Index

_

_CheckRecord() (trtools.utils.tr_harmonizer.TRRecord method) _Cyvcf2FormatDict (class in trtools.utils.tr_harmonizer) _fit_ridge() (trtools.associaTR.OLS method) _HarmonizeAdVNTRRecord() (in module trtools.utils.tr_harmonizer)

_HarmonizeEHRecord() (in module trtools.utils.tr_harmonizer) _HarmonizeGangSTRRecord() (in module trtools.utils.tr_harmonizer) _HarmonizeHipSTRRecord() (in module trtools.utils.tr_harmonizer) _HarmonizePopSTRRecord() (in module trtools.utils.tr_harmonizer)

A

advntr (trtools.utils.tr_harmonizer.VcfTypes attribute) alt_alleles (trtools.utils.tr_harmonizer.TRRecord attribute) append_alleles() (trtools.annotaTR.PgenWriter method) append_alleles_batch() (trtools.annotaTR.PgenWriter method) append_biallelic() (trtools.annotaTR.PgenWriter method) append_biallelic_batch() (trtools.annotaTR.PgenWriter method)

append_dosages() (trtools.annotaTR.PgenWriter method) append_dosages_batch() (trtools.annotaTR.PgenWriter method) append_partially_phased() (trtools.annotaTR.PgenWriter method) append_partially_phased_batch() (trtools.annotaTR.PgenWriter method) ApplyCallFilters() (in module trtools.dumpSTR) ApplyLocusFilters() (in module trtools.dumpSTR) ArgumentDefaultsHelpFormatter (class in trtools.utils.utils)

B

beagleap (trtools.utils.tr_harmonizer.TRDosageTypes attribute) beagleap_norm (trtools.utils.tr_harmonizer.TRDosageTypes attribute) bestguess (trtools.utils.tr_harmonizer.TRDosageTypes attribute)

bestguess_norm (trtools.utils.tr_harmonizer.TRDosageTypes attribute) buffer (trtools.mergeSTR.TextIO property) BuildCallFilters() (in module trtools.dumpSTR) BuildLocusFilters() (in module trtools.dumpSTR)

C

CalcR2() (in module trtools.compareSTR) CallFilterMaxValue (class in trtools.dumpSTR.filters) CallFilterMinValue (class in trtools.dumpSTR.filters) check_region() (in module trtools.compareSTR) CheckAdVNTRFilters() (in module trtools.dumpSTR) CheckAlleleCompatibility() (in module trtools.annotaTR) CheckEHFilters() (in module trtools.dumpSTR) CheckFilters() (in module trtools.dumpSTR) CheckGangSTRFilters() (in module trtools.dumpSTR) CheckHipSTRFilters() (in module trtools.dumpSTR)

CheckLocusFilters() (in module trtools.dumpSTR) CheckLongTRFilters() (in module trtools.dumpSTR) CheckMin() (in module trtools.utils.mergeutils) CheckPopSTRFilters() (in module trtools.dumpSTR) CheckPos() (in module trtools.utils.mergeutils) chrom (trtools.utils.tr_harmonizer.TRRecord attribute) close() (trtools.annotaTR.PgenWriter method) ComputePvalue() (in module trtools.prancSTR) ConfineRange() (in module trtools.prancSTR) create_region_filter() (in module trtools.dumpSTR.filters) CreateAlleleFasta() (in module trtools.simTR)

D

DebugPrintRecordLocations() (in module trtools.utils.mergeutils) default_callback() (in module trtools.utils.mergeutils)

description() (trtools.dumpSTR.filters.FilterBase method) DoneReading() (in module trtools.utils.mergeutils)

E

eh (trtools.utils.tr_harmonizer.VcfTypes attribute) encoding (trtools.mergeSTR.TextIO property) end_pos (trtools.utils.tr_harmonizer.TRRecord attribute)

errors (trtools.mergeSTR.TextIO property) ExtractAB() (in module trtools.prancSTR) ExtractReadVector() (in module trtools.prancSTR)

