uk.ac.sanger.npg.illumina
Class Tile

java.lang.Object
  uk.ac.sanger.npg.illumina.Tile

public class Tile
extends java.lang.Object

Process an illumina tile

Constructor Summary

Tile(java.lang.String intensityDir, java.lang.String baseCallDir, java.lang.String id, int laneNumber, int tileNumber, java.util.HashMap<java.lang.String,int[]> cycleRangeByRead, boolean secondCall, boolean pfFilter, java.lang.String barcodeSeqTagName, java.lang.String barcodeQualTagName)

Method Summary

boolean	checkBCLClusterNumber(int expectedClusterNumber)
boolean	checkSCLClusterNumber(int expectedClusterNumber)
void	closeBaseCallFiles() close all BCL or SCL file in not closed yet
java.lang.String	convertByteArrayToString(byte[] array)
java.lang.String	convertPhredQualByteArrayToFastqString(byte[] array)
java.lang.String	getBaseCallFileName(int cycle, boolean firstCall)
java.util.HashMap<java.lang.String,BCLFileReader[]>	getBclFileReaderListByRead()
java.lang.String	getcLocsFileName()
java.lang.String	getFilterFileName()
java.lang.String	getLocsFileName()
byte[][]	getNextClusterBaseQuals(BCLFileReader[] bclFileList) read bases and qualities for next cluster of one read from its BCL file list
byte[][]	getNextClusterBaseQuals(java.lang.String read) read bases and qualities for next cluster of one read
java.lang.String	getNextClusterSecondBases(SCLFileReader[] sclFileList) read second bases for next cluster of one read from its BCL file list
java.lang.String	getNextClusterSecondBases(java.lang.String read) read second bases for next cluster of one read
java.lang.String	getPosFileName()
java.lang.String	getReadName(java.lang.String[] pos) form read name for one cluster
net.sf.samtools.SAMRecord	getSAMRecord(net.sf.samtools.SAMFileHeader fileHeader, java.lang.String readName, int clusterIndex, byte[][] baseQuals, java.lang.String secondBases, byte[][] baseQualsIndex, byte[][] baseQualsIndex2, int filter, boolean paired, boolean firstRead) write all together for one SAM Record
java.util.HashMap<java.lang.String,SCLFileReader[]>	getSclFileReaderListByRead()
boolean	isIndexed()
boolean	isPairedRead()
static void	main(java.lang.String[] args) test main method
void	openBaseCallFiles() open all BCL or SCL files
void	processTile(net.sf.samtools.SAMFileWriter outputSam) read each cluster and write them to output bam file
void	setSecondBarcodeQualTagName(java.lang.String secondBarcodeQualTagName)
void	setSecondBarcodeSeqTagName(java.lang.String secondBarcodeSeqTagName)

Methods inherited from class java.lang.Object

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

Constructor Detail

Tile

public Tile(java.lang.String intensityDir,
            java.lang.String baseCallDir,
            java.lang.String id,
            int laneNumber,
            int tileNumber,
            java.util.HashMap<java.lang.String,int[]> cycleRangeByRead,
            boolean secondCall,
            boolean pfFilter,
            java.lang.String barcodeSeqTagName,
            java.lang.String barcodeQualTagName)

Parameters:

intensityDir - intensities directory

baseCallDir -

id - instrument with run id, which will be used for read name

laneNumber - the run laneNumber number

tileNumber - this tile number

cycleRangeByRead - cycle range for each read, the hash key could be read1, read2 or readIndex

secondCall - include second base call or not

pfFilter - include PF filtered reads or not

barcodeSeqTagName -

barcodeQualTagName -

Method Detail

processTile

public void processTile(net.sf.samtools.SAMFileWriter outputSam)
                 throws java.lang.Exception

read each cluster and write them to output bam file

Parameters:

outputSam -

Throws:

java.lang.Exception

checkBCLClusterNumber

public boolean checkBCLClusterNumber(int expectedClusterNumber)
                              throws java.lang.Exception

Parameters:

expectedClusterNumber -

Returns:

true if cluster number in bcl file match the one in filter file

Throws:

java.lang.Exception

checkSCLClusterNumber

public boolean checkSCLClusterNumber(int expectedClusterNumber)
                              throws java.lang.Exception

