1.3.1

• locus: add --phasediff to plot difference between phases as output
• locus: add --hidelegend
• segplot: add --vertlabel (vertical labels)
• region: add --bed
• region, locus: add --hidebedlabel
• locus: add --csi (#87)
• locus: bounds checking for highlight region
• wgmeth: avoid crash on read not found

1.3.0

• tools for plotting C-U substitution data (WGBS, EM-seq)
• x and y limits for ridge plots (segplot)
• bugfixes

1.2.11

bugfix release due to packaging issues

1.2.8

Add features:

• add --color_by_phase
• add --smoothed_csv option to output smoothed data to .csv
• add --show_transcripts to locus/region
• add --exonheight to locus

Notable bugfixes and updates:

• fix modbam support for wgmeth when using --phased
• handle cases where the read length is longer than the reference
• remove jitter keyword from violin plots

1.2.7

• region, locus: change --highlight_panels to --highlight_alpha
• region: add gene-specific colours
• enforce --motif should only include IUPAC bases
• region, locus: custom colours if input is list of .bam files with two columns (2nd column being colours)
• add -o, --outfile as option to specify filename for tools with file output.
• various bugfixes

1.2.6

Fixes:

• skip bogus modified base data in .mod bams due to calls outside bounds of hard-clipped secondary/supplementary alignments
• locus/region: use "gene_id" if "gene_name" not in .gtf attributes
• various fixes to mod .bam handling, particularly around single base motifs

Features:

• composite: add --meanplot_cutoff, --output_table, --minelts, --maxelts options
• locus/region: add --plot_coverage option (experimental)
• depreciate db-guppy
• scoredist: support mod .bam

1.2.5

Bugfixes and feature requests:

• locus/region/composite: add --ymin and --ymax options to control vertical range on smoothed methylation plots (#26)
• Try harder to detect .bam files if they don't have the .bam extenstion (#25)
• region: Allow IUPAC codes for normalising region coverage (#22)
• wgmeth: error instead of crash if --phased used on unphased data.

1.2.4

Mostly bugfixes.

• add warning where there are multiple mod calls on the same site (seems to be a nanopolish-specific issue related to inclusion of non-primary alignments that overlap primary alignments)
• add --primary_only option (only really works for mod .bams)
• segplot: tweaks to ridge plot output
• do not require PS tag for phased reads (not all phasing tools output this)

1.2.3

Various bugfixes and minor improvements.

1.2.2

• updates for .bam files with modification tags: all tools should work for both remora and megalodon .bams
• segplot: --ridge_smoothing option, --ref and --motif options for mod .bams
• wgmeth: --motif option for mod .bams
• locus: --ref and --motif options for mod .bams