SequenceUtil (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.util.SequenceUtil

public class SequenceUtil
extends java.lang.Object

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SequenceUtil.SequenceListsDifferException

Nested Classes
Modifier and Type	Class and Description
`static class`	`SequenceUtil.SequenceListsDifferException`

Field Summary

Fields
Modifier and Type	Field and Description
`static byte`	`a` Byte typed variables for all normal bases.
`static byte`	`A` Byte typed variables for all normal bases.
`static byte`	`c` Byte typed variables for all normal bases.
`static byte`	`C` Byte typed variables for all normal bases.
`static byte`	`g` Byte typed variables for all normal bases.
`static byte`	`G` Byte typed variables for all normal bases.
`static byte`	`n` Byte typed variables for all normal bases.
`static byte`	`N` Byte typed variables for all normal bases.
`static byte`	`t` Byte typed variables for all normal bases.
`static byte`	`T` Byte typed variables for all normal bases.
`static byte[]`	`VALID_BASES_LOWER`
`static byte[]`	`VALID_BASES_UPPER`

Constructor Summary

Constructors
Constructor and Description

SequenceUtil()

Constructors
Constructor and Description
`SequenceUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`areSequenceDictionariesEqual(SAMSequenceDictionary s1, SAMSequenceDictionary s2)` Returns true if both parameters are null or equal, otherwise returns false
`static void`	`assertSequenceDictionariesEqual(SAMSequenceDictionary s1, SAMSequenceDictionary s2)` Throws an exception if both parameters are non-null and unequal.
`static void`	`assertSequenceDictionariesEqual(SAMSequenceDictionary s1, SAMSequenceDictionary s2, boolean checkPrefixOnly)` Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only).
`static void`	`assertSequenceDictionariesEqual(SAMSequenceDictionary s1, SAMSequenceDictionary s2, java.io.File f1, java.io.File f2)` Throws an exception if both parameters are non-null and unequal, including the filenames.
`static void`	`assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1, java.util.List<SAMSequenceRecord> s2)` default signature that forces the lists to be the same size
`static void`	`assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1, java.util.List<SAMSequenceRecord> s2, boolean checkPrefixOnly)` Throws an exception only if both (first) parameters are not null optionally check that one list is a (nonempty) prefix of the other.
`static boolean`	`basesEqual(byte lhs, byte rhs)` Efficiently compare two IUPAC base codes, simply returning true if they are equal (ignoring case), without considering the set relationships between ambiguous codes.
`static boolean`	`bisulfiteBasesEqual(boolean negativeStrand, byte read, byte reference)` Returns true if the bases are equal OR if the mismatch can be accounted for by bisulfite treatment.
`static boolean`	`bisulfiteBasesEqual(byte read, byte reference)`
`static boolean`	`bisulfiteBasesMatchWithAmbiguity(boolean negativeStrand, byte read, byte reference)` Same as above, but use `readBaseMatchesRefBaseWithAmbiguity` instead of `basesEqual`.
`static double`	`calculateGc(byte[] bases)` Calculates the fraction of bases that are G/C in the sequence.
`static byte[]`	`calculateMD5(byte[] data, int offset, int len)`
`static java.lang.String`	`calculateMD5String(byte[] data)`
`static java.lang.String`	`calculateMD5String(byte[] data, int offset, int len)`
`static void`	`calculateMdAndNmTags(SAMRecord record, byte[] ref, boolean calcMD, boolean calcNM)` Calculate MD and NM similarly to Samtools, except that N->N is a match.
`static int`	`calculateSamNmTag(SAMRecord read, byte[] referenceBases)` Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
`static int`	`calculateSamNmTag(SAMRecord read, byte[] referenceBases, int referenceOffset)` Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
`static int`	`calculateSamNmTag(SAMRecord read, byte[] referenceBases, int referenceOffset, boolean bisulfiteSequence)` Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see `readBaseMatchesRefBaseWithAmbiguity` method).
`static int`	`calculateSamNmTagFromCigar(SAMRecord record)` Attempts to calculate the predefined NM tag from the SAM spec using the cigar string alone.
`static byte`	`complement(byte b)` Returns the complement of a single byte.
`static int`	`countDeletedBases(Cigar cigar)`
`static int`	`countDeletedBases(SAMRecord read)`
`static int`	`countInsertedBases(Cigar cigar)`
`static int`	`countInsertedBases(SAMRecord read)`
`static int`	`countMismatches(SAMRecord read, byte[] referenceBases)` Calculates the number of mismatches between the read and the reference sequence provided.
