Package htsjdk.samtools.reference

Class FastaSequenceIndexEntry

  • public class FastaSequenceIndexEntry
extends Object
    Hold an individual entry in a fasta sequence index file.

    • Constructor Detail

      • FastaSequenceIndexEntry

        public FastaSequenceIndexEntry​(String contig,
                               long location,
                               long size,
                               int basesPerLine,
                               int bytesPerLine,
                               int sequenceIndex)
        Create a new entry with the given parameters.
        Parameters:
        contig - Contig this entry represents.
        location - Location (byte coordinate) in the fasta file.
        size - The number of bases in the contig.
        basesPerLine - How many bases are on each line.
        bytesPerLine - How many bytes are on each line (includes newline characters).

    • Method Detail

      • getContig

        public String getContig()
        Gets the contig associated with this entry.
        Returns:
        String representation of the contig.

      • setContig

        protected void setContig​(String contig)
        Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries. Provide that capability to other classes w/i the package.
        Parameters:
        contig - New value for the contig.

      • getLocation

        public long getLocation()
        Gets the location of this contig within the fasta.
        Returns:
        seek position within the fasta.

      • getSize

        public long getSize()
        Gets the size, in bytes, of the data in the contig.
        Returns:
        size of the contig bases in bytes.

      • getBasesPerLine

        public int getBasesPerLine()
        Gets the number of bases in a given line.
        Returns:
        Number of bases in the fasta line.

      • getBytesPerLine

        public int getBytesPerLine()
        How many bytes (bases + whitespace) are consumed by the given line?
        Returns:
        Number of bytes in a line.

      • getSequenceIndex

        public int getSequenceIndex()

      • toString

        public String toString()
        For debugging. Emit the contents of each contig line.
        Overrides:
        toString in class Object
        Returns:
        A string representation of the contig line.

      • equals

        public boolean equals​(Object other)
        Compare this index entry to another index entry.
        Overrides:
        equals in class Object
        Parameters:
        other - another FastaSequenceIndexEntry
        Returns:
        True if each has the same name, location, size, basesPerLine and bytesPerLine

      • hashCode

        public int hashCode()
        In general, we expect one entry per contig, so compute the hash based only on the contig.
        Overrides:
        hashCode in class Object
        Returns:
        A unique hash code representing this object.