v1.0.1

Minor release:

• Changed GFF3 / GTF name parsing #43
• Possible fix for segfault using intel macOS #42

GW v1.0.0

New features

• Sort reads by strand or haplolag using sort strand or sort hap commands
• Ideograms as default
• Scale bars as default
• PAF file support
• header command to show bam file header contents
• Track strand now shown with arrow
• Redirect selected reads to a bam file using sam > out.bam or sam >> a.bam etc
• Shortcuts for ylim
• Better keyboard integration
• Load path or session from splash screen
• Backwards compatible .gw.ini
• Cleaner drawing style

Fixes

• Menu interactions and popups work consistently
• More consistent screen updates after applying commands
• Bug in htslib code for mod parsing
• Other minor bug fixes

v0.10.1

v0.10.1

Improvements:

• Ability to add comments to image tiles when labelling
• load command now supports all file types
• save command supports label files
• Better tab-completion for load and save
• Fixed several bugs relating to image clipping
• Several bug fixed for drawing following applying commands

v0.10.0

GW v0.10.0

Improvements

• Up to 20% faster long-read drawing
• Base modifications supported (5mc, 5hmc)
• Session files - pick up where you left off
• Save reads from a region straight to a bam file
• Fully customisable colours
• Ideograms as bed files + customisable ideograms
• Improved themes
• Option to compile gw as c++ library or wasm target
• Add regions of interest with roi command
• Lots of bug fixes

v0.9.3

v0.9.3

• Big performance improvements for large scale regions
• Automatic low memory mode, memory stays low even for chromosome scale views
• Filter/count on read pattern e.g. 'filter pattern == del or pattern == dup'
• Filter/count using named sam flag properties e.g. 'filter ~proper-pair'
• Added options for tag command e.g. 'tag NM' prints NM tag from target read
• Option to output SVG image
• Coloured arcs can be drawn for SVs when loaded as a track
• Fixed longstanding issues involving Mac - Linux X-forwarding
• Several bug fixes

v0.9.1

v0.9.1

New features

• User interface for selecting commands and editing settings
• SNP frequency drawn over coverage track
• Multiple VCF files supported for labelling
• Support for GFF3, GTF, BIGWIG, BIGBED
• Tracks can be expanded and resized with mouse
• More customisation of look; slate theme, turn on/off mismatches, edges, indels
• Faster runtime ~15% on linux, 2x faster image generation
• More model organisms supported out of the box
• Use command box to search for features in tracks, or take notes
• Integration with online genome browsers using online command
• Installers for MacOS (dmg), debian (deb) and Windows (vb script)
• Open a bam file by double-clicking or using Open With (reference genome is automatically)
• Numerous bug fixes

Breaking changes

• GW_LABEL files now contain one extra column with the filename of the original variant file.
• .gw.ini file will need to be replaced.

v0.8.2

v0.8.2

Improvements:

• Added TAB hotkey to switch between image-view and alignment-view
• Added F hotkey to highlight all alignments of selected read
• A box now highlights current region when switching regions using keyboard

Bug fixes:

• Mouse clicks are accurate after window re-size
• Window resizing using SHIFT + ARROW key does not trigger key press events

v0.8.1

v0.8.1

• Fixed regression bug - filter and count commands work again

v0.8.0

• Added window resizing using SHIFT + ARROW_KEY
• New commands/CLI-options to toggle 'insertions', 'mismatches', 'edges', 'soft-clips'
• Better keyboard input
• Command box can also be accessed with '/'
• Filename also shown when mouse is over a region
• -b option can also accept glob patterns e.g. -b '*.bams'
• Long cigars are no longer printed in full
• Can use remote reference genomes from CLI

Bug fixes

• Sticky scrolling when using vcf file

v0.7.0

GW v0.7.0

Improvements:

• Near-constant memory use when drawing static images (reads are no longer buffered unless needed). This allows plotting of whole chromosomes in parallel. To plot the genome use gw hg38 -b your.bam -n -t 16 -o chrom_plots; chromosome information is extracted from the fasta.fai file.
• Region information is encoded in filenames by default, so static images can be later opened and explored dynamically.
• Default 1x1 image grid if only single image provided

v0.6.4

Minor release

Improvements / features added

• :low-mem command to toggle low mem option
• --use-raster option to force drawing on the cpu when using --no-show option

Bug fixes:

• More accurate y-position for mouse clicks
• Deletions drawn correctly when zoomed