Package org.utgenome.format.fasta

FASTA utilities

See:
          Description

Interface Summary
CompactFASTA.PacFileAccess  
GenomeSequence A common interface of genome sequences
OverlappingKmerIterator For walking overlapping k-mer integers
 

Class Summary
CompactACGT Compact array for ACGT (and N) sequences
CompactACGTWriter ACGT sequence compressor
CompactFASTA CompactFASTA is a packed FASTA file, supporting random accesses to sub sequences of a specified chromosome.
CompactFASTAGenerator  
CompactFASTAIndex A sequence index to packed FASTA files
FASTA  
FASTA.RawStringWrapper  
FASTADatabase Fasta2DB creates a SQLite database file from a given FASTA format file
FASTADatabase.Config  
FASTADatabase.NSeq A holder for retrieving compressed genome sequence
FASTADatabase.TextOutput  
FASTAPullParser A pull parser for FASTA format files
FASTASequence A FASTASequence represents an entry in FASTA files
Kmer K-mer integer representation of ACGT.
 

Package org.utgenome.format.fasta Description

FASTA utilities



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