References shown in tiles with additional information provided.
Widgets for setting filters added.
"show qualities" issue fixed.
ver 0.2.12 (2017-Mar-22)
Improvments in error handling.
Compatibility issue with new version of the data tables library addressed.
ver 0.2.11 (2017-Jan-13)
Redefined the formula for estimating the resolution. New unit BasePerPixel should be consistent across different input sequence lengths and window sizes.
ver 0.2.10 (2016-Nov-17)
Scrolling events ignored on zoom (zoom on scroll was not seamless).
Reordered svg elements. Order of elements ~ z coordinate.
ver 0.2.9 (2016-Nov-3)
UI modifications. Better interactivity (Click and drag in the graph area).
Filtered beginnings of reads now set to a fixed value.
ver 0.2.8 (2016-Oct-7)
A bug preventing the loading of some single nucleotide sequences fixed.
Correction in the way VAF (variant allele frequency) is estimated.
ver 0.2.7 (2016-Sep-29)
Small changes in the table of samples formating for a more comprehensive representation of variants and a more unified style in both the samples table and the final exported excel table.
Added proper naming of protein variants for p.(=) and p.? cases.
ver 0.2.6 (2016-Sep-10)
dbSNP annotation added for TP53 now uses exact matching instead of position matching.
Added button to show/hide the help infobox in the variants panel.
Titles, email us, table formatting, quick guide.
Modified export button behaviour; hide when nothing to export.
Delete button in samples table behaviour fixed.
Enabled the delete button on the example file.
ver 0.2.5 (2016-Aug-20)
Position based dbSNP annotation added for TP53. (Column "dbSNP" in the variants table.)
ver 0.2.4 (2016-Aug-11)
"No reference" upload fixed and documented.
Forward beginnings filter initial position updated.
ver 0.2.3 (2016-Aug-4)
Fixed bug causing single strand samples to crash (result of previous update).
Small change in minimap navigation box opacity.
ver 0.2.2 (2016-Aug-2)
Minimap navigation box coloured steel blue (~ magnifier glass) and shadow added to make it "pop-out".
Variant indicators are now strand specific.
Variant indicator scales to peak width.
ver 0.2.1 (2016-Jul-29)
Minimap navigation box appearence and behaviour.
More seamless chromatogram transitions.
Box representing zoomed-in area.
Filters of beginnings of reads stylised in chromatogram and also minimap.
ver 0.1.2 (2016-Jul-27)
Filters of beginnings and ends of reads visualised in minimap.
Reference now case sensitive: exons in uppercase, everything else in lowercase.
It\'s now possible to load samples without a reference, just untick all genes.
ver 0.1.1 (2016-Jul-06)
Implemented brush-able filtering-out of variants from the beginning of reads (the filter is at the end of the reverse sequences since these are reverse complemented).
Added reference selector, with selected references used to autodetect strandedness - not using all references speeds up the upload process.
(0) hovering over '[?]'s will provide quick help tips
(1) select / upload relevant references beforehand, GLASS will align and auto-orientate against them
(2) upload ABI files from supported references, forward and/or reverse, and with unique names
(3) after processing and auto-detection of most file properties, pair / unpair / swap / delete / change reference as necessary
(4) click the blue 'play' button to load the file(s)
(5) when done in 'variants' panel (find separate instructions there), confirmed variants will appear under 'status' and are exportable with the green 'export variants' button
minimap : blue box = resize/move for navigation | boxes = exons/introns | horizontal grey line = full sequence | verticals = variants, ref>pri>sec | red dotted lines = filtered noisy beginnings
chromatogram: click text to print info^ | crosshair + click = drag | zoom-in for extra info (coords..) | sequences, from top = ref, call/pri, mut/sec | pink verticals = variants | grey bars = codons
variants : 'goto' = go to variant on chromatogram | 'x' = ignore for the session | 'confirm' = keep for the session (even if you change parameters) and make them exportable from 'samples' panel