Package htsjdk.samtools.sra

Class SRAUtils

java.lang.Object
htsjdk.samtools.sra.SRAUtils
public class SRAUtils extends Object
Provides some functionality which can be used by other classes Created by andrii.nikitiuk on 10/28/15.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    REFERENCE_ALIGNMENT
    References are stored in SRA table in chunks of 5k bases per row, while last chunk of a reference is less or equal than 5k bases in size (even if the next reference follows).

  • Constructor Summary

    Constructors
    Constructor
    Description
    SRAUtils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static long
    getNumberOfReads(ngs.ReadCollection run)
    Is used to build RecordRangeInfo
    static List<Long>
    getReferencesLengthsAligned(ngs.ReadCollection run)
    Loads reference lengths from a read collection.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • REFERENCE_ALIGNMENT

      public static final int REFERENCE_ALIGNMENT
      References are stored in SRA table in chunks of 5k bases per row, while last chunk of a reference is less or equal than 5k bases in size (even if the next reference follows). So, it will be optimal if we align reference sizes to 5k bases to read by reference rows.
      See Also:

  • Constructor Details

    • SRAUtils

      public SRAUtils()

  • Method Details

    • getNumberOfReads

      public static long getNumberOfReads(ngs.ReadCollection run) throws ngs.ErrorMsg
      Is used to build RecordRangeInfo
      Parameters:
      run - open read collection
      Returns:
      total number of reads (both aligned and unaligned) in SRA archive
      Throws:
      ngs.ErrorMsg

    • getReferencesLengthsAligned

      public static List<Long> getReferencesLengthsAligned(ngs.ReadCollection run) throws ngs.ErrorMsg
      Loads reference lengths from a read collection. Aligns reference lengths by REFERENCE_ALIGNMENT bases for optimal loads of alignments (references are stored in REFERENCE_ALIGNMENT bases chunks in SRA table) Is used to build RecordRangeInfo
      Parameters:
      run - single opened read collection
      Returns:
      list with references lengths
      Throws:
      ngs.ErrorMsg