First release.

This is the first release with the complete pipeline.

Input file:

• Probability table from NanoSplicer (TSV)
• NanoSplicer jwr_checker output (HDF5)
• BAM file (same as what has been input to NanoSplicer)

Output:

• **Option 1:**Default (or specify an output filename with extension .bed): BED file. Each entry corresponds to a unique isoform, and the "score" field (column 5) represents the read counts for each identified isoform.
• Option 2: specify an output filename with extension .gtf). Note: the quantification information is still not included in the GTF output.