Walk finds completely novel allele when presented with mutated allele

[ronald-jaepel]

Same situation as in Issue #13

but this time walk picked an allele that has one additional mutation compared to the original:

Gene	Version	DNA_SNPs	DNA_INDELs	AA_SNPs	AA_INDELs
ctxm	101	2	0	1	0
tem	39	2	0	2	0

Repeat of the debugging locations: The genomes, reads and graphs can be found at:

/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/generated_genomes/2016_05_09_1252/ecoli_K12_MG1655ref.fa

/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/simulated_reads/2016_05_09_1252/ecoli_1.fq.gz or ./ecoli_2.fq.gz

/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/simulated_graphs/2016_05_091252/ecoli.k31.ctx (e.g. ecoli_tem183.k31.ctx)

The databases used are: databases.zip where gn_amr-genesmutated.fasta was used to generate the genomes, reads and graphs while gn_amr-genes.fasta was used as panel for walk

The JSONS output of the atlas runs can be found at: /data1/projects/ronald_jaepel/atlas_test/JSONS/2016_05_09_1252/

[Phelimb]

Also fixed by https://github.com/Phelimb/atlas/commit/ef6a4a9f3b90a8dd1e995140bdf9d8993690d87f (v0.3.11) . I think a similar issue occurs as in #13 at the point of the very low coverage kmers.

@ronald-jaepel How easy would it be for you to rerun all of these analyses?

[ronald-jaepel]

I should be able to do that today.

[ronald-jaepel]

did you change the output .json format?

• before the .json of atlas walk calls included the atlas genotype information, now it doesn't