Dev #4
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Dev #4
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…entries.tsv * roers would not run when the --dedup-seqs flag was passed becuase the output file was created in an inconsistent mode (no .write(true), but .append(false)). This is fixed and the file is now created with .write(true).trunc(true). * write out a duplicate_entries.tsv file when --dedup-seqs is used to track the name of the deduplicated (removed) sequence and the retained sequence to which it maps (matching the behavior of pyroe). TODO: Come up with a more considered policy of which sequence to keep an which to eliminate when deduplicating. Also, decide if we should deduplicate *across* sequence types (spliced/unspliced) or only within.
Record dups
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Several important changes and fixes:
roersto fail with the--dedupoption (due to a fileOpenModemistake).pyroeby writing aduplicate_entries.tsvfile containing, for each deduplicated (removed) sequence, the (retained, duplicate) pair.t2gort2g_3colfiles.polars, unlikepandasbackingpyroe, is multithreaded).spliceureference), the spliced sequence will be retained and the unspliced sequence deduplicated.