bin3C

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specify the last version of biopython (1.76) that supports python2

hyphaltip

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...

cerebis

One huge cluster

8

Hi cerebis, I used bin3c to build mags from hi-c (50G WGS and 30G Hi-C). bin3c two steps ran successfully. But the mags status was a little strange. There are...

orctyr

What is the `--tip-size` used for?

1

In contact_map, there is a param named tip-size I cant understand. its value is initialized none and is not input value. But in count_sites, it is used to partition the...

ruoyu1123

Bumps [pyyaml](https://github.com/yaml/pyyaml) from 3.13 to 5.4. Changelog Sourced from pyyaml's changelog. 5.4 (2021-01-19) yaml/pyyaml#407 -- Build modernization, remove distutils, fix metadata, build wheels, CI to GHA yaml/pyyaml#472 -- Fix for...

dependabot[bot]

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...

cerebis

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...

cerebis

Memory Error while running in VirtualBox

1

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...

cerebis

Installation through pip requires newer pip version

1

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 =...

cerebis

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,...

cerebis