HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
BSD 3-Clause "New" or "Revised" License
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Add flag for cluster-bins to allow multiple gaps per chromosome #215
Issue: fixed-width binning (and external methods for preparing bins) may intentionally leave gaps between adjacent bins where there is little or no data, e.g., regions lacking heterozygous SNPs. This PR adds an optional flag that skips the check currently performed by cluster-bins which requires at most 1 gap per chromosome. Default behavior is unchanged.
Also fixed a bug with allowed keywords mismatch between ArgParsing and cluster-bins.py
Issue: fixed-width binning (and external methods for preparing bins) may intentionally leave gaps between adjacent bins where there is little or no data, e.g., regions lacking heterozygous SNPs. This PR adds an optional flag that skips the check currently performed by
cluster-binswhich requires at most 1 gap per chromosome. Default behavior is unchanged.Also fixed a bug with allowed keywords mismatch between
ArgParsingandcluster-bins.py