PairedEnd
IlluminaAdapters
PairedUmiAssigner
GroupReadsByUmi
PerBase
ConsensusTags
PerRead
ConsensusTags
Personal
ClpGroups
PhaseBlock
vcf
PhaseBlockLengthMetric
vcf
PhaseConcordanceFormatDescription
AssessPhasing
PhaseConcordanceFormatHeaderLine
AssessPhasing
PhaseConcordanceFormatTag
AssessPhasing
PhaseSetFormatDescription
HeaderLines
PhaseSetFormatHeaderLine
HeaderLines
PhaseSetFormatTag
HeaderLines
PhredScore
NumericTypes
PickIlluminaIndices
util
PickLongIndices
util
Pileup
bam
PileupBuilder
bam
PileupEntry
bam
PlotExtension
ErrorRateByReadPositionMetric
PlotsExt
CollectDuplexSeqMetrics
Plus
SamBuilder
PoolingFractionMetric
bam
Precision
PhredScore
ProgressLogger
util
Proportion
Metric
PrunedFormatDescription
HapCut2VcfHeaderLines
PrunedFormatHeaderLine
HapCut2VcfHeaderLines
PrunedFormatTag
HapCut2VcfHeaderLines
pDuplexIdeal
CollectDuplexSeqMetrics
pValue
FishersExactTest
packageList
FgBioMain
packages
BuildToolDocs
paddedString
Alignment
pairOrientation
SamRecord
pair_orientation
InsertSizeMetric
paired
SamRecord
pairedReadsOnly
FilterSomaticVcf
paired_=
SamRecord
parseSampleData
SampleSheet
passing_filter_transcripts
ErccSummaryMetrics
pct_matches
SampleBarcodeMetric
pearsons_correlation
ErccSummaryMetrics
perfect_matches
UmiCorrectionMetrics SampleBarcodeMetric
personal
fulcrumgenomics
pf
SamRecord
pf_=
SamRecord
pf_normalized_matches
SampleBarcodeMetric
pf_one_mismatch_matches
SampleBarcodeMetric
pf_pct_matches
SampleBarcodeMetric
pf_perfect_matches
SampleBarcodeMetric
pf_ratio_this_barcode_to_best_barcode_pct
SampleBarcodeMetric
pf_reads
SampleBarcodeMetric
phaseSet
BlockInfo
phaseSetOption
BlockInfo
phased
BlockInfo
pile
Pileup
platform
FastqToBam
platformModel
AutoGenerateReadGroupsByName DemuxFastqs FastqToBam
platformUnit
DemuxFastqs FastqToBam
plotDescription
FgBioDef
pos
Locus Pileup CoordinateKey ConsensusVariantReviewInfo
pos1
TemplateCoordinateKey
pos2
TemplateCoordinateKey
position
ErrorRateByReadPositionMetric
positionFromOtherEndOfTemplate
Bams
positionInRead
BaseEntry
positionInReadInReadOrder
BaseEntry
positiveStrand
SamRecord
positiveStrand_=
SamRecord
precision
MakeMixtureVcf
predict
DnaFoldPredictor
predictedInsertSize
AutoGenerateReadGroupsByName DemuxFastqs FastqToBam
prefix
EstimateRnaSeqInsertSize
primers
TrimPrimers
printEndingLines
FgBioMain
printStartupLines
FgBioMain
probabilityOfErrorTwoTrials
LogProbability
producePerBaseTags
VanillaUmiConsensusCallerOptions
programGroup
AutoGenerateReadGroupsByName
progress
ConsensusCallingIterator ExtractUmisFromBam
project
Sample
properlyPaired
SamRecord
properlyPaired_=
SamRecord