Added variant callers for benchmarking (resolves #97) #99
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fnothaft
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Jenkins, retest this please. |
jvivian
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Aug 14, 2017
| end_time = time.time() | ||
| log_runtime(job, start_time, end_time, 'fasta_generate_regions') | ||
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| docker_parameters = ['--rm', |
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more DRY to have a base_docker_parameters as you're just extending to add --entrypoint.
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| import subprocess | |||
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| def log_runtime(job, start, end, cmd): | |||
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Given the repetitiveness of having to call time.time() before and after every dockerCall along with this function, would this be better refactored as a decorator for dockerCall?
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Wait 'til you see where I'm going with this in #101...
Added: * FreeBayes * Platypus * 16GT * Strelka (and Manta) * Samtools Mpileup/BCFtools call Also, ported over GATK3 HaplotypeCaller from toil-scripts.
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Rebased. Consider this good to merge for now. |
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