Package picard.util
Class IlluminaUtil
- java.lang.Object
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- picard.util.IlluminaUtil
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public class IlluminaUtil extends Object
Misc utilities for working with Illumina specific files and data
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
IlluminaUtil.IlluminaAdapterPair
Describes adapters used on each pair of strands
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Field Summary
Fields Modifier and Type Field Description static String
BARCODE_DELIMITER
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Constructor Summary
Constructors Constructor Description IlluminaUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static String
barcodeSeqsToString(byte[][] barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITERstatic String
barcodeSeqsToString(String[] barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITERstatic String
barcodeSeqsToString(List<String> barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITERstatic String
byteArrayToString(byte[][] barcodes, String delim)
Concatenates all the barcode sequences with BARCODE_DELIMITERstatic void
convertSolexaQualityAscii_1_1_ToPhredBinary(byte[] solexaQualities)
Converts from Solexa ASCII to Phred binary in place.static byte
getSolexaQualityCharFromFourQualities(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 Integer
getTileFromReadName(String readName)
Parse the tile # from the read name.static byte[]
makePhredBinaryFromSolexaQualityAscii_1_3(String solexaQualities)
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.static byte[]
makePhredBinaryFromSolexaQualityAscii_1_3(String solexaQualities, int offset, int length)
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.static String
stringSeqsToString(String[] barcodes, String delim)
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Field Detail
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BARCODE_DELIMITER
public static final String BARCODE_DELIMITER
- See Also:
- Constant Field Values
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Method Detail
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getTileFromReadName
public static Integer getTileFromReadName(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.
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makePhredBinaryFromSolexaQualityAscii_1_3
public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(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.
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makePhredBinaryFromSolexaQualityAscii_1_3
public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(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.
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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.
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getSolexaQualityCharFromFourQualities
public static byte getSolexaQualityCharFromFourQualities(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.
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barcodeSeqsToString
public static String barcodeSeqsToString(List<String> barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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barcodeSeqsToString
public static String barcodeSeqsToString(String[] barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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barcodeSeqsToString
public static String barcodeSeqsToString(byte[][] barcodes)
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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