java.lang.Object
- htsjdk.samtools.util.GZIIndex

```
public final class GZIIndex
extends Object
```
Represents a .gzi index of a block-compressed file.
The .gzi index is a mapping between the offset of each block in the gzipped file and the uncompressed offset that that block starts with. This mapping is represented by GZIIndex.IndexEntry.
An example of usage for this index for random access a bgzip file using an index generated from raw data. For example, for indexing a compressed FASTA file the .gzi index can be used in conjunction with the FastaSequenceIndex to seek concrete sequences.

See Also:

https://github.com/samtools/htslib/issues/473

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`GZIIndex.GZIIndexer`	Helper class for constructing the GZIindex.
`static class`	`GZIIndex.IndexEntry`	Index entry mapping the block-offset (compressed offset) to the uncompressed offset where the block starts.

Field Summary

Fields
Modifier and Type Field Description

static String DEFAULT_EXTENSION
Deprecated.
since June 2019 Use FileExtensions.GZI instead.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static GZIIndex`	`buildIndex(Path bgzipFile)`	Builds a `GZIIndex` on the fly from a BGZIP file.
`static GZIIndex`	`createIndex(Path bgzipFile, boolean overwrite)`	Creates a `GZIIndex` from a BGZIP file and store it in memory and disk.
`boolean`	`equals(Object obj)`
`List<GZIIndex.IndexEntry>`	`getIndexEntries()`	Gets an unmodifiable list with the index entries.
`int`	`getNumberOfBlocks()`	Gets the number of blocks on the file.
`long`	`getVirtualOffsetForSeek(long uncompressedOffset)`	Gets the virtual offset for seek with `BlockCompressedInputStream.seek(long)`.
`int`	`hashCode()`
`static GZIIndex`	`loadIndex(String source, InputStream indexIn)`	Loads the index from the provided input stream.
`static GZIIndex`	`loadIndex(String source, ReadableByteChannel channel)`	Loads the index from the provided channel.
`static GZIIndex`	`loadIndex(Path indexPath)`	Loads the index from the provided file.
`static Path`	`resolveIndexNameForBgzipFile(Path bgzipFile)`	Gets the default index path for the bgzip file.
`String`	`toString()`
`void`	`writeIndex(OutputStream output)`	Writes this index into the requested path.
`void`	`writeIndex(Path output)`	Writes this index into the requested path.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_EXTENSION
```
@Deprecated
public static final String DEFAULT_EXTENSION
```
    Deprecated.
    since June 2019 Use FileExtensions.GZI instead.
    
    See Also:
    
    Constant Field Values
- Method Detail
  - getNumberOfBlocks
```
public int getNumberOfBlocks()
```
    Gets the number of blocks on the file.
    
    Returns:
    
    the number of blocks.
  - getIndexEntries
```
public List<GZIIndex.IndexEntry> getIndexEntries()
```
    Gets an unmodifiable list with the index entries.
    Note: because the first block corresponds to a dummy index entry (0, 0), the returned list does not include it. Thus, the size of the list is getNumberOfBlocks() - 1.
    
    Returns:
    
    index entries.
  - getVirtualOffsetForSeek
```
public long getVirtualOffsetForSeek(long uncompressedOffset)
```
    Gets the virtual offset for seek with BlockCompressedInputStream.seek(long).
    BlockCompressedInputStream.seek(long) parameter is not a byte-offset, but a special virtual file pointer that specifies the block-offset within the file (BlockCompressedFilePointerUtil.getBlockAddress(long)), and the offset within the block (BlockCompressedFilePointerUtil.getBlockOffset(long)).
    This methods converts the provided byte-offset on the file to the special file pointer used to seek a block-compressed file, using this index to find the block where the byte-offset is located.
    
    Parameters:
    
    uncompressedOffset - the file-offset.
    
    Returns:
    
    virtual offset for BlockCompressedInputStream.
    
    See Also:
    
    BlockCompressedFilePointerUtil
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - writeIndex
```
public void writeIndex(Path output)
                throws IOException
```
    Writes this index into the requested path.
    
    Parameters:
    
    output - the output path.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - writeIndex
```
public void writeIndex(OutputStream output)
                throws IOException
```
    Writes this index into the requested path. NOTE: This method will close out the provided output stream when it finishes writing the index
    
    Parameters:
    
    output - the output file.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - loadIndex
```
public static final GZIIndex loadIndex(Path indexPath)
                                throws IOException
```
    Loads the index from the provided file.
    
    Parameters:
    
    indexPath - the path for the index to load.
    
    Returns:
    
    loaded index.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - loadIndex
```
public static final GZIIndex loadIndex(String source,
                                       InputStream indexIn)
                                throws IOException
```
    Loads the index from the provided input stream.
    
    Parameters:
    
    source - The named source of the reference file (used in error messages). May be null if unknown.
    
    indexIn - the input stream for the index to load.
    
    Returns:
    
    loaded index.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - loadIndex
```
public static final GZIIndex loadIndex(String source,
                                       ReadableByteChannel channel)
                                throws IOException
```
    Loads the index from the provided channel.
    
    Parameters:
    
    source - The named source of the reference file (used in error messages). May be null if unknown.
    
    channel - the channel to read the index from.
    
    Returns:
    
    loaded index.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - buildIndex
```
public static final GZIIndex buildIndex(Path bgzipFile)
                                 throws IOException
```
    Builds a GZIIndex on the fly from a BGZIP file.
    Note that this method does not write the index on disk. Use writeIndex(OutputStream) on the returned object to save the index.
    
    Parameters:
    
    bgzipFile - the bgzip file.
    
    Returns:
    
    in-memory .gzi index.
    
    Throws:
    
    IOException - if an I/O error occurs.
  - createIndex
```
public static GZIIndex createIndex(Path bgzipFile,
                                   boolean overwrite)
                            throws IOException
```
    Creates a GZIIndex from a BGZIP file and store it in memory and disk.
    
    Parameters:
    
    bgzipFile - the bgzip file.
    
    overwrite - if the .fai index already exists override it if true; otherwise, throws a IOException.
    
    Returns:
    
    the in-memory representation for the created index.
    
    Throws:
    
    IOException - if an IO error occurs.
  - resolveIndexNameForBgzipFile
```
public static Path resolveIndexNameForBgzipFile(Path bgzipFile)
```
    Gets the default index path for the bgzip file.

Class GZIIndex

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_EXTENSION

Method Detail

getNumberOfBlocks

getIndexEntries

getVirtualOffsetForSeek

equals

hashCode

toString

writeIndex

writeIndex

loadIndex

loadIndex

loadIndex

buildIndex

createIndex

resolveIndexNameForBgzipFile