Allow `bam` input and other formats of splice junction files

YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

http://yeolab.github.io/outrigger/

BSD 3-Clause "New" or "Revised" License

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Allow `bam` input and other formats of splice junction files #30

Open olgabot opened 8 years ago

olgabot commented 8 years ago

Right now, only csv files are allowed but as files grow larger and larger (especially the GTEX data which has ~9000 samples and ~300,000 junctions), then hdf format should also be accepted. It's unclear how to implement it thoguh because there's so many different formats and pandas.read_csv is already so complicated...