F

FabricateAllele() (in module trtools.utils.utils) field (trtools.dumpSTR.filters.CallFilterMaxValue attribute) (trtools.dumpSTR.filters.CallFilterMinValue attribute) Filter_LocusHrun (class in trtools.dumpSTR.filters) Filter_MaxLocusHet (class in trtools.dumpSTR.filters) Filter_MinLocusCallrate (class in trtools.dumpSTR.filters) Filter_MinLocusHet (class in trtools.dumpSTR.filters) Filter_MinLocusHWEP (class in trtools.dumpSTR.filters) filter_name() (trtools.dumpSTR.filters.Filter_LocusHrun method) (trtools.dumpSTR.filters.Filter_MaxLocusHet method) (trtools.dumpSTR.filters.Filter_MinLocusCallrate method) (trtools.dumpSTR.filters.Filter_MinLocusHet method) (trtools.dumpSTR.filters.Filter_MinLocusHWEP method) (trtools.dumpSTR.filters.FilterBase method)

FilterBase (class in trtools.dumpSTR.filters) fit_regularized() (trtools.associaTR.OLS method) format (trtools.utils.tr_harmonizer.TRRecord attribute) format_nan_precision() (in module trtools.statSTR) full_alleles_end_pos (trtools.utils.tr_harmonizer.TRRecord attribute) full_alleles_pos (trtools.utils.tr_harmonizer.TRRecord attribute)

G

gangstr (trtools.utils.tr_harmonizer.VcfTypes attribute) GangSTRCallBadCI (class in trtools.dumpSTR.filters) GangSTRCallExpansionProbHet (class in trtools.dumpSTR.filters) GangSTRCallExpansionProbHom (class in trtools.dumpSTR.filters) GangSTRCallExpansionProbTotal (class in trtools.dumpSTR.filters) GangSTRCallSpanBoundOnly (class in trtools.dumpSTR.filters) GangSTRCallSpanOnly (class in trtools.dumpSTR.filters) get() (trtools.utils.tr_harmonizer._Cyvcf2FormatDict method) GetAFreq() (in module trtools.statSTR) GetAllCallFilters() (in module trtools.dumpSTR) GetAlleleCounts() (trtools.utils.tr_harmonizer.TRRecord method) GetAlleleFreqs() (trtools.utils.tr_harmonizer.TRRecord method) GetAlleleSeq() (in module trtools.simTR) GetAltAlleles() (in module trtools.mergeSTR) GetAltsByKey() (in module trtools.mergeSTR) GetAndCheckVCFType() (in module trtools.utils.mergeutils) getargs() (in module trtools.annotaTR) (in module trtools.compareSTR) (in module trtools.dumpSTR) (in module trtools.mergeSTR) (in module trtools.prancSTR) (in module trtools.qcSTR) (in module trtools.simTR) (in module trtools.statSTR) GetBubbleLegend() (in module trtools.compareSTR) GetCalledSamples() (trtools.utils.tr_harmonizer.TRRecord method) GetCallRate() (trtools.utils.tr_harmonizer.TRRecord method) GetCanonicalMotif() (in module trtools.utils.utils) GetCanonicalOneStrand() (in module trtools.utils.utils) GetChromOrder() (in module trtools.utils.mergeutils) GetChromOrderEqual() (in module trtools.utils.mergeutils) GetContigs() (in module trtools.utils.utils) GetDosages() (trtools.utils.tr_harmonizer.TRRecord method) GetEntropy() (in module trtools.statSTR) (in module trtools.utils.utils) GetFormatFields() (in module trtools.compareSTR) GetFullStringGenotypes() (trtools.utils.tr_harmonizer.TRRecord method)

