Peter Nguyen

Vcfanno does not use pipes to delimit multiple annotations for a single ALT allele

4

The `by_alt` operation should use pipes (perhaps this could be parameterized) to delimit multiple annotations for a single ALT allele. However when adding BED annotations, vcfanno seems to use commas...

install_data.py requires more than 30 GiB of memory

2

It seems like install_data.py -- in particular https://github.com/davek44/Basset/blob/6ae86b88a8df8607c58590ee84a3702662ac33dc/install_data.py#L113 and https://github.com/davek44/Basset/blob/master/src/seq_hdf5.py#L73 -- requires a lot of memory. It deterministically runs OOM on a GCE instance with 30 GiB of memory. After...

The Docker image lzamparo/basset is great, but it is missing a few things Re Lua, it needs to have ```bash export LUA_PATH="$BASSETDIR/src/?.lua;$LUA_PATH" ``` Re Python, it does not have an...

GenBank parser too sensitive to spacing differences.

5

### Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: ```python import sys; print(sys.version) import platform; print(platform.python_implementation()); print(platform.platform()) import Bio; print(Bio.__version__) ``` ```...