This is a start on beacon oriented tests for the import scripts. They will probably need more work and maybe some restructuring, but I add them as a PR already now in an attempt to make things less confusing when coming back from vacation.
Two new things are tested: the dataset variantcount and callcount, and the parsing of manta files.
Changes made:
Adds test for adding data set counts (--count_calls)
updates travis_script.sh to count these calls for dataset1_1 and dataset2_1
add expected counts to reference.psql
Adds test for importing a manta file (ie mates, breakends)
test data (manta.vcf, slightly modified Swegen data)
reference counts (mates_reference.txt)
update to travis_script.sh, Test 6, to make an import and compare the result.
Describe the pull request:
Pull request long description:
This is a start on beacon oriented tests for the import scripts. They will probably need more work and maybe some restructuring, but I add them as a PR already now in an attempt to make things less confusing when coming back from vacation.
Two new things are tested: the dataset
variantcountandcallcount, and the parsing of manta files.Changes made:
Adds test for adding data set counts (
--count_calls)travis_script.shto count these calls fordataset1_1anddataset2_1reference.psqlAdds test for importing a manta file (ie mates, breakends)
manta.vcf, slightly modified Swegen data)mates_reference.txt)travis_script.sh,Test 6, to make an import and compare the result.