Czhu fix parse rmats

[zhuchcn]

Description

Fixing 3 things here.

1. The skip junctions of SE were not handled correctly.
2. The function that identifies a transcript being mRNA_end_NF did not do its job. This is not related to AS.
3. I added a check in the beginning of each cli to make sure the output files are writable, to avoid waiting for hours to find out the output file has no write permission.

So because of 2, we may have to rerun the SNV only for CPCG samples for benchmark again. I tried CPCG0100 and the difference is pretty small.

Closes #...

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
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[lydiayliu]

Closes #671?