Version 0.7.3 access: - New command equivalent to the now-deprecated `genome2access.py` script. target, antitarget: - Always write output files in 4-column BED format. scatter: - Copy ratios (.cnr) are no longer required. Without this input file, behavior is similar to the now-deprecated `loh` command, but still more flexible. - VCF input file can include multiple tumor samples and PEDIGREE tags; if a tumor sample ID is specified, all PEDIGREE tags will be checked to find the matching normal sample. - VCFs processed by CLC Genomics Server are now parsed correctly. loh: - Deprecated. Use `scatter` with `-v` and no .cnr file instead. segment: - Preliminary support for segmenting SNP allele frequencies from a VCF in addition to total copy number (`-v` option). Details are likely to change in a later release. (#34) - In the `weight` column of the output file, values are now the sum, not the mean, of the weights of the probes covered by that segment. - The `haar` segmentation method is improved to avoid duplicate breakpoints and run much faster. export bed: - Deprecate `--show-all` in favor of `--show` with possible arguments `all` (like --show-all), `ploidy` (default behavior), or `variant` (show the same regions as export vcf). export vcf: - Fix a typo in the SVLEN tag definition in the VCF header -- Number should be 1, not -1 which caused GATK parsing to fail. (#57; thanks @chapmanb) Python library `cnvlib`: - Logging is now done with the Python standard library's `logging` module, making it easier to silence or redirect status messages. In particular, unit tests run more quietly. (#52) - Internal refactoring (including new features in GenomicArray, RegionArray, VariantArray) resulting in changes to the `cnvlib` API , as well as some performance improvements.