SISRS

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index out of range error

5

Getting the following error when trying to run SISRS with the test data provided: ```==== Done Identifying Fixed Sites Without Error ==== 748768 total variable sites (alignment.nex) Traceback (most recent...

kleigeb

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...

anderspitman

Python Port Documentation

4

Hi @anderspitman, After bringing over the new Python port branch, there are a few things that I'm unclear about. Would you mind creating a basic README with usage instructions (how...

BobLiterman

Using Bowtie across multiple nodes, if available

4

Hey @anderspitman, One major bottleneck with SISRS is that the Bowtie mapping steps occur serially, rather than in parallel. In part, this is because Bowtie itself does not run in...

BobLiterman

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.

anderspitman

use compressed data

1

rachelss

Problematic Species

1

Include an option to identify specific taxa which lead to disproportionate amounts of missing data for possible downstream filtering

BobLiterman

If we want to encourage the use of SISRS we should explore ways to make it attractive to users. Readthdocs? Standalone website? Once there's a python port we can look...

rachelss

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.

anderspitman

Assigning Tasks

2

With development of SISRS taking off this semester in two locations, it is important that we figure out who is addressing which issue or pull request. The easiest way to...

reedacartwright