Leandro Lima

A different parallelisation granularity in GATB

2

Dear GATB team, In [pandora](https://github.com/rmcolq/pandora/), we use GATB to make a local assembly of de-novo variants. We are facing a performance issue where we have to perform several thousands local...

Add --update-method to make_prg update

1

Not for this next 0.4.0 release, likely for 0.5.0. Adds a new parameter to `make_prg update`: ``` -m UPDATE_METHOD, --update-method UPDATE_METHOD How to update PRGs. Valid options are (default is...

See https://llvllatrix.wordpress.com/2016/02/19/python-vs-copy-on-write . TLDR: every python object has reference counting. If we are sharing read-only python objects hoping this will be efficient due to copy-on-write optimisation, it might not be...

See https://github.com/iqbal-lab-org/make_prg/pull/37/files/9be3b81420f10319f0f547c24b1be2fff2a6e5e6#r853619797

Ignore `N`s that might have slipped through when updating PRGs

4

When running the 4-way pipeline, updating the E coli PRG with illumina data, I got this error: ``` Traceback (most recent call last): File "/usr/local/bin/make_prg", line 10, in sys.exit(main()) File...

Mabi got confused by this warning message, and I think the common use case for `pandora` is to actually not receive reference sequences for the genes and automatically infer it...

Downsampling reads is an upstream task, not pandora responsibility

See Zam's comment at https://github.com/rmcolq/pandora/pull/335 Basically, we have several common default CLI args for `compare`, `map` and `discover`, see https://github.com/rmcolq/pandora/blob/master/include/compare_main.h https://github.com/rmcolq/pandora/blob/master/include/map_main.h https://github.com/rmcolq/pandora/blob/master/include/denovo_discovery/discover_main.h Would be better if there was a header...