| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/pwm/ |
| H A D | pwm_score_maf.py | 176 def MafBlockScorer(pwm, species, maf): argument
199 def MafMotifScorer(species, maf, motifs): argument
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| /dports/biology/vt/vt-0.57721/ |
| H A D | profile_hwe.cpp | 34 float maf; member
172 float maf = 0; in profile_hwe() local
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| H A D | profile_len.cpp | 31 float maf; member
177 float maf = -1; in profile_len() local
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| /dports/biology/py-bx-python/bx-python-0.8.13/scripts/ |
| H A D | maf_tile_2bit.py | 34 import bx.align.maf as maf namespace
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| H A D | maf_tile_2.py | 38 import bx.align.maf as maf namespace
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| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/ |
| H A D | maf_tests.py | 8 import bx.align.maf as maf namespace
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| /dports/mail/popular/popular-1.5.5/pdm/master/ |
| H A D | libpdm_master.c | 135 FILE *maf; in pdm_auth() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | FuncotatorIntegrationTest.java | 1164 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(mafOutputFile.toPath(),… in testVcfMafConcordance() local
1412 final AnnotatedIntervalCollection maf = runPik3caHg19VcfToMaf(new HashSet<>()); in testVCFToMAFPreservesFields() local
1462 final AnnotatedIntervalCollection maf = runPik3caHg19VcfToMaf(excludedFields); in testVcfToMafHonorsExcludedFields() local
1543 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), nu… in testMafCustomCountFields() local
1599 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), nu… in testMafCustomCountFieldsTumorOnly() local
1732 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), nu… in testNoVariantsProduceMaf() local
1737 private void assertCustomFieldsArePresent(final AnnotatedIntervalCollection maf) { in assertCustomFieldsArePresent()
1762 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outputFile.toPath(), nu… in testEnsureDbSnpInMaf() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ |
| H A D | GermlineFilter.java | 61 final double maf = computeMinorAlleleFraction(vc, filteringEngine, alleleCounts); in calculateErrorProbability() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/ |
| H A D | MafOutputRendererUnitTest.java | 1194 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outFile.toPath(), null); in testCreateMafCompliantOutputMapExclusion() local
1213 …final AnnotatedIntervalCollection maf = AnnotatedIntervalCollection.create(outFile.toPath(), null); in testCreateMafCompliantOutputMapSanitized() local
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| /dports/misc/pyobd/pyobd-0.9.3/debian/pyobd/usr/share/pyobd/ |
| H A D | obd_sensors.py | 29 def maf(code): function
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| /dports/misc/pyobd/pyobd-0.9.3/ |
| H A D | obd_sensors.py | 29 def maf(code): function
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/contamination/ |
| H A D | ContaminationModel.java | 194 final double maf = minorAlleleFractions.get(n); in segmentationRecords() local
228 …genotypeLikelihoods(final PileupSummary site, final double c, final double errorRate, double maf) { in genotypeLikelihoods()
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| H A D | MinorAlleleFractionRecord.java | 94 final double maf = dataLine.getDouble(MinorAlleleFractionTableColumn.MAF); in createRecord() local
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| /dports/science/PETSc/petsc-3.14.1/src/ts/tutorials/ |
| H A D | extchem.c | 332 const PetscScalar *maf; in MassFractionToMoleFraction() local
352 PetscScalar *maf; in MoleFractionToMassFraction() local
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| H A D | extchemfield.c | 438 const PetscScalar **maf; in FormMoleFraction() local
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| /dports/math/timbl/timbl-6.6/src/ |
| H A D | Statistics.cxx | 137 double maf = 0.0; in FScore() local
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| /dports/biology/gcta/gcta_1.26.0_src/ |
| H A D | read_imput.cpp | 88 vector<double> freq, maf, qual, rsq; in read_imp_prob_mach() local
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| H A D | option.cpp | 65 double maf = 0.0, max_maf = 0.0, dose_Rsq_cutoff = 0.0; in option() local
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | BaseNode.java | 104 float maf=(refBase=='N' ? MAF_noref : MAF_sub); in consensus() local
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| /dports/biology/bcftools/bcftools-1.14/plugins/ |
| H A D | guess-ploidy.c | 76 int maf; member
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| /dports/biology/bio-mocha/bcftools-1.14/plugins/ |
| H A D | guess-ploidy.c | 76 int maf; member
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| /dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
| H A D | entry_filters.cpp | 799 double maf=numeric_limits<double>::max(); in filter_sites_by_frequency_and_call_rate() local
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| /dports/databases/db18/db-18.1.40/src/dbinc/ |
| H A D | tcl_db.h | 282 #define MAKE_SITE_LIST(e, h, p, s, pr, vw, el, maf, mao) do { \ argument
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| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | param.h | 47 double maf; variable
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