| 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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