PD-2474: Remove reads from MT genes in Tagsort metrics

[aawdeh]

Remove reads on MT genes from the intronic, exonic, and intergenic counts in Optimus/Multiome. To do this, we did the following:

1. Added the protected variables std::unordered_set<std::string> mito_genes_ to the class MetricGatherer. mito_genes_ are a set of MT genes

2. Added the following additional input parameters to theMetricGatherer class: TagOrder tag_order, std::string gtf_file, std::string mitochondrial_gene_names_filename.

3. Added function isMitochondrial to the class MetricGatherer which returns whether or not a gene is mitochondrial based on the tag_order.

4. Moved function getInterestingMitochondrialGenes in the MetricGatherer constructor.

5. Function parseAlignedReadFields in the MetricGatherer class.

• Added condition if mitochondrial (this calls isMitochondrial) to check if the gene is mitochondrial or not before counting the number of reads_mapped_uniquely_, reads_mapped_exonic_, reads_mapped_intronic_, reads_mapped_intronic_as_ and reads_mapped_multiple_.

7. Function ingestLine in the CellMetricGatherer class.

• Added condition if mitochondrial (this calls isMitochondrial) in if statement to check if gene is mitochondrial or not.

[ekiernan]

This looked good! Thank you for demoing. I think as long as the number of MT reads matches what is expected as discussed, this can be merged.