`static int`	`countMismatches(SAMRecord read, byte[] referenceBases, boolean bisulfiteSequence)` Calculates the number of mismatches between the read and the reference sequence provided.
`static int`	`countMismatches(SAMRecord read, byte[] referenceBases, int referenceOffset)` Calculates the number of mismatches between the read and the reference sequence provided.
`static int`	`countMismatches(SAMRecord read, byte[] referenceBases, int referenceOffset, boolean bisulfiteSequence)` Calculates the number of mismatches between the read and the reference sequence provided.
`static int`	`countMismatches(SAMRecord read, byte[] referenceBases, int referenceOffset, boolean bisulfiteSequence, boolean matchAmbiguousRef)`
`static java.util.List<byte[]>`	`generateAllKmers(int length)` Generates all possible unambiguous kmers (upper-case) of length and returns them as byte[]s.
`static java.lang.String`	`getSamReadNameFromFastqHeader(java.lang.String fastqHeader)` Returns a read name from a FASTQ header string suitable for use in a SAM/BAM file.
`static boolean`	`isBisulfiteConverted(byte read, byte reference)`
`static boolean`	`isBisulfiteConverted(byte read, byte reference, boolean negativeStrand)` Checks for bisulfite conversion, C->T on the positive strand and G->A on the negative strand.
`static boolean`	`isNoCall(byte base)` returns true if the value of base represents a no call
`static boolean`	`isValidBase(byte b)` Returns true if the byte is in [acgtACGT].
`static java.lang.String`	`makeCigarStringWithIndelPossibleClipping(int alignmentStart, int readLength, int referenceSequenceLength, int indelPosition, int indelLength)` Create a cigar string for a gapped alignment, which may have soft clipping at either end
`static java.lang.String`	`makeCigarStringWithPossibleClipping(int alignmentStart, int readLength, int referenceSequenceLength)` Create a simple ungapped cigar string, which might have soft clipping at either end
`static byte[]`	`makeReferenceFromAlignment(SAMRecord rec, boolean includeReferenceBasesForDeletions)` Produce reference bases from an aligned SAMRecord with MD string and Cigar.
`static java.lang.String`	`makeSoftClipCigar(int clipLength)`
`static boolean`	`readBaseMatchesRefBaseWithAmbiguity(byte readBase, byte refBase)` Efficiently compare two IUPAC base codes, one coming from a read sequence and the other coming from a reference sequence, using the reference code as a 'pattern' that the read base must match.
`static void`	`reverse(byte[] array, int offset, int len)`
`static void`	`reverseComplement(byte[] bases)` Reverses and complements the bases in place.
`static void`	`reverseComplement(byte[] bases, int offset, int len)`
`static java.lang.String`	`reverseComplement(java.lang.String sequenceData)` Calculate the reverse complement of the specified sequence (Stolen from Reseq)
`static void`	`reverseQualities(byte[] quals)` Reverses the quals in place.
`static int`	`sumQualitiesOfMismatches(SAMRecord read, byte[] referenceBases)` Calculates the sum of qualities for mismatched bases in the read.
`static int`	`sumQualitiesOfMismatches(SAMRecord read, byte[] referenceBases, int referenceOffset)` Calculates the sum of qualities for mismatched bases in the read.
`static int`	`sumQualitiesOfMismatches(SAMRecord read, byte[] referenceBases, int referenceOffset, boolean bisulfiteSequence)` Calculates the sum of qualities for mismatched bases in the read.
`static byte`	`upperCase(byte base)`
`static byte[]`	`upperCase(byte[] bases)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - a
```
public static final byte a
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    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - c
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public static final byte c
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - g
```
public static final byte g
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - t
```
public static final byte t
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - n
```
public static final byte n
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - A
```
public static final byte A
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - C
```
public static final byte C
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - G
```
public static final byte G
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - T
```
public static final byte T
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - N
```
public static final byte N
```
    Byte typed variables for all normal bases.
    
