Matthew DeMaere
Matthew DeMaere
An oversight has been discovered in the simulation of WGS pairs. Despite the possibility that real WGS pairs can span neighbouring contigs when occurring at contig-ends, during simulation in sim3C,...
Just realized that if a chromosome is defined as being in more than one copy, there is no possibility that it will interact with its twin(s). The probability draws are...
Real data from the S.stipitis genome demonstrates the characteristic X modulation of _trans_ interactions. This pattern is theorised to be due to spatial organisation of chromosomes. In particular, the collective...
https://github.com/cerebis/bin3C/blob/76ad2a94597b92b21e1d2054a1917c277e06cb1b/mzd/contact_map.py#L537 This will produce an uncaught exception if the 'HD' record does not existing the BAM file. We need to either check for 'HD' or place this call in a...
Currently data is stored simply compressing pickled python classes. This approacj was chosen over other serialisation methods as a good-enough and quick approach. However, as time passes and the codebase...
Without thorough testing to show otherwise, it must be assumed that bin3C relies on BWA MEM to build the BAM file, while also relying that BWA MEM was run with...
Dear cerebis, I am having a similar problem. I managed to generate the contact map but it's 58 Mb and when I run it in virtualbox (ubuntu) I got the...
With older version of Pip (mid v9 and earlier) did not support direct github URLs. ``` Exception: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 215, in main status =...
Certain experimental details can be modified post map creation and would eliminate needless re-runs if a change is desired due to such events as a metadata error at invocation time,...