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The GAlignmentPairs class is a container for genomic alignment pairs.
● Data Source:
BioConductor
● Keywords: classes, methods
● Alias: GAlignmentPairs-class, class:GAlignmentPairs
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The GAlignments class is a simple container which purpose is to store a set of genomic alignments that will hold just enough information for supporting the operations described below.
● Data Source:
BioConductor
● Keywords: classes, methods
● Alias: GAlignments-class, class:GAlignments
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The GAlignmentsList class is a container for storing a collection of GAlignments objects.
● Data Source:
BioConductor
● Keywords: classes, methods
● Alias: GAlignmentsList, GAlignmentsList-class, class:GAlignmentsList
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The GappedReads class extends the GAlignments class.
● Data Source:
BioConductor
● Keywords: classes, methods
● Alias: GappedReads-class, class:GappedReads
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The OverlapEncodings class is a container for storing the "overlap encodings" returned by the encodeOverlaps function.
● Data Source:
BioConductor
● Keywords: classes, methods
● Alias: OverlapEncodings, OverlapEncodings-class, class:OverlapEncodings
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Utility functions for low-level CIGAR manipulation.
● Data Source:
BioConductor
● Keywords: manip
● Alias: cigar-utils
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mapToAlignments
(Package: GenomicAlignments) :
Map range coordinates between reads and genome space using
Map range coordinates between reads (local) and genome (reference) space using the CIGAR in a GAlignments object.
● Data Source:
BioConductor
● Keywords: methods, utilities
● Alias: coordinate-mapping-methods
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coverage-methods
(Package: GenomicAlignments) :
Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object
coverage methods for GAlignments, GAlignmentPairs, GAlignmentsList, and BamFile objects.
● Data Source:
BioConductor
● Keywords: methods, utilities
● Alias: coverage-methods
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In the context of an RNA-seq experiment, encoding the overlaps between the aligned reads and the transcripts of a given gene model can be used for detecting those overlaps that are compatible with the splicing of the transcript.
● Data Source:
BioConductor
● Keywords: methods, utilities
● Alias: encodeOverlaps-methods
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In the context of an RNA-seq experiment, findCompatibleOverlaps (or countCompatibleOverlaps) can be used for finding (or counting) hits between reads and transcripts that are compatible with the splicing of the transcript.
● Data Source:
BioConductor
● Keywords: methods, utilities
● Alias: findCompatibleOverlaps-methods
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providing 
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