    See Also:
    
    Constant Field Values
  - VALID_BASES_UPPER
```
public static final byte[] VALID_BASES_UPPER
```
  - VALID_BASES_LOWER
```
public static final byte[] VALID_BASES_LOWER
```
- Constructor Detail
  - SequenceUtil
```
public SequenceUtil()
```
- Method Detail
  - reverseComplement
```
public static java.lang.String reverseComplement(java.lang.String sequenceData)
```
    Calculate the reverse complement of the specified sequence (Stolen from Reseq)
    
    Parameters:
    
    sequenceData -
    
    Returns:
    
    reverse complement
  - basesEqual
```
public static boolean basesEqual(byte lhs,
                                 byte rhs)
```
    Efficiently compare two IUPAC base codes, simply returning true if they are equal (ignoring case), without considering the set relationships between ambiguous codes.
  - readBaseMatchesRefBaseWithAmbiguity
```
public static boolean readBaseMatchesRefBaseWithAmbiguity(byte readBase,
                                                          byte refBase)
```
    Efficiently compare two IUPAC base codes, one coming from a read sequence and the other coming from a reference sequence, using the reference code as a 'pattern' that the read base must match. We take ambiguous codes into account, returning true if the set of possible bases represented by the read value is a (non-strict) subset of the possible bases represented by the reference value. Since the comparison is directional, make sure to pass read / ref codes in correct order.
  - isNoCall
```
public static boolean isNoCall(byte base)
```
    returns true if the value of base represents a no call
  - isValidBase
```
public static boolean isValidBase(byte b)
```
    Returns true if the byte is in [acgtACGT].
  - calculateGc
```
public static double calculateGc(byte[] bases)
```
    Calculates the fraction of bases that are G/C in the sequence.
  - assertSequenceListsEqual
```
public static void assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
                                            java.util.List<SAMSequenceRecord> s2)
```
    default signature that forces the lists to be the same size
    
    Parameters:
    
    s1 - a list of sequence headers
    
    s2 - a second list of sequence headers
  - assertSequenceListsEqual
```
public static void assertSequenceListsEqual(java.util.List<SAMSequenceRecord> s1,
                                            java.util.List<SAMSequenceRecord> s2,
                                            boolean checkPrefixOnly)
```
    Throws an exception only if both (first) parameters are not null optionally check that one list is a (nonempty) prefix of the other.
    
    Parameters:
    
    s1 - a list of sequence headers
    
    s2 - a second list of sequence headers
    
    checkPrefixOnly - a flag specifying whether to only look at the first records in the lists. This will then check that the records of the smaller dictionary are equal to the records of the beginning of the larger dictionary, which can be useful since sometimes different pipelines choose to use only the first contigs of a standard reference.
  - areSequenceDictionariesEqual
```
public static boolean areSequenceDictionariesEqual(SAMSequenceDictionary s1,
                                                   SAMSequenceDictionary s2)
```
    Returns true if both parameters are null or equal, otherwise returns false
    
    Parameters:
    
    s1 - a list of sequence headers
    
    s2 - a second list of sequence headers
  - assertSequenceDictionariesEqual
```
public static void assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
                                                   SAMSequenceDictionary s2)
```
    Throws an exception if both parameters are non-null and unequal.
    
    Parameters:
    
    s1 - a list of sequence headers
    
    s2 - a second list of sequence headers
  - assertSequenceDictionariesEqual
```
public static void assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
                                                   SAMSequenceDictionary s2,
                                                   boolean checkPrefixOnly)
```
    Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only).
    
