Jim Robinson

Thanks @cviner this is helpful. I understand that it is definitely possible for multiple modifications to be specified for a single position, each with a probability. This is common now...

@jkbonfield I'm making a lot of noise I guess, but maybe this is will be helpful. If I struggle with this I suspect someone else will. So after studying the...

Yes, if someone could ping this issue again in February I will look at it. On Thu, Jan 5, 2017 at 12:38 AM, nchernia wrote: > @jrobinso If you could...

@lbergelson File encoding should be irrelevant, this is a raw byte stream. Regardless of other issues casting in.read() to a byte before that test is incorrect, I think. A positive...

InputStream.read() is supposed to return an integer between 0 and 255, or -1 if EOF, there is no encoding involved. So 1/2 of the values it can legally return will...

It's a weird convention, but its been like that since the beginning. I suppose the contract is for an "int" specifically so they can have a return value (-1) which...

@lbergelson I still don't see what encoding has to do with this class, which is a stream reader for raw bytes. You can decode these bytes anyway you please, but...

@lbergelson OK, yes, sorry, I was focused on the test in question, the part below. It is most definitely a bug to cast the result from in.read() to a byte...

Here's the relevant text for GFF format, which I think is pretty typical among genomic file formats. The term "plain text" might be ambiguous, but I think is understand to...

The reference server has been down for almost 2 years so I'm closing this.