org.mulinlab.varnote.utils.database.index

Class Index

java.lang.Object

org.mulinlab.varnote.utils.database.index.Index

Direct Known Subclasses:

TbiIndex, VannoIndex

public abstract class Index
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	buf
protected Format	format
protected htsjdk.samtools.util.BlockCompressedInputStream	is
protected int	mBc
protected java.util.Map<java.lang.String,java.lang.Integer>	mChr2tid
protected int	mEc
protected java.util.Map<java.lang.Integer,java.lang.Long>	minOffForChr
protected int	mMeta
protected int	mPreset
protected int	mSc
protected java.lang.String[]	mSeq
protected int	mSkip
protected java.util.Map<java.lang.Integer,java.lang.String>	mTid2chr

Constructor Summary

Constructors

Constructor and Description
Index(htsjdk.samtools.util.BlockCompressedInputStream is)
Index(java.lang.String indexPath, boolean useJDK)

Method Summary

Modifier and Type	Method and Description
int	chr2tid(java.lang.String chr) return chromosome ID or -1 if it is unknown
java.util.Set<java.lang.String>	getChromosomes() return the chromosomes in that tabix file
abstract java.lang.String[]	getColumnNames()
Format	getFormat()
htsjdk.samtools.util.BlockCompressedInputStream	getIs()
java.util.Map<java.lang.String,java.lang.Integer>	getmChr2tid()
java.util.Map<java.lang.Integer,java.lang.Long>	getMinOffForChr()
java.lang.Long	getMinOffForChr(int tid)
int	getmMeta()
java.lang.String[]	getmSeq()
int	getmSeqLen()
int[]	parseReg(java.lang.String reg) Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
void	read()
protected abstract void	readFormat()
protected abstract void	readIndex()
protected abstract void	readMagic()
protected void	readSeq()
java.lang.String	tid2chr(int tid)

Methods inherited from class java.lang.Object

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

Field Detail

mPreset

protected int mPreset

mSc

protected int mSc

mBc

protected int mBc

mEc

protected int mEc

mMeta

protected int mMeta

mSeq

protected java.lang.String[] mSeq

mChr2tid

protected java.util.Map<java.lang.String,java.lang.Integer> mChr2tid

mTid2chr

protected java.util.Map<java.lang.Integer,java.lang.String> mTid2chr

mSkip

protected int mSkip

is

protected htsjdk.samtools.util.BlockCompressedInputStream is

minOffForChr

protected java.util.Map<java.lang.Integer,java.lang.Long> minOffForChr

format

protected Format format

buf

protected byte[] buf

Constructor Detail

Index

public Index(java.lang.String indexPath,
             boolean useJDK)

Index

public Index(htsjdk.samtools.util.BlockCompressedInputStream is)

Method Detail

getmChr2tid

public java.util.Map<java.lang.String,java.lang.Integer> getmChr2tid()

read

public void read()
          throws java.io.IOException

Throws:

java.io.IOException

getFormat

public Format getFormat()

readMagic

protected abstract void readMagic()
                           throws java.io.IOException

Throws:

java.io.IOException

readFormat

protected abstract void readFormat()
                            throws java.io.IOException

Throws:

java.io.IOException

readSeq

protected void readSeq()
                throws java.io.IOException

Throws:

java.io.IOException

readIndex

protected abstract void readIndex()
                           throws java.io.IOException

Throws:

java.io.IOException

chr2tid

public int chr2tid(java.lang.String chr)

return chromosome ID or -1 if it is unknown

tid2chr

public java.lang.String tid2chr(int tid)

getChromosomes

public java.util.Set<java.lang.String> getChromosomes()

return the chromosomes in that tabix file

parseReg

public int[] parseReg(java.lang.String reg)

Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"

Parameters:

reg - Region string

Returns:

An array where the three elements are sequence_id, region_begin and region_end. On failure, sequence_id==-1.

getmMeta

public int getmMeta()

getMinOffForChr

public java.lang.Long getMinOffForChr(int tid)

getMinOffForChr

public java.util.Map<java.lang.Integer,java.lang.Long> getMinOffForChr()

getmSeq

public java.lang.String[] getmSeq()

getmSeqLen

public int getmSeqLen()

getIs

public htsjdk.samtools.util.BlockCompressedInputStream getIs()

getColumnNames

public abstract java.lang.String[] getColumnNames()