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Include small samples of 2bit/BB/bam files for easier testing

Open armish opened this issue 9 years ago • 2 comments

We currently depend on external 2bit (for reference) and BB (for genes) files for testing/demoing. Instead, it would be great to have relatively small slices of them in the repository.

These will include the following files that span the range chr17:7500000-7515000

  • [ ] a slice of the hg19.2bit file
  • [ ] a slice of the ensGene.bb file
  • [ ] a small bam files with unpaired reads

armish avatar Sep 17 '15 16:09 armish

one problem is that there's no such thing as a 2bit "slice" — each chromosome always starts at position 1. We could work around this by making a ShiftedTwoBit class that wraps TwoBit, but this might be confusing for our introductory example.

danvk avatar Sep 17 '15 16:09 danvk

ah, I see. That 2bit file will require some more thinking then.

armish avatar Sep 17 '15 16:09 armish