    Parameters:
    
    s1 - a list of sequence headers
    
    s2 - a second list of sequence headers
    
    checkPrefixOnly - a flag specifying whether to only look at the first records in the lists. This will then check that the records of the smaller dictionary are equal to the records of the beginning of the larger dictionary, which can be useful since sometimes different pipelines choose to use only the first contigs of a standard reference.
  - assertSequenceDictionariesEqual
```
public static void assertSequenceDictionariesEqual(SAMSequenceDictionary s1,
                                                   SAMSequenceDictionary s2,
                                                   java.io.File f1,
                                                   java.io.File f2)
```
    Throws an exception if both parameters are non-null and unequal, including the filenames.
  - makeCigarStringWithPossibleClipping
```
public static java.lang.String makeCigarStringWithPossibleClipping(int alignmentStart,
                                                                   int readLength,
                                                                   int referenceSequenceLength)
```
    Create a simple ungapped cigar string, which might have soft clipping at either end
    
    Parameters:
    
    alignmentStart - raw aligment start, which may result in read hanging off beginning or end of read
    
    Returns:
    
    cigar string that may have S operator at beginning or end, and has M operator for the rest of the read
  - makeCigarStringWithIndelPossibleClipping
```
public static java.lang.String makeCigarStringWithIndelPossibleClipping(int alignmentStart,
                                                                        int readLength,
                                                                        int referenceSequenceLength,
                                                                        int indelPosition,
                                                                        int indelLength)
```
    Create a cigar string for a gapped alignment, which may have soft clipping at either end
    
    Parameters:
    
    alignmentStart - raw alignment start, which may result in read hanging off beginning or end of read
    
    readLength -
    
    referenceSequenceLength -
    
    indelPosition - number of matching bases before indel. Must be > 0
    
    indelLength - length of indel. Positive for insertion, negative for deletion.
    
    Returns:
    
    cigar string that may have S operator at beginning or end, has one or two M operators, and an I or a D.
  - makeSoftClipCigar
```
public static java.lang.String makeSoftClipCigar(int clipLength)
```
  - countMismatches
```
public static int countMismatches(SAMRecord read,
                                  byte[] referenceBases)
```
    Calculates the number of mismatches between the read and the reference sequence provided.
  - countMismatches
```
public static int countMismatches(SAMRecord read,
                                  byte[] referenceBases,
                                  int referenceOffset)
```
    Calculates the number of mismatches between the read and the reference sequence provided.
  - countMismatches
```
public static int countMismatches(SAMRecord read,
                                  byte[] referenceBases,
                                  int referenceOffset,
                                  boolean bisulfiteSequence)
```
    Calculates the number of mismatches between the read and the reference sequence provided.
    
    Parameters:
    
    referenceBases - Array of ASCII bytes that covers at least the the portion of the reference sequence to which read is aligned from getReferenceStart to getReferenceEnd.
    
    referenceOffset - 0-based offset of the first element of referenceBases relative to the start of that reference sequence.
    
    bisulfiteSequence - If this is true, it is assumed that the reads were bisulfite treated and C->T on the positive strand and G->A on the negative strand will not be counted as mismatches.
  - countMismatches
```
public static int countMismatches(SAMRecord read,
                                  byte[] referenceBases,
                                  int referenceOffset,
                                  boolean bisulfiteSequence,
                                  boolean matchAmbiguousRef)
```
  - countMismatches
```
public static int countMismatches(SAMRecord read,
                                  byte[] referenceBases,
                                  boolean bisulfiteSequence)
```
    Calculates the number of mismatches between the read and the reference sequence provided.
    
    Parameters:
    
    referenceBases - Array of ASCII bytes that covers at least the the portion of the reference sequence to which read is aligned from getReferenceStart to getReferenceEnd.
    
    bisulfiteSequence - If this is true, it is assumed that the reads were bisulfite treated and C->T on the positive strand and G->A on the negative strand will not be counted as mismatches.
  - sumQualitiesOfMismatches
```
public static int sumQualitiesOfMismatches(SAMRecord read,
                                           byte[] referenceBases)
```
    Calculates the sum of qualities for mismatched bases in the read.
    
    Parameters:
    
    referenceBases - Array of ASCII bytes in which the 0th position in the array corresponds to the first element of the reference sequence to which read is aligned.
  - sumQualitiesOfMismatches
```
public static int sumQualitiesOfMismatches(SAMRecord read,
                                           byte[] referenceBases,
                                           int referenceOffset)
```
    Calculates the sum of qualities for mismatched bases in the read.
    
