Searched refs:pedFile (Results 1 – 6 of 6) sorted by relevance
54 pedFile = sys.argv[1] variable75 for line in open(pedFile):
28 for (final GATKPath pedFile : pedigreeFiles) { in addSamplesFromPedigreeFiles()29 Collection<Sample> samples = addSamplesFromPedigreeArgument(pedFile); in addSamplesFromPedigreeFiles()
284 String pedFile = "MendelianViolationEval.ped"; in testVEMendelianViolationEvaluator() local287 …" -R " + b37Reference + " --eval " + vcfFile + " -ped "+ getTestFilePath(pedFile) +" -no-ev -EV Me… in testVEMendelianViolationEvaluator()297 String pedFile = "PhaseByTransmission.IntegrationTest.goodFamilies.ped"; in testMVEvalFamilyStrat() local299 …w IntegrationTestSpec(" -R " + b37Reference + " -ped " + getTestFilePath(pedFile) + " -eval " + ge… in testMVEvalFamilyStrat()
3 NuclearPedigree::NuclearPedigree(const char* pedFile) in NuclearPedigree() argument5 htsFile *hts = hts_open(pedFile, "r"); in NuclearPedigree()
105 NuclearPedigree(const char* pedFile);
714 final String pedFile = getToolTestDataDir() + "CEUtrio.ped"; in testMendelianViolationSelection() local717 …baseTestString(" -ped " + pedFile + " --mendelian-violation --mendelian-violation-qual-threshold 0… in testMendelianViolationSelection()727 final String pedFile = getToolTestDataDir() + "CEUtrio.ped"; in testInvertMendelianViolationSelection() local730 …on --mendelian-violation-qual-threshold 0 --invert-mendelian-violation -ped " + pedFile, testFile), in testInvertMendelianViolationSelection()