Package picard.util
Class IlluminaUtil
java.lang.Object
picard.util.IlluminaUtil
Misc utilities for working with Illumina specific files and data
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
Describes adapters used on each pair of strands -
Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic 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 Details
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BARCODE_DELIMITER
- See Also:
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Constructor Details
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IlluminaUtil
public IlluminaUtil()
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Method Details
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getTileFromReadName
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
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. -
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
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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barcodeSeqsToString
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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barcodeSeqsToString
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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stringSeqsToString
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byteArrayToString
Concatenates all the barcode sequences with BARCODE_DELIMITER- Parameters:
barcodes
-- Returns:
- A single string representation of all the barcodes
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