v1.1.0

• update conda recipe for AmpliconClassifier version 1.0.0, which adds ecDNA context reporting
• Update documentation in GUIDE.md
• Bugfix to GroupedAnalysisAmpSuite.py invokation of AmpliconSuite-pipeline.py
• improve install.sh --finalize_only when docker or singularity is used (thanks Owen Chapman)
• add test output files to compare against in test_outputs/ directory
• add script to get timing log get_AA_log_timing.sh from multiple samples to help evaluate runtime on large batches of samples
• add script to evaluate how commonly specific regions end up in seed files from a collection of bed files seed_overlap_counts.sh
• fix behavior of --no_filter
• --sv_vcf arg in docker and singularity uses absolute path of file

v1.0.0

1.0.0 is here! Not because of huge new improvements to the pipeline in this release, but because the features and codebase are finally stabilizing.

• Adds support for AA v1.3.r6, which provides users with two new arguments
  • --sv_vcf, --sv_vcf_no_filter/
  • These allow AA to use externally provided SV calls from a VCF file
• Log last_modified date from AA data repo
• Improve usability of --completed_AA_runs mode
• Update github links in container files, documentation, wrapper arguments, and lift singularity scipy version cap
• Bugfixes to GroupedAnalysisAmpSuite.py
• Improve install.sh
• Differentiate various license, report the AA license explicitly since it is not the BSD-2-Clause
• Include copy number flow in cycles_to_bed.py
• Documentation updates

v0.1555.2

• Reallow --ref to be optional if bam file is given
• Require --ref if --completed_AA_runs is given
• Update conda build recipe for local builds
• Bugfix to the default --AA_insert_sdevs argument specified by GroupedAnalysisAmpSuite.py

v0.1555.1

• Updates to GroupedAnalysisAmpSuite.py to add a --no_union option if users want to run multiple samples in a batch but not take union of the seeds.
• add --uninstall option to installer and fix bugs in installer script
• Fix potential issue with concurrent docker/singularity image deployment
• Update conda recipe
• update documentation.
• better logging about issues finding data repo

v0.1546.1

Create a release for packaging with conda.