Indexes are 0-base not 1-base

hoffmangroup / umap

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Indexes are 0-base not 1-base #17

Open niederhuth opened 1 month ago

niederhuth commented 1 month ago

While running the scripts from the command line with --job_id, I noticed that each step skips the first set of chromosomes/coordinates in the chrsize.tsv and chrsize_index.tsv. Digging into this, it looks like these are not being read in as 0-base index, rather than a 1-base index.

EricR86 commented 3 weeks ago

The TSV is, as far as I can tell and remember, supposed to be 1-based. There is a good chance that this is a bug. How did you verify that the first job by ID was being skipped?