v1.5.2

• Correctly handle low CN non-ecDNA human-viral amplicons for GRCh38_viral ref samples
• Do not report empty bed files

v1.5.1

• When converting intervals back to 0-based half-open from fully closed interval, bugfix to intervals being reported 1bp longer than they should be.
• lncRNA annotations created using GENCODE database.
• Added check_SV_support.py script and refactor read support analysis code.
• Catch edge case where no CN states found in ecDNA context analysis.
• Expose p-value threshold argument for similarity filtering to user.
• Decrease stringency for similarity-based filtering of linear amps.
• Add optional argument to do --make_results_table, the consolidate report of classification outputs that previously required running a separate make_results_table.py script.
• Add script to liftover AC files between ref versions (@Sspandau)
• Add script to create directory of softlinks to sashimi plots by amplicon classification type.

v1.4.2

• bugfix to make_input.sh when no amplicons present
• logging improvements and bugfixes
• improve legacy version usability for easier comparison of legacy to current
• improve results_comparator.py
• rewrite make_input.sh and bugfixes
• Includes updates which were not actually included in the prior release:
  • modifications to default params to increase stringency of ecDNA identification for small, low CN focal amps
  • 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

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

v1.3.3

Bugfix to counts file when ecDNA filtered in final cycle check

v1.3.2

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

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