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Created by jrobinso on 9/22/15 .
Manages data loading for a sin gle alignment file. Shared be tween alignment, coverage...
Packs alignments such that the re is no overlap
A wrapper for an AlignmentQuer yReader that caches query res ults
abstract class BaseAlignmentCounts
Genomic interval showing which areas have had reads removed (downsampled)
Developmental track to explore display of conservation scor es.
Created by jrobinso on 2/10/17 .
Some alignment formats are par sed as Features. This is all getting rather circular, ...
Created by jrobinso on 3/22/16 .
Experimental class for phasing alignments for high ploidy r egions.
Created by jrobinso on 12/22/1 6. Experimental class to test strategies for drawing i...
Created by jrobinso on 1/13/17 .
Created by jrobinso on 1/12/17 .
Class for experimenting with 1 0X linked reads.
Convenience class for storing map from group -> list of ali gnments packed into rows ...
Stores objects by position so they can be looked up by inex act position (contains)
Created by jrobinso on 12/20/1 6. Some simple statistics to distinguish dna, rna, and...
A row of alignments, packed to minimize empty space
abstract class SAMAlignment
Write SAM/BAM Alignments to a file or stream
Created by jrobinso on 3/31/16 .
A helper class for computing s plice junctions from alignmen ts. Junctions are filtere...
Track which displays features, typically showing regions of the genome in a qualitat...
abstract class AbstractTrack
Created by jrobinson on 5/3/16 .
Created by jrobinson on 6/3/16 .
insertionMaps 0..* 0..*