GetGenotypeCounts() (trtools.utils.tr_harmonizer.TRRecord method) GetGenotypeIndicies() (trtools.utils.tr_harmonizer.TRRecord method) GetHardyWeinbergBinomialTest() (in module trtools.utils.utils) GetHeader() (in module trtools.statSTR) GetHet() (in module trtools.statSTR) GetHeterozygosity() (in module trtools.utils.utils) GetHomopolymerRun() (in module trtools.utils.utils) GetHWEP() (in module trtools.statSTR) GetID() (in module trtools.mergeSTR) GetIncrementAndComparability() (in module trtools.utils.mergeutils) GetInfoItem() (in module trtools.mergeSTR) GetLengthGenotypes() (trtools.utils.tr_harmonizer.TRRecord method) GetLocusKey() (in module trtools.annotaTR) GetMaxAllele() (trtools.utils.tr_harmonizer.TRRecord method) GetMaxDelta() (in module trtools.simTR) GetMaxPloidy() (trtools.utils.tr_harmonizer.TRRecord method) GetMean() (in module trtools.statSTR) (in module trtools.utils.utils) GetMinRecords() (in module trtools.utils.mergeutils) GetMode() (in module trtools.statSTR) (in module trtools.utils.utils) GetNAlleles() (in module trtools.statSTR) GetNextRecords() (in module trtools.utils.mergeutils) GetNumSamples() (in module trtools.statSTR) (trtools.utils.tr_harmonizer.TRRecord method) GetPGenPvarWriter() (in module trtools.annotaTR) GetPos() (in module trtools.utils.mergeutils) GetQualityScores() (trtools.utils.tr_harmonizer.TRRecord method) GetReason() (trtools.dumpSTR.filters.Reason method) GetRefAllele() (in module trtools.mergeSTR) GetSamplePloidies() (trtools.utils.tr_harmonizer.TRRecord method) GetSamples() (in module trtools.utils.mergeutils) GetSharedSamples() (in module trtools.utils.mergeutils) GetStringGenotypes() (trtools.utils.tr_harmonizer.TRRecord method) GetTempDir() (in module trtools.simTR) GetThresh() (in module trtools.statSTR) GetVariance() (in module trtools.statSTR) (in module trtools.utils.utils)

H

handle_overlaps() (in module trtools.compareSTR) HarmonizeIfNotNone() (in module trtools.mergeSTR) HarmonizeRecord() (in module trtools.utils.tr_harmonizer) HasFabricatedAltAlleles() (trtools.utils.tr_harmonizer.TRRecord method) HasFabricatedRefAllele() (trtools.utils.tr_harmonizer.TRRecord method) HasFullStringGenotypes() (trtools.utils.tr_harmonizer.TRRecord method) HasLengthAltGenotypes() (in module trtools.utils.tr_harmonizer) (trtools.utils.tr_harmonizer.TRRecordHarmonizer method) HasLengthRefGenotype() (in module trtools.utils.tr_harmonizer) (trtools.utils.tr_harmonizer.TRRecordHarmonizer method)

HasQualityScore() (trtools.utils.tr_harmonizer.TRRecordHarmonizer method) HasQualityScores() (trtools.utils.tr_harmonizer.TRRecord method) hessian() (trtools.associaTR.OLS method) hessian_factor() (trtools.associaTR.OLS method) hipstr (trtools.utils.tr_harmonizer.VcfTypes attribute) HipSTRCallFlankIndels (class in trtools.dumpSTR.filters) HipSTRCallMinSuppReads (class in trtools.dumpSTR.filters) HipSTRCallStutter (class in trtools.dumpSTR.filters)

I

InferRepeatSequence() (in module trtools.utils.utils) InferVCFType() (in module trtools.utils.tr_harmonizer) info (trtools.utils.tr_harmonizer.TRRecord attribute)

InitReaders() (in module trtools.utils.mergeutils) IsBeagleVCF() (in module trtools.utils.tr_harmonizer) (trtools.utils.tr_harmonizer.TRRecordHarmonizer method)

J

Just_C_Pred() (in module trtools.prancSTR)

Just_F_Pred() (in module trtools.prancSTR)

K

keys() (trtools.utils.tr_harmonizer._Cyvcf2FormatDict method)

L

Likelihood_mosaic() (in module trtools.prancSTR) line_buffering (trtools.mergeSTR.TextIO property) LoadMetadataFromRefPanel() (in module trtools.annotaTR) LoadReaders() (in module trtools.utils.mergeutils) (in module trtools.utils.utils)

