CNV performallelefractionsegmentation: tag doc

[sooheelee]

• No example command since there is no WDL for me to reference. FYI @LeeTL1220 @achevali.
• tag doc and mention that the tumorHets file is from GetHetCoverage.

[samuelklee]

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.

[sooheelee]

@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.

[samuelklee]

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()
    };

[sooheelee]

This is missing the documentation tag.