Package htsjdk.samtools

Interface SAMFileSpan

All Superinterfaces:
Cloneable
All Known Implementing Classes:
BAMFileSpan
public interface SAMFileSpan extends Cloneable
A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query.

  • Method Summary

    Modifier and Type
    Method
    Description
    SAMFileSpan
    getContentsFollowing()
    Gets a pointer over the data immediately following this span.
    boolean
    isEmpty()
    Does this file span point to any data, or is it completely empty?
    SAMFileSpan
    removeContentsBefore(SAMFileSpan fileSpan)
    Remove all pointers in this file span before the given file span starts.

  • Method Details

    • getContentsFollowing

      SAMFileSpan getContentsFollowing()
      Gets a pointer over the data immediately following this span.
      Returns:
      The a pointer to data immediately following this span.

    • removeContentsBefore

      SAMFileSpan removeContentsBefore(SAMFileSpan fileSpan)
      Remove all pointers in this file span before the given file span starts.
      Parameters:
      fileSpan - The filespan before which to eliminate.
      Returns:
      The portion of the chunk list after the given chunk.

    • isEmpty

      boolean isEmpty()
      Does this file span point to any data, or is it completely empty?
      Returns:
      True if the file span is empty, false otherwise.