Commit 03ce7a67 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

journal update

parent 20505da6
......@@ -3,4 +3,21 @@ https://gitlab.cs.uni-duesseldorf.de/hoeckesfeld/snakemake-ngs-spa-typing
## 10.11.20 - 17.11.20
This week I could get the hilbert to run the snakemake workflow. A few parameters needed to be tweaked (7c2f06fd).
The plan at the moment, is, to find a feasible probability for V\O kmers. For this I implemented
a script calcDistanceMatrixVkmers.py . TODO: embed the resulting .npz in the ckmer script.
\ No newline at end of file
a script calcDistanceMatrixVkmers.py . TODO: embed the resulting .npz in the ckmer script.
## 18.11.20 - 24.11.20
This week I coded the import of .npz files into the c++ script. For this I needed to adapt the CMake script and also the docker image.
This gets more and more complicated, since my local machine cannot handle the memory needs. Also i defined my expectation value for unobserved kmers:
```math
e_k = error rate
a = e_k / (e_k +1)
```
-> a is the chance of one mutated base, so (1-a) is the chance of no mutation of the base
So the chance of mutating from kmer a to kmer b is:
```
a^{mutated_bases} * (1-a)^{unmutated bases}
```
This results in a expectation value for an unobserved kmer:
```
E = sum over all si in Spatype: a^{mutated_bases} * (1-a)^{unmutated bases}
```
......@@ -81,10 +81,10 @@ rule calcLikelihoods:
deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))),
itersetType = config['itersetType'],
#cluster exectuion
cpus = '1',
mem = '4G',
cpus = '8',
mem = '15G',
gpus = '0',
walltime = '01:30:00'
walltime = '00:30:00'
singularity:
'docker://phspo/ckmertools:iterationset-tests'
shell:
......
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