picard.util

Class IlluminaUtil

java.lang.Object

picard.util.IlluminaUtil

public class IlluminaUtil
extends java.lang.Object

Misc utilities for working with Illumina specific files and data

Author:

jburke@broadinstitute.org

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IlluminaUtil.IlluminaAdapterPair Describes adapters used on each pair of strands

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BARCODE_DELIMITER

Constructor Summary

Constructors

Constructor and Description
IlluminaUtil()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	barcodeSeqsToString(byte[][] barcodes) Concatenates all the barcode sequences with BARCODE_DELIMITER
static java.lang.String	barcodeSeqsToString(java.util.List<java.lang.String> barcodes) Concatenates all the barcode sequences with BARCODE_DELIMITER
static java.lang.String	barcodeSeqsToString(java.lang.String[] barcodes) Concatenates all the barcode sequences with BARCODE_DELIMITER
static java.lang.String	byteArrayToString(byte[][] barcodes, java.lang.String delim) Concatenates all the barcode sequences with BARCODE_DELIMITER
static void	convertSolexaQualityAscii_1_1_ToPhredBinary(byte[] solexaQualities) Converts from Solexa ASCII to Phred binary in place.
static byte	getSolexaQualityCharFromFourQualities(java.lang.String[] qualities, int cycleNumber, htsjdk.samtools.util.FormatUtil formatter) Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
static java.lang.Integer	getTileFromReadName(java.lang.String readName) Parse the tile # from the read name.
static byte[]	makePhredBinaryFromSolexaQualityAscii_1_3(java.lang.String solexaQualities) Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
static byte[]	makePhredBinaryFromSolexaQualityAscii_1_3(java.lang.String solexaQualities, int offset, int length) Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
static java.lang.String	stringSeqsToString(java.lang.String[] barcodes, java.lang.String delim)

Methods inherited from class java.lang.Object

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

Field Detail

BARCODE_DELIMITER

public static final java.lang.String BARCODE_DELIMITER

See Also:

Constant Field Values

Constructor Detail

IlluminaUtil

public IlluminaUtil()

Method Detail

getTileFromReadName

public static java.lang.Integer getTileFromReadName(java.lang.String readName)

Parse the tile # from the read name. If we find that there are other elements needed from the read name, it might be a good idea to put makeReadName() and various get..() methods into a new class.

Parameters:

readName - As produced by IlluminaUtil.makeReadName()

Returns:

tile number, or null if read name is not in correct format.

makePhredBinaryFromSolexaQualityAscii_1_3

public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(java.lang.String solexaQualities)

Convert from Solexa-scaled ASCII qualities to Phred-scaled binary. The only difference is Solexa qualities have 64 added to the phred binary to make them printable.

Parameters:

solexaQualities - Printable ASCII qualities.

Returns:

binary Phred-scaled qualities.

makePhredBinaryFromSolexaQualityAscii_1_3

public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(java.lang.String solexaQualities,
                                                               int offset,
                                                               int length)

Convert from Solexa-scaled ASCII qualities to Phred-scaled binary. The only difference is Solexa qualities have 64 added to the phred binary to make them printable.

Parameters:

solexaQualities - Printable ASCII qualities.

offset - Character at which to start conversion.

length - Number of characters to convert.

Returns:

binary Phred-scaled qualities.

convertSolexaQualityAscii_1_1_ToPhredBinary

public static void convertSolexaQualityAscii_1_1_ToPhredBinary(byte[] solexaQualities)

Converts from Solexa ASCII to Phred binary in place. These are the older-style qualities rather than Phred qualities with a different addend to make them printable.

getSolexaQualityCharFromFourQualities

public static byte getSolexaQualityCharFromFourQualities(java.lang.String[] qualities,
                                                         int cycleNumber,
                                                         htsjdk.samtools.util.FormatUtil formatter)

Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...]. The best quality from the 4 qualities for the cycle is found, and then it is ASCII-ized by adding 64.

Parameters:

qualities - Array of integer quality strings.

cycleNumber - Which cycle to get quality for.

formatter - For converting decimal strings to ints.

Returns:

best quality for the given cycle.

Throws:

PicardException - if the best quality ASCII value is > 255.

barcodeSeqsToString

public static java.lang.String barcodeSeqsToString(java.util.List<java.lang.String> barcodes)

Concatenates all the barcode sequences with BARCODE_DELIMITER

Parameters:

barcodes -

Returns:

A single string representation of all the barcodes

barcodeSeqsToString

public static java.lang.String barcodeSeqsToString(java.lang.String[] barcodes)

Concatenates all the barcode sequences with BARCODE_DELIMITER

Parameters:

barcodes -

Returns:

A single string representation of all the barcodes

barcodeSeqsToString

public static java.lang.String barcodeSeqsToString(byte[][] barcodes)

Concatenates all the barcode sequences with BARCODE_DELIMITER

Parameters:

barcodes -

Returns:

A single string representation of all the barcodes

stringSeqsToString

public static java.lang.String stringSeqsToString(java.lang.String[] barcodes,
                                                  java.lang.String delim)

byteArrayToString

public static java.lang.String byteArrayToString(byte[][] barcodes,
                                                 java.lang.String delim)

Concatenates all the barcode sequences with BARCODE_DELIMITER

Parameters:

barcodes -

Returns:

A single string representation of all the barcodes