Closed sooheelee closed 7 years ago
Copying comments from closed branch:
No example command since there is no WDL for me to reference. FYI @LeeTL1220 @achevali.
There is no WDL because this tool is experimental. In general, you should be able to put together example command lines from the integration tests for a tool.
tag doc and mention that the tumorHets file is from GetHetCoverage.
We should probably say that the tumorHets file is from GetBayesianHetCoverage, preferably, but can also come from GetHetCoverage.
@samuelklee I looked into the IntegrationTest and did not see an obvious command structure or references to files in our resource suite except for the file that I give an example of.
The following block from PerformAlleleFractionSegmentationIntegrationTest can be translated into a command line (with a little bit of work):
final String[] arguments = {
"-" + ExomeStandardArgumentDefinitions.TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME, snpFile.getAbsolutePath(),
"-" + PerformAlleleFractionSegmentation.INITIAL_NUM_STATES_SHORT_NAME, Integer.toString(initialNumStates),
"-" + ExomeStandardArgumentDefinitions.SEGMENT_FILE_SHORT_NAME, outputSegmentFile.getAbsolutePath()
};
This is missing the documentation tag.