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Genes under 30x#1

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rklocke wants to merge 10 commits intomainfrom
genes_under_30x
Open

Genes under 30x#1
rklocke wants to merge 10 commits intomainfrom
genes_under_30x

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@rklocke rklocke commented May 6, 2024

  • Add functionality (find_low_coverage_genes.py) to return a report containing genes with coverage under a certain percentage threshold at 30x, which takes inputs:
    • A file from Sambamba (-i)
    • Optional parameter of the name of the output file (-o)
    • Optional parameter of a threshold (-t) to find genes under that percentage at 30x
  • Add unit testing for above functions
  • Update README to reflect usage of the tool and provide example commands
  • Add example output data for thresholds of 100% and 98%
  • Add requirements.txt for required packages

@rklocke rklocke added the enhancement New feature or request label May 6, 2024
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