Add max_depth option for pysam.pileup in BaseCellCounter.py and SingleCellGenotype.py

cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data

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Closed ArthurDondi closed 2 months ago

ArthurDondi commented 3 months ago

Added a max_dp option in BaseCellCounter.py and SingleCellGenotype.py as discussed in #63
For the int(DP) and int(NC) filters in BaseCellCalling.step1.py, swapped min_reads and min_cells (from #16)