Versions in this module Expand all Collapse all v0 v0.1.1 Apr 6, 2021 v0.1.0 Apr 6, 2021 Changes in this version + const IlluminaReadName5Fields + const IlluminaReadName5FieldsTileField + const IlluminaReadName7Fields + const IlluminaReadName7FieldsTileField + const IlluminaReadName8Fields + const IlluminaReadName8FieldsTileField + func ChoosePrimary(entries []DuplicateEntry) int + func GetLibrary(readGroupLibrary map[string]string, record *sam.Record) string + func NewAux(name string, val interface{}) sam.Aux + func NewRecord(name string, ref *sam.Reference, pos int, flags sam.Flags, matePos int, ...) *sam.Record + func NewRecordAux(name string, ref *sam.Reference, pos int, flags sam.Flags, matePos int, ...) *sam.Record + func NewRecordSeq(name string, ref *sam.Reference, pos int, flags sam.Flags, matePos int, ...) *sam.Record + func NewTestOutput(dir string, index int, format string) string + func ReadRecords(t *testing.T, path string) []*sam.Record + func RunTestCases(t *testing.T, header *sam.Header, cases []TestCase) + func SetupAndMark(ctx context.Context, provider bamprovider.Provider, opts *Opts) error + type BagProcessor func([]*IntermediateDuplicateSet) []*IntermediateDuplicateSet + type BagProcessorFactory interface + Create func() BagProcessor + type DuplicateEntry interface + BaseQScore func() int + FileIdx func() uint64 + Name func() string + type IndexedPair struct + Left IndexedSingle + Right IndexedSingle + func (p IndexedPair) BaseQScore() int + func (p IndexedPair) FileIdx() uint64 + func (p IndexedPair) GetR1R2() (r1 *sam.Record, r2 *sam.Record) + func (p IndexedPair) Name() string + type IndexedSingle struct + FileIdx_ uint64 + R *sam.Record + func (s IndexedSingle) BaseQScore() int + func (s IndexedSingle) FileIdx() uint64 + func (s IndexedSingle) Name() string + type IntermediateDuplicateSet struct + Corrected map[string]string + Pairs []DuplicateEntry + Singles []DuplicateEntry + type MarkDuplicates struct + Opts *Opts + Provider bamprovider.Provider + func (m *MarkDuplicates) Mark(shards []bam.Shard) (*MetricsCollection, error) + type Metrics struct + ReadPairDups int + ReadPairOpticalDups int + ReadPairsExamined int + SecondarySupplementary int + UnmappedReads int + UnpairedDups int + UnpairedReads int + func (m *Metrics) Add(other *Metrics) + func (m *Metrics) String() string + type MetricsCollection struct + HighCoverageIntervals []coverageInterval + LibraryMetrics map[string]*Metrics + OpticalDistance [][]int64 + func (mc *MetricsCollection) AddDistance(bagSize, distance int) + func (mc *MetricsCollection) AddHighCovInterval(interval coverageInterval) + func (mc *MetricsCollection) Get(library string) *Metrics + func (mc *MetricsCollection) Merge(other *MetricsCollection) + type OpticalDetector interface + Detect func(readGroupLibrary map[string]string, pairs []DuplicateEntry, bestIndex int) []string + GetRecordProcessor func() bampair.RecordProcessor + RecordProcessorsDone func() (int, int) + type Opts struct + BagProcessorFactories []BagProcessorFactory + BamFile string + ClearExisting bool + CoverageMax int + DiskMateShards int + EmitUnmodifiedFields bool + Format string + HighCoverageIntervalFile string + IndexFile string + IntDI bool + KnownUmis []byte + MetricsFile string + MinBases int + OpticalDetector OpticalDetector + OpticalHistogram string + OpticalHistogramMax int + OutputPath string + Padding int + Parallelism int + QueueLength int + RemoveDups bool + ScavengeUmis int + ScratchDir string + Seed int64 + SeparateSingletons bool + ShardSize int + StrandSpecific bool + TagDups bool + TileSizeFile string + UmiFile string + UseUmis bool + type Orientation uint8 + func GetR1R2Orientation(p *IndexedPair) Orientation + type PhysicalLocation struct + Lane int + Section int + Surface int + Swath int + TileName int + TileNumber int + X int + Y int + func ParseLocation(qname string) PhysicalLocation + type TestCase struct + Opts Opts + TRecords []TestRecord + type TestRecord struct + DupFlag bool + ExpectedAuxs []sam.Aux + R *sam.Record + UnexpectedTags []sam.Tag + type TileOpticalDetector struct + OpticalDistance int + func (t *TileOpticalDetector) Detect(readGroupLibrary map[string]string, duplicates []DuplicateEntry, bestIndex int) []string + func (t *TileOpticalDetector) GetRecordProcessor() bampair.RecordProcessor + func (t *TileOpticalDetector) RecordProcessorsDone() (int, int)