Package htsjdk.samtools.sra

package htsjdk.samtools.sra
  • Classes
    Class
    Description
    ReferenceCache
    That is a thread-safe wrapper for a list of cache Reference objects.
    SRAAccession
    Describes a single SRA accession for SRA read collection Also provides app string functionality and allows to check if working SRA is supported on the running platform Important: due to checks performed in SRAAccession.isValid(), we won't recognise any accessions other than ones that follow the pattern "^[SED]RR[0-9]{6,9}$", e.g.
    SRAAlignmentIterator
    Iterator for aligned reads.
    SRAIndexedSequenceFile
    Allows reading Reference data from SRA
    SRALazyRecord
    Extends SAMRecord so that any of the fields will be loaded only when needed.
    SRAUnalignmentIterator
    Iterator for unaligned reads.
    SRAUtils
    Provides some functionality which can be used by other classes Created by andrii.nikitiuk on 10/28/15.