Class 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 Detail

      • 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:
        Constant Field Values
    • Constructor Detail

      • SRAUtils

        public SRAUtils()
    • Method Detail

      • 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