Releases: kcleal/gw
Releases · kcleal/gw
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
onlinecommand - 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.inifile 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
v0.6.3
v0.6.2
v0.6.1
Features/Improvements:
- New
--low-memflag for command line, reduces memory by around 30%. This drops tags and qual values from sequencing data. Useful for plotting very large regions, or even entire chromosomes - New
--tlen-yand:tlen-yoption/command, scales y-axis by template length in a similar way to samplot --cov VALand:cov VALcan be used to threshold the coverage profile:varcommand has been updated so you can print target variant information, .e.g:var info.SUwill print SU column from info- New
:snapshotcommand, to save screenshots. Can optional be used with a filename:s view.pngor can even parse variant info into the file name e.g.:snapshot {chrom}_{pos}_{info.SU}.png :gridcommand to control the size of the image grid e.g.:grid 8x8- Drawings arranged on pixel boundaries, so now looks a bit cleaner, especially on low res screens.
Bug fixes:
- Better border position between rows
- Out of bounds error for reference track
- Raster images work again