Support for UCSC Style Chromosome IDs

raphael-group / THetA

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.

http://compbio.cs.brown.edu/projects/theta/

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Support for UCSC Style Chromosome IDs #12

Closed DarioS closed 7 years ago

DarioS commented 7 years ago

                       ...
    2. chromosome number (Integer) - chromosome on which the interval
       occurs
                       ...

This seems unnecessarily restrictive and creates extra work for the end user. Why not allow values like chr1 and chrM ? I've seen other bioinformatics Python packages with this unusual limitation, too.

gsatas commented 7 years ago

Thank you for bringing this to our attention. The code already accepted chrmN format and we updated the code to accept chrN format. The manual has been updated the manual to describe allowed formats.