Please do not guess file types

[diekhans]

ssCorrect.py attempt to guess if a BED or STAR junction file was passed in can silently fail and produce incorrect results.

Please do not try to be easy to use by "guessing" and silently ignore, have explicit command line arguments for STAR vs BED.

This "save time" feature waste da lot of hours. Be rigorous.

[diekhans]

Have two options one for shortreads from BED and the other from STAR junction files will also help guide people that they should not be using junctions_from_bam with STAR BAMs.

By default, STAR doesn't output the XS tag. It is there for cuff links compatibility. It also has some side effects that someone running STAR might not want (discards reads with non-canonical). Probably, the doc should say, "you really should use STAR junctions file if you use STAR"

[diekhans]

this overlaps #381