v0.5.2

Re-organize legacy files. Make compatible with upcoming conda package of AmpliconSuite. Classifications unchanged from 0.5.1.

v0.5.1

• bugfixes to AmpRepo table generation
• add hybrid viral classification ("Virus") for GRCh38_viral samples
• improve classification of hybrid-human viral ecDNA
• enforce a minimum size on total size focally amplified BFB regions (20kbp)
• renames classification "Linear amplification" to "Linear" and "Complex non-cyclic" to "Complex-non-cyclic" to remove spaces from class names.
• warn users if --ref arg appears swapped between GRCh37 and hg19.

v0.4.16

Improved filtering of low CN regions from Linear and CNC bed files. Result table creation bugfixes.

v0.4.15

Version 0.4.15 improves handling of sample and run metadata during the result table generation

v0.4.14

• Better filtering of invalid inds from BFB calling.
• Prevent negative entropy/complexity values
• Ignore same graph.txt comparisons in feature_similarity.py (overlapping features)
• Bonferroni correction on similarity filter pvalue
• Update mm10/GRCh38_viral patch regions

v0.4.13

Improvements to summary tables, feature similarity, and GRCh38_viral usage.

v0.4.11

• Refactor to separate output writing from classification steps.
• Add --filter_similar which filters highly similar amplicons using the amplicon similarity score.
• Make --annotate_cycles_file default
• Write a file of amplicon basic properties.
• Update the JSON table writing.

This version update will not affect classification results from the prior version, unless --filter_similar is set.

v0.4.10

Update README.md