Propagated all hidden arguments in gCNV CASE mode from the given model #7464
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…d CopyNumberCallingConfig arguments from the input model configuration.
mwalker174
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Sep 14, 2021
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Let's add a documentation and checks on the Java side for when users try to specify hidden parameters with this:
final CommandLineArgumentParser clpParser = (CommandLineArgumentParser) getCommandLineParser();
final boolean isOutputSet = clpParser.getNamedArgumentDefinitionByAlias(StandardArgumentDefinitions.OUTPUT_LONG_NAME).getHasBeenSet();
and throw an error.
| * then specified by a file contained in the model directory, all interval-related arguments are ignored in this | ||
| * mode, and all model intervals must be present in all of the input count files. The tool output in CASE mode | ||
| * is only the "-calls" subdirectory and is organized similarly to that in COHORT mode.</p> | ||
| * then specified by a file contained in the model directory,and all model intervals must be present in all of the |
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directory,and -> directory, and
| * mode, and all model intervals must be present in all of the input count files. The tool output in CASE mode | ||
| * is only the "-calls" subdirectory and is organized similarly to that in COHORT mode.</p> | ||
| * then specified by a file contained in the model directory,and all model intervals must be present in all of the | ||
| * input count files. All interval-related arguments (e.g. {@code interval-psi-scale} argument) are ignored in this |
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(e.g. {@code interval-psi-scale} argument) -> (e.g. {@code interval-psi-scale})
| * is only the "-calls" subdirectory and is organized similarly to that in COHORT mode.</p> | ||
| * then specified by a file contained in the model directory,and all model intervals must be present in all of the | ||
| * input count files. All interval-related arguments (e.g. {@code interval-psi-scale} argument) are ignored in this | ||
| * mode, however an advanced user can adjust various sample-related (e.g. {@code sample-psi-scale}) and global |
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mode, however -> mode. However,
| * input count files. All interval-related arguments (e.g. {@code interval-psi-scale} argument) are ignored in this | ||
| * mode, however an advanced user can adjust various sample-related (e.g. {@code sample-psi-scale}) and global | ||
| * (e.g. {@code p_alt}) arguments for custom applications of the tool. Inference-related (e.g. | ||
| * {@code min_training_epochs}) arguments can be adjusted as well. The tool output in CASE mode is only the "-calls" |
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Inference-related (e.g. {@code min_training_epochs}) arguments -> Inference-related arguments (e.g. {@code min_training_epochs})
|
Random request, but maybe let's add a link to the white paper at https://github.com/broadinstitute/gatk/blob/master/docs/CNV/germline-cnv-caller-model.pdf while you're touching up the tool docs? |
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@samuelklee I will add that to the documentation as well. |
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@mwalker174 Thank you for the comments! Back to you |
…if any arguments not applicable in CASE mode were set by the user.
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mwalker174
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Sep 17, 2021
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gCNV in the CASE mode now fills in all hidden DenoisingModelConfig and CopyNumberCallingConfig arguments from the input model configuration.
This addresses issue #6994