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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Ability to specify a user provided configuration yaml file or ability to change presets #172

Closed xunjieli closed 5 years ago

xunjieli commented 5 years ago

We are experimenting with different GLnexus parameters. It will be very helpful if the standalone GLnexus program (glnexus_cli) can accept a flag to parse a user-supplied yaml config file instead of using one of the presets.

This feature request might be equivalent to what you wrote in the code here:

https://github.com/dnanexus-rnd/GLnexus/blob/master/src/cli_utils.cc#L463

// hard-coded configuration presets for unifier & genotyper. TODO: these
// should reside in some user-modifiable yml file
static const char* config_presets_yml = R"eof(
...

Either solution will work for us, so we can use the released binaries with different params. Thank you.

mlin commented 5 years ago

Sorry the documentation is poor but if you give --config custom.yml (where custom.yml is anything ending in .yml) it will treat it as a filename to read. The contents of the file should have genotyper_config and unifier_config at the top level.

ref: https://github.com/dnanexus-rnd/GLnexus/blob/c673f41ba3bf48872ec8c28364db5f79f9c47d72/src/cli_utils.cc#L888-L891

xunjieli commented 5 years ago

Neat! Didn't see that. thank you.