Anders Pitman

bamtools throws an exception when attempting to open stdin when spawned as a subprocess by Node.js. The solution is to build bamtools with: `cmake -DEnableNodeJS=true` This is mentioned in the...

RAL

6

Also added a Command Abstract Base Class and cleaned up the other commands a bit

Port to Python

76

@reedacartwright and I wanted to start a conversation about possibly porting the bash portions of SISRS to Python. We both feel this would make it easier to maintain in the...

Pretty sure it's not needed since I made our own script for camparing bam files

Sorted for python 3

2

In order to generate test data that could be compared to a python 3 run of sisrs, a few changes were necessary. This mostly had to do with sorting things...

Add unit testing/continuous integration

43

It would be good to implement at least some basic testing and CI. The first step would be to come up with a standard small dataset to run against.

Is BBMap really a hard dependency?

5

It's a pain to install (especially for continuous integration) and it appears we're only using one small script (rename.sh) from it.

Check out kcptun

1

https://github.com/xtaci/kcptun

Hi @japaric, from looking through the code it appears there aren't any 64 bit representations. Is that true, or am I reading it wrong? There's a lot of macro magic...

I'm on Firefox 63, attempting to stream a large (18GB) text file. The stream is slowing to a crawl and my memory is blowing up. Are there specific options I...