LoadSingleReader() (in module trtools.utils.utils) locid (trtools.annotaTR.RefMatchTypes attribute) loglike() (trtools.associaTR.OLS method) LongestPerfectRepeat() (in module trtools.utils.utils) longtr (trtools.utils.tr_harmonizer.VcfTypes attribute)

M

main() (in module trtools.annotaTR) (in module trtools.associaTR) (in module trtools.compareSTR) (in module trtools.dumpSTR) (in module trtools.mergeSTR) (in module trtools.prancSTR) (in module trtools.qcSTR) (in module trtools.simTR) (in module trtools.statSTR) MakeWriter() (in module trtools.dumpSTR) MaximizeMosaicLikelihoodBoth() (in module trtools.prancSTR) MayHaveImpureRepeats() (in module trtools.utils.tr_harmonizer) (trtools.utils.tr_harmonizer.TRRecordHarmonizer method) MergeRecords() (in module trtools.mergeSTR) module trtools.annotaTR trtools.associaTR trtools.compareSTR trtools.dumpSTR trtools.dumpSTR.filters trtools.mergeSTR trtools.prancSTR trtools.qcSTR trtools.simTR trtools.statSTR trtools.utils.common trtools.utils.mergeutils trtools.utils.tr_harmonizer trtools.utils.utils

motif (trtools.utils.tr_harmonizer.TRRecord attribute) MSG() (in module trtools.utils.common)

N

name (trtools.dumpSTR.filters.CallFilterMaxValue attribute) (trtools.dumpSTR.filters.CallFilterMinValue attribute) (trtools.dumpSTR.filters.Filter_LocusHrun attribute) (trtools.dumpSTR.filters.Filter_MaxLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusCallrate attribute) (trtools.dumpSTR.filters.Filter_MinLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHWEP attribute) (trtools.dumpSTR.filters.FilterBase attribute) (trtools.dumpSTR.filters.GangSTRCallBadCI attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbHet attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbHom attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbTotal attribute) (trtools.dumpSTR.filters.GangSTRCallSpanBoundOnly attribute) (trtools.dumpSTR.filters.GangSTRCallSpanOnly attribute) (trtools.dumpSTR.filters.HipSTRCallFlankIndels attribute) (trtools.dumpSTR.filters.HipSTRCallMinSuppReads attribute) (trtools.dumpSTR.filters.HipSTRCallStutter attribute) (trtools.dumpSTR.filters.PopSTRCallRequireSupport attribute) (trtools.dumpSTR.filters.Reason attribute)

newlines (trtools.mergeSTR.TextIO property) NewOverallFormatBin() (in module trtools.compareSTR) NewOverallPeriod() (in module trtools.compareSTR)

O

OLS (class in trtools.associaTR) OutputBubblePlot() (in module trtools.compareSTR) OutputChromCallrate() (in module trtools.qcSTR) OutputDiffRefBias() (in module trtools.qcSTR) OutputDiffRefHistogram() (in module trtools.qcSTR) OutputFileTypes (class in trtools.annotaTR) OutputLocusMetrics() (in module trtools.compareSTR)

OutputOverallMetrics() (in module trtools.compareSTR) OutputQualityLocusStrat() (in module trtools.qcSTR) OutputQualityPerCall() (in module trtools.qcSTR) OutputQualityPerLocus() (in module trtools.qcSTR) OutputQualityPerSample() (in module trtools.qcSTR) OutputQualitySampleStrat() (in module trtools.qcSTR) OutputSampleCallrate() (in module trtools.qcSTR) OutputSampleMetrics() (in module trtools.compareSTR)

P

ParseCoordinates() (in module trtools.simTR) perform_gwas() (in module trtools.associaTR) perform_gwas_helper() (in module trtools.associaTR) pgen (trtools.annotaTR.OutputFileTypes attribute)

PgenWriter (class in trtools.annotaTR) PlotAlleleFreqs() (in module trtools.statSTR) popstr (trtools.utils.tr_harmonizer.VcfTypes attribute) PopSTRCallRequireSupport (class in trtools.dumpSTR.filters) pos (trtools.utils.tr_harmonizer.TRRecord attribute)

