John St. John

TODO: - Determine if a site is a known DBSNP site within the MuTect genotyper. Any ideas for this @fnothaft? - Calculate the sum of phred scores for mismatching bases...

I have the same `java.lang.ClassNotFoundException: org.apache.spark.streaming.twitter.TwitterReceiver` issue now that I fixed the `scalaVersion := "2.10.3"` thing.

Oh interesting. Yeah that check is in place to avoid the situation where the reads get out of sync. The length 91 thing seems to be confusing it. You could...

So that’s the function that does the comparison. Looks like your quickest option would be to add a return true; (before that first if) as the first line of the...

You wouldn’t want to ignore that… it’s saying that read 1 and read 2 are not actually from the same fragment! I would do some manual qc on the data...

Also you’re outputting one file as .fq and the other as .fq.gz. Pretty sure you didn’t mean to do that? On Jul 21, 2022, 7:32 PM -0700, bahiyahazli ***@***.***>, wrote:...

Hmm.. there seems to have been a change in compilers going to 10.9 that broke things. Remove “-Werror” from the makefile, install macports, install gcc version 4.7 in there, and...

Thanks for the info! I will go through and do that unless someone beats me to it with a pull request ( I will not have time to do this...

Of course! Sorry for the super late response.

Hello, I am not actively working on this. At a high level we would probably want to wrap the file IO operations in a function that optionally does gzip output....