Package ngs

Interface ReadCollection

public interface ReadCollection

Represents an NGS-capable object with a collection of Reads, References and Alignments.

Each of the basic content types may be accessed by id as either a standalone object, or more commonly through an Iterator over a selected collection of objects.

Reads are grouped by ReadGroup. When not specifically assigned, Reads will be placed into the default ReadGroup.

  • Method Details

    • getName

      String getName() throws ErrorMsg

      Access the simple name of the ReadCollection. This name is generally extracted from the "spec" used to create the object, but may also be mapped to a canonical name if one may be determined and differs from that given in the spec.

      if the name is extracted from "spec" and contains well-known file extensions that do not form part of a canonical name (e.g. ".sra"), they will be removed.

      Returns:
      the simple name of the ReadCollection
      Throws:
      ErrorMsg - if the name cannot be retrieved
      See Also:

    • getReadGroups

      ReadGroupIterator getReadGroups() throws ErrorMsg
      Access all non-empty ReadGroups. Iterator will contain at least one ReadGroup unless the ReadCollection itself is empty.
      Returns:
      an unordered Iterator of ReadGroups
      Throws:
      ErrorMsg - only upon an error accessing data

    • hasReadGroup

      boolean hasReadGroup(String spec)
      Parameters:
      spec - the name of a contained read group
      Returns:
      true if a call to "getReadGroup()" should succeed

    • getReadGroup

      ReadGroup getReadGroup(String spec) throws ErrorMsg
      Access a single ReadGroup by name.
      Parameters:
      spec - the name of a contained read group
      Returns:
      an instance of the designated ReadGroup
      Throws:
      ErrorMsg - if specified ReadGroup is not found
      ErrorMsg - upon an error accessing data

    • getReferences

      ReferenceIterator getReferences() throws ErrorMsg
      Access all References having aligned Reads. Iterator will contain at least one ReadGroup unless no Reads are aligned.
      Returns:
      an unordered Iterator of References
      Throws:
      ErrorMsg - upon an error accessing data

    • hasReference

      boolean hasReference(String spec)
      Parameters:
      spec - the name of a contained Reference
      Returns:
      true if a call to "getReference()" should succeed

    • getReference

      Reference getReference(String spec) throws ErrorMsg
      Access a single Reference by name spec.
      Parameters:
      spec - a common or canonical name of a contained reference
      Returns:
      an instance of the designated Reference
      Throws:
      ErrorMsg - if the Reference is not found
      ErrorMsg - upon an error accessing data

    • getAlignment

      Alignment getAlignment(String alignmentId) throws ErrorMsg
      Access a single Alignment by id. The object id is unique within any given ReadCollection, and may designate an Alignment of any category. Note Excessive usage may create pressure on JVM and System memory.
      Parameters:
      alignmentId - the ID of the alignment to return
      Returns:
      an individual Alignment instance
      Throws:
      ErrorMsg - if Alignment is not found
      ErrorMsg - upon an error accessing data

    • getAlignments

      AlignmentIterator getAlignments(int categories) throws ErrorMsg
      Select Alignments by AlignmentCategory.
      Parameters:
      categories - is a bitfield of AlignmentCategory
      Returns:
      an iterator of all Alignments from specified categories
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentCount

      long getAlignmentCount() throws ErrorMsg
      Count all Alignments within the ReadCollection
      Returns:
      0 if there are no aligned Reads, > 0 otherwise
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentCount

      long getAlignmentCount(int categories) throws ErrorMsg
      Count selected Alignments within the ReadCollection
      Parameters:
      categories - is a bitfield of AlignmentCategory
      Returns:
      count of all alignments
      Throws:
      ErrorMsg - upon an error accessing data
      See Also:

    • getAlignmentRange

      AlignmentIterator getAlignmentRange(long first, long count) throws ErrorMsg
      getAlignmentRange
      Parameters:
      first - is an unsigned ordinal into set
      count - the number of alignments
      Returns:
      an iterator across a range of Alignments
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentRange

      AlignmentIterator getAlignmentRange(long first, long count, int categories) throws ErrorMsg
      getAlignmentRange
      Parameters:
      first - is an unsigned ordinal into set
      count - number of alignments
      categories - provides a means of filtering by AlignmentCategory
      Returns:
      an iterator across a range of Alignments
      Throws:
      ErrorMsg - upon an error accessing data

    • getRead

      Read getRead(String readId) throws ErrorMsg
      getRead
      Parameters:
      readId - the ID of the Read to return
      Returns:
      an individual Read
      Throws:
      ErrorMsg - if Read does not exist

    • getReads

      ReadIterator getReads(int categories) throws ErrorMsg
      getReads
      Parameters:
      categories - provides a means of filtering by ReadCategory
      Returns:
      an iterator of all contained machine Reads
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadCount

      long getReadCount() throws ErrorMsg
      getReadCount
      Returns:
      the number of reads in the collection
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadCount

      long getReadCount(int categories) throws ErrorMsg
      getReadCount
      Parameters:
      categories - provides an optional means of filtering by ReadCategory
      Returns:
      the number of reads in the collection
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadRange

      ReadIterator getReadRange(long first, long count) throws ErrorMsg
      getReadRange
      Parameters:
      first - is an unsigned ordinal into set
      count - the number of reads
      Returns:
      an iterator across a range of Reads
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadRange

      ReadIterator getReadRange(long first, long count, int categories) throws ErrorMsg
      getReadRange
      Parameters:
      first - is an unsigned ordinal into set
      count - the number of reads
      categories - provides an optional means of filtering by ReadCategory
      Returns:
      an iterator across a range of Reads
      Throws:
      ErrorMsg - upon an error accessing data