filters

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Versions in this module

v4

v4.1.6

Aug 19, 2020

v4.1.5

Jul 24, 2019

Changes in this version

type BaseRecalibrator

+ func (recal *BaseRecalibrator) RecalibrateWithMaxCycle(reads *sam.Sam, maxCycle int) (tables BaseRecalibratorTables)

type BaseRecalibratorTables

+ func (recal BaseRecalibratorTables) ApplyBQSRWithMaxCycle(quantizeLevels int, sqqList []uint8, maxCycle int) sam.Filter

v4.1.4

May 23, 2019

v4.1.3

Apr 29, 2019

v4.1.2

Apr 8, 2019

Changes in this version

+ type DuplicatesCountsHistograms struct

v4.1.1

Jan 28, 2019

v4.1.0

Jan 21, 2019

Changes in this version

type DuplicatesCtrMap

+ func MarkOpticalDuplicatesWithPixelDistance(reads *sam.Sam, pairs *sync.Map, deterministic bool, opticalPixelDistance int) DuplicatesCtrMap

v4.0.1

Nov 8, 2018

v4.0.0

Oct 18, 2018

Changes in this version

+ var X0 = utils.Intern("X0")

+ var X1 = utils.Intern("X1")

+ var XG = utils.Intern("XG")

+ var XM = utils.Intern("XM")

+ var XO = utils.Intern("XO")

+ func AddOrReplaceReadGroup(readGroup utils.StringMap) sam.Filter

+ func AddPGLine(newPG utils.StringMap) sam.Filter

+ func AddREFID(header *sam.Header) sam.AlignmentFilter

+ func CleanSam(header *sam.Header) sam.AlignmentFilter

+ func KeepOptionalFields(tags []string) sam.Filter

+ func MarkDuplicates(alsoOpticals bool) (sam.Filter, *sync.Map, *sync.Map)

+ func PrintDuplicatesMetrics(input, output, metrics string, removeDuplicates bool, ctrs DuplicatesCtrMap) (err error)

+ func PrintDuplicatesMetricsToIntermediateFile(name string, ctrs DuplicatesCtrMap) (err error)

+ func RemoveDuplicateReads(_ *sam.Header) sam.AlignmentFilter

+ func RemoveMappingQualityLessThan(mq int) sam.Filter

+ func RemoveNonExactMappingReads(_ *sam.Header) sam.AlignmentFilter

+ func RemoveNonExactMappingReadsStrict(header *sam.Header) sam.AlignmentFilter

+ func RemoveNonOverlappingReads(bed *bed.Bed) sam.Filter

+ func RemoveOptionalFields(tags []string) sam.Filter

+ func RemoveOptionalReads(header *sam.Header) sam.AlignmentFilter

+ func RemoveUnmappedReads(_ *sam.Header) sam.AlignmentFilter

+ func RemoveUnmappedReadsStrict(_ *sam.Header) sam.AlignmentFilter

+ func RenameChromosomes(header *sam.Header) sam.AlignmentFilter

+ func ReplaceReferenceSequenceDictionary(dict []utils.StringMap) sam.Filter

+ func ReplaceReferenceSequenceDictionaryFromSamFile(samFile string) (f sam.Filter, err error)

+ type BaseRecalibrator struct

+ func NewBaseRecalibrator(knownSites []string, referenceFasta string) (recal *BaseRecalibrator)

+ func (recal *BaseRecalibrator) Recalibrate(reads *sam.Sam) (tables BaseRecalibratorTables)

+ type BaseRecalibratorTables struct

+ Contexts bqsrTable

+ Cycles bqsrTable

+ QualityScores bqsrTable

+ func LoadAndCombineBQSRTables(bqsrPath string) (BaseRecalibratorTables, error)

+ func NewBaseRecalibratorTables() BaseRecalibratorTables

+ func (recal *BaseRecalibratorTables) PrintBQSRTables(name string) error

+ func (recal *BaseRecalibratorTables) PrintBQSRTablesToIntermediateFile(name string) error

+ func (recal BaseRecalibratorTables) ApplyBQSR(quantizeLevels int, sqqList []uint8) sam.Filter

+ func (recal BaseRecalibratorTables) Err() error

+ func (recal BaseRecalibratorTables) FinalizeBQSRTables()

+ type DuplicatesCtr struct

+ ReadPairDuplicates int

+ ReadPairOpticalDuplicates int

+ ReadPairsExamined int

+ SecondaryOrSupplementaryReads int

+ UnmappedReads int

+ UnpairedReadDuplicates int

+ UnpairedReadsExamined int

+ type DuplicatesCtrMap struct

+ Map map[string]*DuplicatesCtr

+ func LoadAndCombineDuplicateMetrics(metricsPath string) DuplicatesCtrMap

+ func MarkOpticalDuplicates(reads *sam.Sam, fragments, pairs *sync.Map, deterministic bool) DuplicatesCtrMap

+ func (ctrMap DuplicatesCtrMap) Err() error

Other modules containing this package

github.com/exascience/elprep

github.com/exascience/elprep/v5

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