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).

v1.2.2

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

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

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

v1.1.4

AC version 1.1.4

• Remove unused check for AC_SRC in feature_similarity.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.

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

v1.1.2

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

v1.1.1

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

v1.1.0

--- This release is broken and fixed in 1.1.1 ---

• 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

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.