bdgenomics.mango.alignments.AlignmentSummary¶

class bdgenomics.mango.alignments.AlignmentSummary(spark, ac, alignmentDataset, sample=1.0)[source]¶

AlignmentSummary class. AlignmentSummary provides scrollable visualization of alignments based on genomic regions.

__init__(spark, ac, alignmentDataset, sample=1.0)[source]¶

Initializes an AlignmentSummary class.

Args:

param alignmentDataset:
param spark:	SparkSession
param ac:	ADAMContext
	bdgenomics.adam.Dataset.AlignmentRecoDatasetataset
param sample:	fraction of reads to sample from

Methods

`__init__`(spark, ac, alignmentDataset[, sample])	Initializes an AlignmentSummary class.
`getCoverageDistribution`([bin_size])	Computes coverage distribution for this AlignmentDataset.
`getFragmentDistribution`()	Computes fragment distribution for this AlignmentDataset.
`getIndelDistribution`([bin_size])	Computes insertion and deletion distribution for this AlignmentDataset
`getMapQDistribution`()	Computes mapping quality distribution for this AlignmentDataset.
`viewPileup`(contig, start, end[, reference, …])	Visualizes a portion of this AlignmentDataset in a scrollable pileup widget