Mango Pyspark API Documentation¶
bdgenomics.mango Package¶
bdgenomics.mango provides hooks for visualizing genomic data on top of Apache Spark. Available visualizations are supported for alignments, coverage, variants and features.
Alignments¶
AlignmentSummary(spark, ac, alignmentDataset) |
AlignmentSummary class. |
FragmentDistribution(ss, alignmentDataset[, …]) |
FragmentDistribution class. |
MapQDistribution(ss, alignmentDataset[, sample]) |
MapQDistribution class. |
IndelDistribution(ss, alignmentDataset[, …]) |
IndelDistribution class. |
Coverage¶
CoverageDistribution(ss, coverageDataset[, …]) |
CoverageDistribution class. |
Features¶
FeatureSummary(ac, dataset) |
FeatureSummary class. |
Variants¶
VariantSummary(ac, dataset) |
VariantSummary class. |
Genotypes¶
GenotypeSummary(spark, ac, genotypeDataset) |
GenotypeSummary class. |
VariantsPerSampleDistribution(ss, …[, sample]) |
VariantsPerSampleDistribution class. |
HetHomRatioDistribution(ss, genotypeDataset) |
HetHomRatioDistribution class. |
GenotypeCallRatesDistribution(ss, …[, sample]) |
GenotypeCallRatesDistribution class. |