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Added numerical-stability tests and updated test data for all ModelSegments single-sample and multiple-sample modes. #7652

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merged 7 commits into from
Jun 25, 2022
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Added an explicit check that minimum-total-allele-count-case is set t…
…o zero when running ModelSegments in matched-normal mode.
samuelklee committed Jun 24, 2022

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commit 5fe2f221647c7e86771f14274d488dc39a7a5eef
Original file line number Diff line number Diff line change
@@ -746,6 +746,12 @@ private void setModesAndValidateArguments() {
"Must provide at least one denoised-copy-ratios file or allelic-counts file.");
Utils.validateArg(!(inputAllelicCountsFiles.isEmpty() && inputNormalAllelicCountsFile != null),
"Must provide an allelic-counts file for the case sample to run in matched-normal mode.");
Utils.validateArg(!(inputNormalAllelicCountsFile != null && genotypingArguments.minTotalAlleleCountCase > 0),
"The minimum total count for filtering allelic counts in case samples must be set to zero in matched-normal mode. " +
"If the effect of statistical noise due to low depth in case samples on segmentation is a concern, " +
"consider using only denoised copy ratios or externally preprocessing allelic-count files " +
"to remove sites that are poorly covered across all samples.");


runMode = (inputDenoisedCopyRatiosFiles.size() > 1 || inputAllelicCountsFiles.size() > 1)
? RunMode.MULTIPLE_SAMPLE