Pair<X extends Comparable<X>,Y extends Comparable<Y>> |
Simple Pair class.
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PGTagArgumentCollection |
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
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PhysicalLocationInt |
Small class that provides access to the physical location information about a cluster.
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PhysicalLocationShort |
Small class that provides access to the physical location information about a cluster.
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PrimaryAlignmentKey |
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file
(assuming the file is valid).
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ReadNameParser |
Provides access to the physical location information about a cluster.
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RepresentativeReadIndexer |
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
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SamComparison |
Compare two SAM/BAM files.
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SAMComparisonArgumentCollection |
Argument collection for SAM comparison
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