v0.4.2 - Bugfix and Enhancement

v0.4.2

Notes

This is a minor bug fix and enhancement release with the following changes:

Linelist

• Issue #70: Fix missing sc2rf version from recombinant_classifier_dataset
• Issue #74: Correctly identify XN-like and XP-like. Previously, these were just assigned XN/XP regardless of whether the estimated breakpoints conflicted with the curated ones.
• Issue #76: Mark undesignated lineages with no matching sc2rf lineage as unpublished.

Plot

• Issue #71: Only truncate cluster_id while plotting, not in table generation.
• Issue #72: For all plots, truncate the legend labels to a set number of characters. The exception to this are parent labels (clade,lineage) because the full label is informative.
• Issue #73, #75: For all plots except breakpoints, lineages will be defined by the column recombinant_lineage_curated. Previously it was defined by the combination of recombinant_lineage_curated and cluster_id, which made cluttered plots that were too difficult to interpret.
• New parameter --lineage-col was added to scripts/plot_breakpoints.py to have more control on whether we want to plot the raw lineage (lineage) or the curated lineage (recombinant_lineage_curated).

Commits

• 8953ef03 docs: add CHANGELOG for v0.4.2
• 7ec5ccc6 docs: add notes for v0.4.2
• 1b3b1f1d script: restore column name to recombinant_classifer_dataset
• 901caf98 script: restore recombinant_lineage_curated of -like lineages
• d6be9611 script: change internal delim of classifier for #70
• cdb4a78a script: fix recombinant_classifier missing sc2rf for #70
• bf7a4e57 script: mark undesignated lineages with no matching sc2rf lineage as unpublished for #76
• 46f6d754 workflow: update linelists and plotting for #74 and #75
• c03dd3be script: don't split largest by cluster id for #73
• e9802e79 script: majority of plots will not split by cluster_id for #73
• bafb38fb script: fix cluster ID truncation for issue #71
• ab712593 resources: curate and test breakpoints for proposed895