R

rawalleles (trtools.annotaTR.RefMatchTypes attribute) Reason (class in trtools.dumpSTR.filters) record_id (trtools.utils.tr_harmonizer.TRRecord attribute) ref_allele (trtools.utils.tr_harmonizer.TRRecord attribute) RefMatchTypes (class in trtools.annotaTR) ReverseComplement() (in module trtools.utils.utils) run() (in module trtools.annotaTR) (in module trtools.associaTR) (in module trtools.compareSTR) (in module trtools.dumpSTR) (in module trtools.mergeSTR) (in module trtools.prancSTR) (in module trtools.qcSTR) (in module trtools.simTR) (in module trtools.statSTR)

S

score() (trtools.associaTR.OLS method) SF() (in module trtools.prancSTR)

SimulateReads() (in module trtools.simTR) StutterProb() (in module trtools.prancSTR)

T

TextIO (class in trtools.mergeSTR) threshold (trtools.dumpSTR.filters.CallFilterMaxValue attribute) (trtools.dumpSTR.filters.CallFilterMinValue attribute) (trtools.dumpSTR.filters.Filter_MaxLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusCallrate attribute) (trtools.dumpSTR.filters.Filter_MinLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHWEP attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbHet attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbHom attribute) (trtools.dumpSTR.filters.GangSTRCallExpansionProbTotal attribute) (trtools.dumpSTR.filters.HipSTRCallFlankIndels attribute) (trtools.dumpSTR.filters.HipSTRCallMinSuppReads attribute) (trtools.dumpSTR.filters.HipSTRCallStutter attribute) (trtools.dumpSTR.filters.PopSTRCallRequireSupport attribute) TRDosageTypes (class in trtools.utils.tr_harmonizer) TrimAlleles() (in module trtools.annotaTR) trimmedalleles (trtools.annotaTR.RefMatchTypes attribute) TRRecord (class in trtools.utils.tr_harmonizer) TRRecordHarmonizer (class in trtools.utils.tr_harmonizer) trtools.annotaTR module trtools.associaTR module

trtools.compareSTR module trtools.dumpSTR module trtools.dumpSTR.filters module trtools.mergeSTR module trtools.prancSTR module trtools.qcSTR module trtools.simTR module trtools.statSTR module trtools.utils.common module trtools.utils.mergeutils module trtools.utils.tr_harmonizer module trtools.utils.utils module

U

UniqueLengthGenotypeMapping() (trtools.utils.tr_harmonizer.TRRecord method) UniqueLengthGenotypes() (trtools.utils.tr_harmonizer.TRRecord method) UniqueStringGenotypeMapping() (trtools.utils.tr_harmonizer.TRRecord method) UniqueStringGenotypes() (trtools.utils.tr_harmonizer.TRRecord method)

UpdateComparisonResults() (in module trtools.compareSTR) UpdateVCFHeader() (in module trtools.annotaTR) uselength (trtools.dumpSTR.filters.Filter_MaxLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHWEP attribute)

V

ValidateAlleleFreqs() (in module trtools.utils.utils) vcf (trtools.annotaTR.OutputFileTypes attribute) vcffile (trtools.utils.tr_harmonizer.TRRecordHarmonizer attribute) vcfrecord (trtools.utils.tr_harmonizer.TRRecord attribute)

vcftype (trtools.dumpSTR.filters.Filter_MaxLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHet attribute) (trtools.dumpSTR.filters.Filter_MinLocusHWEP attribute) (trtools.utils.tr_harmonizer.TRRecordHarmonizer attribute) VcfTypes (class in trtools.utils.tr_harmonizer)

W

WARNING() (in module trtools.utils.common) weights (trtools.associaTR.OLS attribute) whiten() (trtools.associaTR.OLS method) WriteCombinedFastqs() (in module trtools.simTR)

WriteLocLog() (in module trtools.dumpSTR) WriteMergedHeader() (in module trtools.mergeSTR) WritePvarVariant() (in module trtools.annotaTR) WriteSampleData() (in module trtools.mergeSTR) WriteSampLog() (in module trtools.dumpSTR)