CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams

This repository contains java code for a simple command to get cell level mapping information (number of reads that are intronic, intergenic, multimapped, etc) from the output in CellRanger (tested with CellRanger v5 and v6 using the include introns flag, should work with more recent versions as well though no gurantees. Should work on spaceranger output as well, and both single nuc and single cell data).