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bamstats

package module

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Versions in this module

v0

v0.3.5

Nov 19, 2019

v0.3.4

Nov 5, 2019

v0.3.3

Sep 4, 2019

v0.3.2

Nov 14, 2018

v0.3.1

Nov 6, 2018

v0.3.0

Nov 2, 2018

Changes in this version

+ var GitCommit = ""

v0.2.0

Jul 22, 2016

Changes in this version

+ const MinorVersionNumber

+ const VersionNumber

+ var PreVersionString = ""

+ func NewOutput(output string) io.Writer

+ func OutputJSON(writer io.Writer, stats interface{})

+ func QueryIndex(index *rtreego.Rtree, begin, end float64) []rtreego.Spatial

+ func Version() string

+ type CoverageStats struct

+ Continuous ElementStats

+ Split ElementStats

+ Total ElementStats

+ func NewCoverageStats() *CoverageStats

+ func (s *CoverageStats) Collect(record *sam.Record, index *RtreeMap)

+ func (s *CoverageStats) Finalize()

+ func (s *CoverageStats) Merge(others chan Stats)

+ func (s *CoverageStats) Update(other Stats)

+ type ElementStats struct

+ Exon int

+ ExonIntron int

+ Intergenic int

+ Intron int

+ Other int

+ Total int

+ func (s *ElementStats) Update(other ElementStats)

+ type Feature struct

+ Element string

+ func (f *Feature) Bounds() *rtreego.Rect

+ func (f *Feature) Chr() string

+ func (f *Feature) End() float64

+ func (f *Feature) Start() float64

+ type GeneralStats struct

+ Pairs MappedPairsStats

+ Reads MappingsStats

+ func NewGeneralStats() *GeneralStats

+ func (s *GeneralStats) Collect(r *sam.Record, index *RtreeMap)

+ func (s *GeneralStats) Finalize()

+ func (s *GeneralStats) Merge(others chan Stats)

+ func (s *GeneralStats) Update(other Stats)

+ type MappedPairsStats struct

+ InsertSizes TagMap

+ func NewMappedPairsStats() *MappedPairsStats

+ func (s *MappedPairsStats) FilterInsertSizes(percent float64)

+ func (s *MappedPairsStats) Update(other MappedPairsStats)

+ func (s *MappedPairsStats) UpdateUnmapped()

+ type MappedReadsStats struct

+ Mapped TagMap

+ Total int

+ Unmapped int

+ func NewMappedReadsStats() *MappedReadsStats

+ func (s *MappedReadsStats) Unique() int

+ func (s *MappedReadsStats) Update(other MappedReadsStats)

+ type MappingsStats struct

+ Mappings MultimapStats

+ func (s *MappingsStats) Update(other MappingsStats)

+ func (s *MappingsStats) UpdateMappingsRatio()

+ type MultimapStats struct

+ Count int

+ Ratio float64

+ type RtreeMap map[string]*rtreego.Rtree

+ func CreateIndex(fname string) *RtreeMap

+ func (t RtreeMap) Get(chr string) *rtreego.Rtree

+ type Stats interface

+ Collect func(record *sam.Record, index *RtreeMap)

+ Finalize func()

+ Merge func(others chan Stats)

+ Update func(other Stats)

+ type StatsMap map[string]Stats

+ func Process(bamFile string, annotation string, cpu int, maxBuf int, reads int, uniq bool) (StatsMap, error)

+ func (sm *StatsMap) Merge(stats chan StatsMap)

+ type TagMap map[int]int

+ func (tm *TagMap) UnmarshalJSON(b []byte) (err error)

+ func (tm TagMap) MarshalJSON() ([]byte, error)

+ func (tm TagMap) Total() (sum int)

+ func (tm TagMap) Update(other TagMap)