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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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P
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R
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S
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T
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U
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W
_
_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)
ApplyCallFilters() (in module trtools.dumpSTR)
ApplyLocusFilters() (in module trtools.dumpSTR)
ArgumentDefaultsHelpFormatter (class in trtools.utils.utils)
B
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)
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)
CheckMin() (in module trtools.utils.mergeutils)
CheckPopSTRFilters() (in module trtools.dumpSTR)
CheckPos() (in module trtools.utils.mergeutils)
chrom (trtools.utils.tr_harmonizer.TRRecord attribute)
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.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)
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)
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)
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)
LoadReaders() (in module trtools.utils.mergeutils)
(in module trtools.utils.utils)
LoadSingleReader() (in module trtools.utils.utils)
loglike() (trtools.associaTR.OLS method)
LongestPerfectRepeat() (in module trtools.utils.utils)
M
main() (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.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)
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)
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
Reason (class in trtools.dumpSTR.filters)
record_id (trtools.utils.tr_harmonizer.TRRecord attribute)
ref_allele (trtools.utils.tr_harmonizer.TRRecord attribute)
ReverseComplement() (in module trtools.utils.utils)
run() (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)
TRRecord (class in trtools.utils.tr_harmonizer)
TRRecordHarmonizer (class in trtools.utils.tr_harmonizer)
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)
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)
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)
WriteSampleData() (in module trtools.mergeSTR)
WriteSampLog() (in module trtools.dumpSTR)
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