https://github.com/ampliconsuite/ampliconclassifier - v1.4.1

• small modifications to default params to increase stringency of ecDNA identification
• remove deprecated edges-related info from --verbose_classification
• refactor global vars into config JSON file, allow users to modify with --config to set additional params
• refactor variable names for readability, move some functions into utils

- Python
Published by jluebeck 12 months ago

https://github.com/ampliconsuite/ampliconclassifier - v1.3.3

Bugfix to counts file when ecDNA filtered in final cycle check

- Python
Published by jluebeck about 1 year ago

https://github.com/ampliconsuite/ampliconclassifier - v1.3.2

• Fix logging issue when no focal amps found
• Enable compatibility with ecSimulator amplicons

- Python
Published by jluebeck about 1 year ago

https://github.com/ampliconsuite/ampliconclassifier - v1.3.1

• Improves assignment of regions to focal amp features and unknown.
• Better filtering of tandem dup amps.
• Refactor breakpoint graph reading, graph representation, similarity functions.
• Summary map arg is now optional (location autodetected).

- Python
Published by jluebeck about 1 year ago

https://github.com/ampliconsuite/ampliconclassifier - v1.2.2

Bugfix to usage in non-batch mode, where one amplicon is provided only from --cycles and --graph arguments

- Python
Published by jluebeck over 1 year ago

https://github.com/ampliconsuite/ampliconclassifier - v1.2.1

• refactor method for gene reporting
• add NCBI gene ID to gene tables and final results table
• genes now reported in final results table even if 5-prime end is missing
• add module versions to final results table
• add warning if summary map file missing

- Python
Published by jluebeck over 1 year ago

https://github.com/ampliconsuite/ampliconclassifier - v1.2.0

• 0bp and 1bp segments in decomposed AA cycles no longer contribute to identification of foldbacks, improving BFB detection
• bugfix for --add_chr_tag arg in ecDNA context analysis
• handle empty bed file edge case in ecDNA context analysis

- Python
Published by jluebeck almost 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.1.4

AC version 1.1.4

• Remove unused check for ACSRC in `featuresimilarity.py`
• Add ecDNA context to result table
• Bugfixes for annotation file reading
• Correct off-by-one error in cycle length calculation (was 1bp too short)
• Do not allow --filter_similar with --ref GRCh38_viral as viral amplicon boundaries are conserved and this would filter oncoviral cases inappropriately.

- Python
Published by jluebeck about 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.1.3

AC version 1.1.3

• provides bugfixes for feature & amplicon similarity calculations on mm10-aligned samples
• fix occasional crash during classification of GRCh38_viral-aligned samples

- Python
Published by jluebeck about 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.1.2

Adds a bugfix to a rare situation where genomically overlapping ecDNA are reported

- Python
Published by jluebeck over 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.1.1

This tagged release incorporates a fix for a critical bug (crash) in 1.1.0.

- Python
Published by jluebeck over 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.1.0

• bugfixes to high-CN BFB detection with many foldbacks
• handle old AA graph files w/o homology info
• better handling of graph and cycles files not found by ecDNA context method

- Python
Published by jluebeck over 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v1.0.0

• adds ecDNA genomic context reporting to enable analysis of ecDNA origins
• refactor to place library files into a directory (will simplify conda packaging)
• add warning if input file cannot be generated
• tweak filtering criteria for --filter_similar argument

Version incremented to 1.0.0 as method is becoming stable.

- Python
Published by jluebeck over 2 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.5.4

• Incorporates functionality of make_input.sh directly into amplicon_classifier.py
• Users can now give a directory of AA outputs to the classifier with --AA_results, bypasing the need to make the .input file.
• Makes reading of graph file more robust
• Tweaks --filter_similar multiple comparisons p-val adjustment
• Bugfix to gene names changed for hg38
• Documentation updates

- Python
Published by jluebeck almost 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.5.3

• Adds filtering of amplicons with too many foldback-like artifacts for improved BFB detection
• remove index.html generation
• documentation updates

- Python
Published by jluebeck almost 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.5.2

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

- Python
Published by jluebeck almost 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - 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.

- Python
Published by jluebeck about 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.4.16

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

- Python
Published by jluebeck about 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.4.15

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

- Python
Published by jluebeck about 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - 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

- Python
Published by jluebeck over 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.4.13

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

- Python
Published by jluebeck over 3 years ago

https://github.com/ampliconsuite/ampliconclassifier - 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.

- Python
Published by jluebeck almost 4 years ago

https://github.com/ampliconsuite/ampliconclassifier - v0.4.10

- Python
Published by jluebeck almost 4 years ago