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Versions in this module

v5

v5.1.3

Apr 27, 2022

v5.1.2

Feb 9, 2022

v5.1.1

Oct 4, 2021

v5.1.0

Oct 1, 2021

v5.0.2

May 19, 2021

v5.0.1

Feb 3, 2021

v5.0.0

Dec 8, 2020

Changes in this version

+ const FixedHighQDMessage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

+ 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 ClearDuplicateFlag(_ *sam.Header) sam.AlignmentFilter

+ func CombineVcfOutputs(vcfPath, vcfOutput string)

+ func FilterReadsBySampleName(sampleName *string) sam.Filter

+ func HaplotypeCallAln(hdr *sam.Header) sam.AlignmentFilter

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

+ func LoadAndCombineDuplicateMetrics(metricsPath string) map[string]*DuplicatesCtr

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

+ func MarkOpticalDuplicates(reads *sam.Sam, pairs *sync.Map, opticalPixelDistance int) map[string]*DuplicatesCtr

+ func PrintDuplicatesMetrics(metrics, commandLine string, ctrs map[string]*DuplicatesCtr)

+ func PrintDuplicatesMetricsToIntermediateFile(name string, ctrs map[string]*DuplicatesCtr)

+ 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) sam.Filter

+ type BaseRecalibrator struct

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

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

+ type BaseRecalibratorTables struct

+ Contexts bqsrTable

+ Cycles bqsrTable

+ QualityScores bqsrTable

+ func LoadAndCombineBQSRTables(bqsrPath string) *BaseRecalibratorTables

+ func NewBaseRecalibratorTables() BaseRecalibratorTables

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

+ func (recal *BaseRecalibratorTables) FinalizeBQSRTables()

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

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

+ type DuplicatesCtr struct

+ ReadPairDuplicates int

+ ReadPairOpticalDuplicates int

+ ReadPairsExamined int

+ SecondaryOrSupplementaryReads int

+ UnmappedReads int

+ UnpairedReadDuplicates int

+ UnpairedReadsExamined int

+ type HaplotypeCaller struct

+ func NewHaplotypeCaller(reference *fasta.MappedFasta, referenceConfidence string, ...) *HaplotypeCaller

+ func (hc *HaplotypeCaller) CallVariants(input *sam.Sam, sampleName, vcfOutput string, bedRegions bed.Bed)

+ func (hc *HaplotypeCaller) Close()

Other modules containing this package

github.com/exascience/elprep

github.com/exascience/elprep/v4