v1.9.0

basemodfreq track

• add scale option for the y axis: ymin and ymax

v1.8.1

make scale_min work with show_negative

v1.8.0

bigwig track

• added scale_min parameter (when using a custom scale)
• added lw parameter for setting the line width

v1.7.0

• bigwig track: add show_negative option to also display negative values (by default, only positive values are shown)
• sv track: add support for bedpe format
• sv track: fix an issue where files were not correctly parsed if chromosome names had a "chr" prefix.

v1.6.3

• New track type: ase (allele-specific expression). Shows variant allele frequency for SNPs in genes, in DNA and RNA, in order to display if some genes are expressed from only one allele. See the documentation. This requires preprocessed data generated by fast_ase.
• bed track: added use_file_colors option to use colors provided in the bed file (ninth column), show_strand to show the orientation of each interval. By default, overlapping intervals will now be displayed on multiple rows, unless collapsed is set to true.
• GUI: added tooltips to explain the effect of each parameter.

v1.5.0

• Improved support for gtf and gff3 formats for the gene track.
• Fixed bigwig track when displaying small regions.
• Added parameters for various tracks:
  • chr_prefix for the chr_axis track
  • min_height for the sv track
  • show_strand for the bed track

v1.4.0

• Added group autoscale for bigwig and coverage tracks.
• Added support for gff3 format for gene annotations.
• Improved the GUI for the copynumber track.
• Fixed various bugs reported by users:
  • now correctly handles vcf files with indels for sv tracks.
  • now correctly handles tsv input for sv tracks.
  • now correctly plots copynumber tracks in circular layout, when only CNVs are provided.
  • fixed a bug with the "scale per region" option of bigwig tracks.
  • now correctly handles HiC data that has not been normalized, for hic tracks.

v1.3.0

• chr_axis track: add lw_scale parameter.
• alignments track: add more parameters for displaying split reads.
• basemod_freq track: add support for all-tab bedmethyl file format.
• Windows: fix int overflow when showing all chromosomes.
• Added several warnings.

v1.2

• Better error messages (e.g. if an input file is missing or has the wrong format).
• New warning messages.
• GUI: now displays a panel once the figure is successfully generated, with buttons to open the generated figure or its directory.
• Add ticks_angle option for chr_axis track and show_gene_names option for genes track.
• Various bug fixes.

v1.1.0

General

• Added built-in support for mm10 in addition to hg19 and hg38 (but any other reference genome can be used, if you manually provide the files).
  -Removed requirement for the chr_arms file for custom reference genomes.

Regions

• Now allows region start and end to be given as strings, and also accepts commas.

Tracks

basemod_freq

• Added support for bedgraph and 3-column tsv file formats, in addition to bam and bedmethyls.
• Added parameters: style, smooth, gap_frac.

bigwig and coverage tracks

• Added "upside_down" parameter.

genes

• Improved spacing between genes.

Misc

• Various bug fixes