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Feature: Automatically determine sample type using gene expression
- [ ] add "housekeeping genes" parameter to config.json
- [ ] add code to build "housekeeping" salmon index files for determining sample type
- [ ] add code to sequentially load these index files and quantify the first 1e6 reads
- [ ] add code to sum counts for "housekeeping" quant.sf files and determine most likely sample type composition
- [ ] add argument parser to expose new auto sample type determination
h/t @singerj