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This field was missing from the INFO header which broke the scoring step (error related to plugin not defined in VCF header). The introduced header definition is copied from test_vcf_annotated.vcf file. Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
…s to VCF fixture Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
This is a better option than the default logging module since it provides process level insight as well as prints logging output to stdout/err.
Errors in run method is not visible on stdout/err by default. Log error and stacktrace. Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
When subprocess compound scorers fails and stops decreasing semaphore counter, while main process is in queue join() waiting for completion, we have a deadlock. Avoid this situation by checking subprocess states before joining on queue so that processing can be aborted properly and errors made visible. Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
This patch adds functionality to rescore a VCF (potentially with a different score config) and append the scoring results to the VCF where the score annotations are suffixed. Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
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For @ramprasadn reference building genmod docker container for rescoring.
This PR contains just changes from #180 and export to .sif image makefile target.