Parameters:

expectedClusterNumber -

Returns:

true if cluster number in scl file match the one in filter file

Throws:

java.lang.Exception

openBaseCallFiles

public void openBaseCallFiles()
                       throws java.lang.Exception

open all BCL or SCL files

Throws:

java.lang.Exception

closeBaseCallFiles

public void closeBaseCallFiles()

close all BCL or SCL file in not closed yet

getNextClusterBaseQuals

public byte[][] getNextClusterBaseQuals(java.lang.String read)
                                 throws java.lang.Exception

read bases and qualities for next cluster of one read

Parameters:

read -

Returns:

next cluster base and quality value as byte array for a read

Throws:

java.lang.Exception

getNextClusterBaseQuals

public byte[][] getNextClusterBaseQuals(BCLFileReader[] bclFileList)
                                 throws java.lang.Exception

read bases and qualities for next cluster of one read from its BCL file list

Parameters:

bclFileList -

Returns:

next cluster base and quality value as byte array from BCL file list

Throws:

java.lang.Exception

getNextClusterSecondBases

public java.lang.String getNextClusterSecondBases(java.lang.String read)
                                           throws java.lang.Exception

read second bases for next cluster of one read

Parameters:

read -

Returns:

get next cluster second bases for a read

Throws:

java.lang.Exception

getNextClusterSecondBases

public java.lang.String getNextClusterSecondBases(SCLFileReader[] sclFileList)
                                           throws java.lang.Exception

read second bases for next cluster of one read from its BCL file list

Parameters:

sclFileList -

Returns:

get next cluster second bases from SCL file list

Throws:

java.lang.Exception

getSAMRecord

public net.sf.samtools.SAMRecord getSAMRecord(net.sf.samtools.SAMFileHeader fileHeader,
                                              java.lang.String readName,
                                              int clusterIndex,
                                              byte[][] baseQuals,
                                              java.lang.String secondBases,
                                              byte[][] baseQualsIndex,
                                              byte[][] baseQualsIndex2,
                                              int filter,
                                              boolean paired,
                                              boolean firstRead)

write all together for one SAM Record

Parameters:

fileHeader -

readName -

clusterIndex -

baseQuals -

secondBases -

baseQualsIndex -

baseQualsIndex2 -

filter -

paired -

firstRead -

Returns:

SAM record

getReadName

public java.lang.String getReadName(java.lang.String[] pos)

form read name for one cluster

Parameters:

pos -

Returns:

whole read name

getBaseCallFileName

public java.lang.String getBaseCallFileName(int cycle,
                                            boolean firstCall)

Parameters:

cycle -

firstCall -

Returns:

BCL or SCL base call file name

convertPhredQualByteArrayToFastqString

public java.lang.String convertPhredQualByteArrayToFastqString(byte[] array)

Parameters:

array -

Returns:

fastq quality string from phred qual byte array

convertByteArrayToString

public java.lang.String convertByteArrayToString(byte[] array)

Parameters:

array -

Returns:

string from a byte array

getcLocsFileName

public java.lang.String getcLocsFileName()

Returns:

the cLocsFileName

getFilterFileName

public java.lang.String getFilterFileName()

Returns:

the filterFileNameLocal

isPairedRead

public boolean isPairedRead()

Returns:

the pairedRead

isIndexed

public boolean isIndexed()

Returns:

the indexed

getBclFileReaderListByRead

public java.util.HashMap<java.lang.String,BCLFileReader[]> getBclFileReaderListByRead()

Returns:

the bclFileReaderListByRead

getSclFileReaderListByRead

public java.util.HashMap<java.lang.String,SCLFileReader[]> getSclFileReaderListByRead()

Returns:

the sclFileReaderListByRead

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

test main method

Parameters:

args -

Throws:

java.lang.Exception

getPosFileName

public java.lang.String getPosFileName()

Returns:

the posFileName

getLocsFileName

public java.lang.String getLocsFileName()

Returns:

the locsFileName

setSecondBarcodeSeqTagName

public void setSecondBarcodeSeqTagName(java.lang.String secondBarcodeSeqTagName)

Parameters:

secondBarcodeSeqTagName - the secondBarcodeSeqTagName to set

setSecondBarcodeQualTagName

public void setSecondBarcodeQualTagName(java.lang.String secondBarcodeQualTagName)

Parameters:

secondBarcodeQualTagName - the secondBarcodeQualTagName to set