    Parameters:
    
    referenceBases - Array of ASCII bytes that covers at least the the portion of the reference sequence to which read is aligned from getReferenceStart to getReferenceEnd.
    
    referenceOffset - 0-based offset of the first element of referenceBases relative to the start of that reference sequence.
  - sumQualitiesOfMismatches
```
public static int sumQualitiesOfMismatches(SAMRecord read,
                                           byte[] referenceBases,
                                           int referenceOffset,
                                           boolean bisulfiteSequence)
```
    Calculates the sum of qualities for mismatched bases in the read.
    
    Parameters:
    
    referenceBases - Array of ASCII bytes that covers at least the the portion of the reference sequence to which read is aligned from getReferenceStart to getReferenceEnd.
    
    referenceOffset - 0-based offset of the first element of referenceBases relative to the start of that reference sequence.
    
    bisulfiteSequence - If this is true, it is assumed that the reads were bisulfite treated and C->T on the positive strand and G->A on the negative strand will not be counted as mismatches.
  - countInsertedBases
```
public static int countInsertedBases(Cigar cigar)
```
  - countDeletedBases
```
public static int countDeletedBases(Cigar cigar)
```
  - countInsertedBases
```
public static int countInsertedBases(SAMRecord read)
```
  - countDeletedBases
```
public static int countDeletedBases(SAMRecord read)
```
  - calculateSamNmTag
```
public static int calculateSamNmTag(SAMRecord read,
                                    byte[] referenceBases)
```
    Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
  - calculateSamNmTag
```
public static int calculateSamNmTag(SAMRecord read,
                                    byte[] referenceBases,
                                    int referenceOffset)
```
    Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
    
    Parameters:
    
    referenceOffset - 0-based offset of the first element of referenceBases relative to the start of that reference sequence.
  - calculateSamNmTag
```
public static int calculateSamNmTag(SAMRecord read,
                                    byte[] referenceBases,
                                    int referenceOffset,
                                    boolean bisulfiteSequence)
```
    Calculates the predefined NM tag from the SAM spec: (# of mismatches + # of indels) For the purposes for calculating mismatches, we do not yet support IUPAC ambiguous codes (see readBaseMatchesRefBaseWithAmbiguity method).
    
    Parameters:
    
    referenceOffset - 0-based offset of the first element of referenceBases relative to the start of that reference sequence.
    
    bisulfiteSequence - If this is true, it is assumed that the reads were bisulfite treated and C->T on the positive strand and G->A on the negative strand will not be counted as mismatches.
  - calculateSamNmTagFromCigar
```
public static int calculateSamNmTagFromCigar(SAMRecord record)
```
    Attempts to calculate the predefined NM tag from the SAM spec using the cigar string alone. It may calculate incorrectly if ambiguous operators (Like M) are used. Needed for testing infrastructure: SAMRecordSetBuilder
  - complement
```
public static byte complement(byte b)
```
    Returns the complement of a single byte.
  - reverseComplement
```
public static void reverseComplement(byte[] bases)
```
    Reverses and complements the bases in place.
  - reverseQualities
```
public static void reverseQualities(byte[] quals)
```
    Reverses the quals in place.
  - bisulfiteBasesEqual
```
public static boolean bisulfiteBasesEqual(boolean negativeStrand,
                                          byte read,
                                          byte reference)
```
    Returns true if the bases are equal OR if the mismatch can be accounted for by bisulfite treatment. C->T on the positive strand and G->A on the negative strand do not count as mismatches.
  - bisulfiteBasesEqual
```
public static boolean bisulfiteBasesEqual(byte read,
                                          byte reference)
```
  - bisulfiteBasesMatchWithAmbiguity
```
public static boolean bisulfiteBasesMatchWithAmbiguity(boolean negativeStrand,
                                                       byte read,
                                                       byte reference)
```
    Same as above, but use readBaseMatchesRefBaseWithAmbiguity instead of basesEqual. Note that isBisulfiteConverted is not affected because it only applies when the reference base is non-ambiguous.
  - isBisulfiteConverted
```
public static boolean isBisulfiteConverted(byte read,
                                           byte reference,
                                           boolean negativeStrand)
```
    Checks for bisulfite conversion, C->T on the positive strand and G->A on the negative strand.
  - isBisulfiteConverted
```
public static boolean isBisulfiteConverted(byte read,
                                           byte reference)
```
  - makeReferenceFromAlignment
```
public static byte[] makeReferenceFromAlignment(SAMRecord rec,
                                                boolean includeReferenceBasesForDeletions)
```
    Produce reference bases from an aligned SAMRecord with MD string and Cigar.
    
