Index

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__init__() (bdgenomics.mango.alignments.AlignmentSummary method) (bdgenomics.mango.alignments.FragmentDistribution method) (bdgenomics.mango.alignments.IndelDistribution method) (bdgenomics.mango.alignments.MapQDistribution method) (bdgenomics.mango.coverage.CoverageDistribution method) (bdgenomics.mango.features.FeatureSummary method) (bdgenomics.mango.genotypes.GenotypeCallRatesDistribution method) (bdgenomics.mango.genotypes.GenotypeSummary method) (bdgenomics.mango.genotypes.HetHomRatioDistribution method) (bdgenomics.mango.genotypes.VariantsPerSampleDistribution method) (bdgenomics.mango.pileup.pileupViewer.PileupViewer method) (bdgenomics.mango.pileup.sources.BamDataSource method) (bdgenomics.mango.pileup.sources.BigBedDataSource method) (bdgenomics.mango.pileup.sources.GA4GHAlignmentJson method) (bdgenomics.mango.pileup.sources.GA4GHAlignmentSource method) (bdgenomics.mango.pileup.sources.GA4GHFeatureJson method) (bdgenomics.mango.pileup.sources.GA4GHFeatureSource method) (bdgenomics.mango.pileup.sources.GA4GHVariantJson method) (bdgenomics.mango.pileup.sources.GA4GHVariantSource method) (bdgenomics.mango.pileup.sources.TwoBitDataSource method) (bdgenomics.mango.pileup.sources.VcfDataSource method) (bdgenomics.mango.pileup.track.Track method) (bdgenomics.mango.variants.VariantSummary method)

A

AlignmentSummary (class in bdgenomics.mango.alignments)

B

BamDataSource (class in bdgenomics.mango.pileup.sources) bdgenomics.mango (module) bdgenomics.mango.alignments (module) bdgenomics.mango.coverage (module) bdgenomics.mango.features (module) bdgenomics.mango.genotypes (module)

bdgenomics.mango.pileup (module) bdgenomics.mango.pileup.pileupViewer (module) bdgenomics.mango.pileup.sources (module) bdgenomics.mango.pileup.track (module) bdgenomics.mango.variants (module) BigBedDataSource (class in bdgenomics.mango.pileup.sources)

C

CoverageDistribution (class in bdgenomics.mango.coverage)

F

FeatureSummary (class in bdgenomics.mango.features)

FragmentDistribution (class in bdgenomics.mango.alignments)

G

GA4GHAlignmentJson (class in bdgenomics.mango.pileup.sources) GA4GHAlignmentSource (class in bdgenomics.mango.pileup.sources) GA4GHFeatureJson (class in bdgenomics.mango.pileup.sources) GA4GHFeatureSource (class in bdgenomics.mango.pileup.sources)

GA4GHVariantJson (class in bdgenomics.mango.pileup.sources) GA4GHVariantSource (class in bdgenomics.mango.pileup.sources) GenotypeCallRatesDistribution (class in bdgenomics.mango.genotypes) GenotypeSummary (class in bdgenomics.mango.genotypes)

H

HetHomRatioDistribution (class in bdgenomics.mango.genotypes)

I

IndelDistribution (class in bdgenomics.mango.alignments)

M

MapQDistribution (class in bdgenomics.mango.alignments)

P

PileupViewer (class in bdgenomics.mango.pileup.pileupViewer)

T

Track (class in bdgenomics.mango.pileup.track) track_from_json() (in module bdgenomics.mango.pileup.track) track_to_json() (in module bdgenomics.mango.pileup.track)

tracks_from_json() (in module bdgenomics.mango.pileup.track) tracks_to_json() (in module bdgenomics.mango.pileup.track) TwoBitDataSource (class in bdgenomics.mango.pileup.sources)

V

VariantsPerSampleDistribution (class in bdgenomics.mango.genotypes)

VariantSummary (class in bdgenomics.mango.variants) VcfDataSource (class in bdgenomics.mango.pileup.sources)