Tobias Neumann

Fit Awesome-CV formatting to list of publications

14

Hi, great CV template, I like it a lot. Very well structured, too. The only thing missing (or I couldn't find it) is a publications section where one could e.g....

Check if chromosome names match bam/bed

6

Currently an empty iterator will be returned if the chromosome names from bed do not match the ones from the fasta file. We should check this and implement a warning.

Unknown behaviour read > max read length

2

Currently only tcperreadpos crashes if a read is found > than a manually set max read length. Add some checks if such behaviour is observed and throw warnings or even...

Reverse stranded support

3

Currently only stranded data is supported. Some protocols will deliver reversely stranded data, we should add support for this.

https://github.com/t-neumann/slamdunk/blob/master/slamdunk/utils/misc.py#L91

Make tcperutrpos static window size configurable as a parameter. Now it's hard-coded 250bp.

Error when chromosome names contain "-". Apparently the current parser also splits on dashes.

Multimapper ordering random between Docker and PyPi version. Affects reads multimapping within the same UTR since then alignment is chosen randomly which depends on the output order.

SNP info flag discrepancies between Docker and PyPI version.

-filterbed automatically sets -m during filtering, but -n still has to be set >1 to actually work. Suggesting to set -n 100 if -filterbed is provided.