    Parameters:
    
    rec - Must contain non-empty CIGAR and MD attribute.
    
    includeReferenceBasesForDeletions - If true, include reference bases that are deleted in the read. This will make the returned array not line up with the read if there are deletions.
    
    Returns:
    
    References bases corresponding to the read. If there is an insertion in the read, reference contains '-'. If the read is soft-clipped, reference contains '0'. If there is a skipped region and includeReferenceBasesForDeletions==true, reference will have Ns for the skipped region.
  - reverse
```
public static void reverse(byte[] array,
                           int offset,
                           int len)
```
  - reverseComplement
```
public static void reverseComplement(byte[] bases,
                                     int offset,
                                     int len)
```
  - calculateMD5String
```
public static java.lang.String calculateMD5String(byte[] data)
                                           throws java.security.NoSuchAlgorithmException
```
    Throws:
    
    java.security.NoSuchAlgorithmException
  - calculateMD5String
```
public static java.lang.String calculateMD5String(byte[] data,
                                                  int offset,
                                                  int len)
```
  - calculateMD5
```
public static byte[] calculateMD5(byte[] data,
                                  int offset,
                                  int len)
```
  - calculateMdAndNmTags
```
public static void calculateMdAndNmTags(SAMRecord record,
                                        byte[] ref,
                                        boolean calcMD,
                                        boolean calcNM)
```
    Calculate MD and NM similarly to Samtools, except that N->N is a match.
    
    Parameters:
    
    record - Input record for which to calculate NM and MD. The appropriate tags will be added/updated in the record
    
    ref - The reference bases for the sequence to which the record is mapped
    
    calcMD - A flag indicating whether to update the MD tag in the record
    
    calcNM - A flag indicating whether to update the NM tag in the record
  - upperCase
```
public static byte upperCase(byte base)
```
  - upperCase
```
public static byte[] upperCase(byte[] bases)
```
  - generateAllKmers
```
public static java.util.List<byte[]> generateAllKmers(int length)
```
    Generates all possible unambiguous kmers (upper-case) of length and returns them as byte[]s.
  - getSamReadNameFromFastqHeader
```
public static java.lang.String getSamReadNameFromFastqHeader(java.lang.String fastqHeader)
```
    Returns a read name from a FASTQ header string suitable for use in a SAM/BAM file. Any letters after the first space are ignored. Ths method also strips trailing "/1" or "/2" so that paired end reads have the same name.
    
    Parameters:
    
    fastqHeader - the header from a FastqRecord.
    
    Returns:
    
    a read name appropriate for output in a SAM/BAM file.

Class SequenceUtil

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

a

c

g

t

n

A

C

G

T

N

VALID_BASES_UPPER

VALID_BASES_LOWER

Constructor Detail

SequenceUtil

Method Detail

reverseComplement

basesEqual

readBaseMatchesRefBaseWithAmbiguity

isNoCall

isValidBase

calculateGc

assertSequenceListsEqual

assertSequenceListsEqual

areSequenceDictionariesEqual

assertSequenceDictionariesEqual

assertSequenceDictionariesEqual

assertSequenceDictionariesEqual

makeCigarStringWithPossibleClipping

makeCigarStringWithIndelPossibleClipping

makeSoftClipCigar

countMismatches

countMismatches

countMismatches

countMismatches

countMismatches

sumQualitiesOfMismatches

sumQualitiesOfMismatches

sumQualitiesOfMismatches

countInsertedBases

countDeletedBases

countInsertedBases

countDeletedBases

calculateSamNmTag

calculateSamNmTag

calculateSamNmTag

calculateSamNmTagFromCigar

complement

reverseComplement

reverseQualities

bisulfiteBasesEqual

bisulfiteBasesEqual

bisulfiteBasesMatchWithAmbiguity

isBisulfiteConverted

isBisulfiteConverted

makeReferenceFromAlignment

reverse

reverseComplement

calculateMD5String

calculateMD5String

calculateMD5

calculateMdAndNmTags

upperCase

upperCase

generateAllKmers

getSamReadNameFromFastqHeader