Exposed maximum copy ratio and point size for CNV plotting tools. #6482
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@bhanugandham Comms may be interested in increasing the |
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@fleharty mind reviewing? This is pretty boilerplate, but it's possible that I've erred in my copy-paste-editing somewhere... |
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| @Test(expectedExceptions = IllegalArgumentException.class) | ||
| public void testMinimumContigLength() { | ||
| final File outputDir = createTempDir("testDir"); | ||
| final String[] arguments = { | ||
| "--" + CopyNumberStandardArgument.STANDARDIZED_COPY_RATIOS_FILE_LONG_NAME, STANDARDIZED_COPY_RATIOS_FILE.getAbsolutePath(), | ||
| "--" + CopyNumberStandardArgument.DENOISED_COPY_RATIOS_FILE_LONG_NAME, DENOISED_COPY_RATIOS_FILE.getAbsolutePath(), | ||
| "-" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, SEQUENCE_DICTIONARY_WITH_NO_CONTIGS_ABOVE_MINIMUM_LENGTH_FILE.getAbsolutePath(), | ||
| "--" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, SEQUENCE_DICTIONARY_WITH_NO_CONTIGS_ABOVE_MINIMUM_LENGTH_FILE.getAbsolutePath(), |
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Why does this StandardArgumentDefinitions us "--" but the next one for OUTPUT_SHORT_NAME uses only "-".
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Short names use -, long names use --. It just happens that the short and long names for sequence dictionary are the same for the CNV plotting tools, but this line of code would've broken if that was ever changed.
| @@ -81,7 +99,7 @@ public void testNonExistentStandardizedFile() { | |||
| final String[] arguments = { | |||
| "--" + CopyNumberStandardArgument.STANDARDIZED_COPY_RATIOS_FILE_LONG_NAME, "Non-existent-file", | |||
| "--" + CopyNumberStandardArgument.DENOISED_COPY_RATIOS_FILE_LONG_NAME, DENOISED_COPY_RATIOS_FILE.getAbsolutePath(), | |||
| "-" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, SEQUENCE_DICTIONARY_FILE.getAbsolutePath(), | |||
| "--" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, SEQUENCE_DICTIONARY_FILE.getAbsolutePath(), | |||
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Do StandardArgumentDefinitions use "-" or "--"?
Closes #6391.
Closes #5748.
Note that the *.denoisedLimit4.png output has been removed from the PlotDenoisedCopyRatios tool and the corresponding WDL task. The default behavior has changed slightly, in that the remaining *.denoised.png output is now delimited to maximum copy ratio = 4.0 (instead of covering the entire range in the data). @fleharty @droazen we may want to mention this in the release notes.