Package htsjdk.samtools.reference

Class FastaSequenceIndex

java.lang.Object
htsjdk.samtools.reference.FastaSequenceIndex
All Implemented Interfaces:
Iterable<FastaSequenceIndexEntry>
public class FastaSequenceIndex extends Object implements Iterable<FastaSequenceIndexEntry>
Reads/writes a fasta index file (.fai), as generated by `samtools faidx`.

  • Constructor Details

    • FastaSequenceIndex

      public FastaSequenceIndex(File indexFile)
      Build a sequence index from the specified file.
      Parameters:
      indexFile - File to open.
      Throws:
      FileNotFoundException - if the index file cannot be found.

    • FastaSequenceIndex

      public FastaSequenceIndex(Path indexFile)
      Build a sequence index from the specified file.
      Parameters:
      indexFile - File to open.
      Throws:
      FileNotFoundException - if the index file cannot be found.

    • FastaSequenceIndex

      public FastaSequenceIndex(InputStream in)
      Build a sequence index from the specified input stream.
      Parameters:
      in - InputStream to read from.

    • FastaSequenceIndex

      protected FastaSequenceIndex()
      Empty, protected constructor for unit testing.

  • Method Details

    • add

      protected void add(FastaSequenceIndexEntry indexEntry)
      Add a new index entry to the list. Protected for unit testing.
      Parameters:
      indexEntry - New index entry to add.

    • rename

      protected void rename(FastaSequenceIndexEntry entry, String newName)
      Renames the existing index entry to the new index entry with the specified name.
      Parameters:
      entry - entry to update.
      newName - New name for the index entry.

    • equals

      public boolean equals(Object other)
      Compare two FastaSequenceIndex objects for equality.
      Overrides:
      equals in class Object
      Parameters:
      other - Another FastaSequenceIndex to compare
      Returns:
      True if index has the same entries as other instance, in the same order

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • write

      public void write(Path indexFile) throws IOException
      Writes this index to the specified path.
      Parameters:
      indexFile - index file to output the index in the .fai format
      Throws:
      IOException - if an IO error occurs.

    • hasIndexEntry

      public boolean hasIndexEntry(String contigName)
      Does the given contig name have a corresponding entry?
      Parameters:
      contigName - The contig name for which to search.
      Returns:
      True if contig name is present; false otherwise.

    • getIndexEntry

      public FastaSequenceIndexEntry getIndexEntry(String contigName)
      Retrieve the index entry associated with the given contig.
      Parameters:
      contigName - Name of the contig for which to search.
      Returns:
      Index entry associated with the given contig.
      Throws:
      SAMException - if the associated index entry can't be found.

    • iterator

      public Iterator<FastaSequenceIndexEntry> iterator()
      Creates an iterator which can iterate through all entries in a fasta index.
      Specified by:
      iterator in interface Iterable<FastaSequenceIndexEntry>
      Returns:
      iterator over all fasta index entries.

    • size

      public int size()
      Returns the number of elements in the index.
      Returns:
      Number of elements in the index.