- `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
1.2.1
- `locus`: add --bed option to draw custom annotations - `locus`: indicate annotation direction with ">>" (+) or "<<" (-) - `locus`: add --phase_labels option to replace HP tags with names when using --color_by_hp - `locus`: bugfix keep legend z-order on top - `composite`: bugfix --mincalls
1.2.0
- Re-worked the `composite` function to allow for multiple samples and phasing with a simplified input. - [segplot: preserve sample order in ridge plot](https://github.com/adamewing/methylartist/commit/86224307149028be355bcf0a131c69a58973946b)