscellaneous rendering issues when switching between contigs.

New in 1.10.03.04

NEW: Added support for indexed BAM assemblies.
NEW: Added a new navigation bar for moving the viewing window around within a larger BAM assembly.
NEW: Implemented background (multicore) thread support for calculating auxiliary display data, meaning large contigs can now be viewed instantly.
NEW: Various implementation changes mean less memory is now used for large contigs.
NEW: The Open Assembly dialog is now significantly quicker at detecting the assembly type.
NEW: The page left/right controls now hide when the edges of the display are reached.
NEW: Added options to the Preferences Dialog to enable/disable disk caching (where supported).
NEW: Loading a very large number of features is now much faster.
NEW: The bp coordinates (data set/BAM window and current view) are now shown on the overview images.
CHG: Updated the mismatch code to ignore regions of reads that extend beyond the left or right ends of the consensus.
BUG: Fixed a problem with files being ignored when passed to Tablet on the command line.
BUG: Fixed a bug which caused Tablet to not exit correctly when a filter had been applied in the Contigs Table.
BUG: Fixed multiple issues with AFG parsing related to clr and gap tags.
BUG: The unpadded read length was no longer being shown in the popup information box.

New in 1.10.02.08

NEW: Added (experimental) support for BAM, using in-memory only reading for now, NOT indexed support.
NEW: Support for most CIGAR operations, with the positions of Insertions being tagged as features for now.
NEW: Displayed consensus sequences now use 8 bytes per base less memory.
NEW: Added a (prefs-file only) option to disable all disk caching for maximum performance at the expense of memory.
NEW: The Contigs Table now lists read vs consensus mismatch percentage information.
CHG: Some miscellaneous changes to cache support to speed up read retrieval.
BUG: Fixed a memory-leak problem with display-time objects not being removed after closing a contig.
BUG: Tablet now only deletes the cache files it creates, rather than every file in its cache directory.

New in 1.10.01.28

NEW: Added a right-click "save a summary of read information (per contig)" option to the contigs table.
NEW: Tablet can now read from http streams (supported on the command line and the Open Assembly dialog).
NEW: Tablet can now read from compressed gzip data streams (http or file).
NEW: Features outside the scope of the current contig are now highlighted in red in the Features Table.
NEW: Features with a Name= tag in a GFF3 file will now show this name in the Features Table.
NEW: Added an option to toggle on or off the use of regular expressions in searches.
CHG: The Importing Assembly dialog now shows its progress in MB/s too.
CHG: Removed support for consensus tags in ACE files. GFF3 formatted files are now the only way to import features.
BUG: Loading the same features file twice will no longer result in duplicate entries.

New in 1.09.12.14

NEW: Added an option to export coverage summary information to a file on disk.
NEW: Added an explicit cancel option to the progress dialogs (even though closing the dialog did cancel them anyway).
NEW: Added a right-click "copy-to-clipboard" option for the contigs table data.
CHG: The Application Menu now contains an "Export" sub menu with multiple items, including the old Export Image option.
CHG: Tidied up and enhanced Table's file-handling error messages, to ensure file and line number is always given.
BUG: Fixed a problem with the current contig getting reselected when sorting the contigs table.
BUG: Fixed an issue with the "Are you sure..." warning messages sometimes appearing multiple times.
BUG: Fixed several rendering issues with the new stack-based names overlay.
BUG: Fixed a problem with ACE file parsing when badly formatted consensus tags are present.

New in 1.09.12.08

NEW: Tablet has now appeared in a Bioinformatics publication so we've moved the version number to 1.xx
NEW: Packing data on contigs with very high read coverage is now significantly faster.
NEW: All tables now show tooltips with more readable information about the row under the mouse.
NEW: The Features table tooltips will show padded *and* unpadded coordinate spaces at the same time, ordered by the "Features are padded" checkbox selection.
NEW: The Search results (for reads) table is now sortable.
NEW: Added a link to regular expression help for searching for reads.
NEW: Added an option to overlay read names onto the display (stacked view only).
NEW: Additional coverage data is now available as a tooltip when the mouse is over the coverage or coverage overview panels.
CHG: Tablet now monitors the cache folder location and warns if it is invalid/inaccessible.
BUG: The Features control panel tab was still showing text when selected.
BUG: Fixed a problem with MAQ files being incorrectly identified as SAM.
BUG: Changed the default cache folder location to avoid a problem with it getting locked out on multi-user systems.

New in 0.09.11.25

NEW: Added support for finding reads by name (across current or all contigs), with graphical pinpointing.
CHG: The "Contigs Browser" is now the "Control Panel", containing contig, features, and search tabs.

New in 0.09.11.06

NEW: Added experimental support for reading SAM assembly files. Note that BAM is not supported yet.
BUG: Fixed a problem with read data not getting copied to the clipboard.

New in 0.09.11.04

NEW: The full path to recently accessed assemblies (rather than just their name) is now available via tooltips.
BUG: The version of Tablet displayed in its title bar was wrong if Tablet was started from a directory other than its own.
BUG: Fixed some GUI layout issues that were affecting Linux installs.

New in 0.09.10.30

NEW: Tablet now uses up to 50% less memory per assembly than in previous versions.
NEW: The Import Assembly dialog has had a complete redesign to make it easier to use.
NEW: SOAP or MAQ assemblies can now be loaded without having to provide reference or consensus data in an additional file.
NEW: The location of the (temporary) assembly cache directory can now be specified in the Tablet Options dialog.
NEW: Tablet pop-up warnings can now be toggled on or off via the Tablet Options dialog.
NEW: Added Ribbon controls for iterating backwards or forwards through the list of features.
NEW: Feature positions can now be tagged as either padded or unpadded.
BUG: Running "tablet <somefile>" from the command line now behaves properly regardless of the directory level used.

New in 0.09.10.02

BUG: Fixed a parsing error with fasta/fastq files.

New in 0.09.10.01

NEW: Tablet now prompts before closing or exiting if an assembly is loaded.
NEW: Added controls to the list of features to allow it to be filtered by type.
CHG: Made various changes to the installers to improve Linux compatibility and to provide "What's New" information at update time.
BUG: Fixed an issue with checking for updates that was causing very slow startup times on some systems.
BUG: Keyboard shortcuts for zooming were not working via the numeric keypad.

New in 0.09.09.11

CHG: Significant reduction in the time required to pack reads when dealing with large contigs.
BUG: Fixed a problem with protein translations when the sequence didn't start with known characters.
BUG: Copy-to-clipboard operations were copying the read orientation incorrectly.

New in 0.09.09.07

NEW: First public release of Tablet.