org.utgenome.format.fasta
Class CompactFASTAIndex

java.lang.Object
  org.utgenome.format.fasta.CompactFASTAIndex

public class CompactFASTAIndex
extends Object

A sequence index to packed FASTA files

Author:

leo

Field Summary

String	description Full description written in FASTA file ( > chr1 ...
int	length sequence length
String	name sequence name (e.g., chr1, scaffold2)
long	offset Offset from the beginning of the packed file

Constructor Summary

CompactFASTAIndex()

Method Summary

static List<CompactFASTAIndex>	load(Reader indexFile)
static List<CompactFASTAIndex>	load(URL indexFile)
CytoBand	toCytoBand() Convert to cyto band

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

public String name

sequence name (e.g., chr1, scaffold2)

description

public String description

Full description written in FASTA file ( > chr1 ... ), without '>' indicator

offset

public long offset

Offset from the beginning of the packed file

length

public int length

sequence length

Constructor Detail

CompactFASTAIndex

public CompactFASTAIndex()

Method Detail

load

public static List<CompactFASTAIndex> load(URL indexFile)
                                    throws org.xerial.core.XerialException,
                                           IOException

Throws:

org.xerial.core.XerialException

IOException

load

public static List<CompactFASTAIndex> load(Reader indexFile)
                                    throws org.xerial.core.XerialException,
                                           IOException

Throws:

org.xerial.core.XerialException

IOException

toCytoBand

public CytoBand toCytoBand()

Convert to cyto band

Returns: