htsjdk.samtools

Class SAMUtils

java.lang.Object

htsjdk.samtools.SAMUtils

public final class SAMUtils
extends java.lang.Object

Utilty methods.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_PHRED_SCORE

Constructor Summary

Constructors

Constructor and Description
SAMUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	calculateReadGroupRecordChecksum(java.io.File input, java.io.File referenceFasta) Calculate a hash code from identifying information in the RG (read group) records in a SAM file's header.
static void	chainSAMProgramRecord(SAMFileHeader header, SAMProgramRecord program) Chains program in front of the first "head" item in the list of SAMProgramRecords in header.
static boolean	cigarMapsNoBasesToRef(Cigar cigar) Determines if a cigar has any element that both consumes read bases and consumes reference bases (e.g.
static int	combineMapqs(int m1, int m2) Hokey algorithm for combining two MAPQs into values that are comparable, being cognizant of the fact that in MAPQ world, 1 > 255 > 0.
static int	compareMapqs(int mapq1, int mapq2)
static byte[]	compressedBasesToBytes(int length, byte[] compressedBases, int compressedOffset) Convert from a byte array with basese stored in nybbles, with =, A, C, G, T represented as 0, 1, 2, 4, 8, 15, to a a byte array containing =AaCcGgTtNn represented as ASCII.
static void	fastqToPhred(byte[] fastq) Converts printable qualities in Sanger fastq format to binary phred scores.
static int	fastqToPhred(char ch) Convert a single printable ASCII FASTQ format phred score to binary phred score.
static byte[]	fastqToPhred(java.lang.String fastq) Convert a string with phred scores in printable ASCII FASTQ format to an array of binary phred scores.
static long	findVirtualOffsetOfFirstRecordInBam(java.io.File bamFile) Returns the virtual file offset of the first record in a BAM file - i.e.
static java.util.List<AlignmentBlock>	getAlignmentBlocks(Cigar cigar, int alignmentStart, java.lang.String cigarTypeName) Given a Cigar, Returns blocks of the sequence that have been aligned directly to the reference sequence.
static java.lang.String	getCanonicalRecordName(SAMRecord record) Returns a string that is the the read group ID and read name separated by a colon.
static java.util.List<AlignmentBlock>	getMateAlignmentBlocks(SAMRecord rec)
static int	getMateAlignmentEnd(SAMRecord rec) This method uses the MateCigar value as determined from the attribute MC.
static Cigar	getMateCigar(SAMRecord rec) Returns the Mate Cigar or null if there is none.
static Cigar	getMateCigar(SAMRecord rec, boolean withValidation) Returns the Mate Cigar or null if there is none.
static int	getMateCigarLength(SAMRecord rec)
static java.lang.String	getMateCigarString(SAMRecord rec) Returns the Mate Cigar String as stored in the attribute 'MC'.
static int	getMateUnclippedEnd(SAMRecord rec)
static int	getMateUnclippedStart(SAMRecord rec)
static int	getUnclippedEnd(int alignmentEnd, Cigar cigar)
static int	getUnclippedStart(int alignmentStart, Cigar cigar)
static boolean	hasMateCigar(SAMRecord rec) Checks to see if it is valid for this record to have a mate CIGAR (MC) and then if there is a mate CIGAR available.
static void	makeReadUnmapped(SAMRecord rec)
static java.lang.String	phredToFastq(byte[] data) Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.
static java.lang.String	phredToFastq(byte[] buffer, int offset, int length) Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.
static char	phredToFastq(int phredScore) Convert a single binary phred score to printable ASCII representation, ala FASTQ format.
static void	processValidationError(SAMValidationError validationError, ValidationStringency validationStringency)
static void	processValidationErrors(java.util.List<SAMValidationError> validationErrors, long samRecordIndex, ValidationStringency validationStringency) Handle a list of validation errors according to the validation stringency.
static boolean	recordMapsEntirelyBeyondEndOfReference(SAMRecord record) Tests if the provided record is mapped entirely beyond the end of the reference (i.e., the alignment start is greater than the length of the sequence to which the record is mapped).
static java.util.List<SAMValidationError>	validateCigar(SAMRecord rec, Cigar cigar, java.lang.Integer referenceIndex, java.util.List<AlignmentBlock> alignmentBlocks, long recordNumber, java.lang.String cigarTypeName) Run all validations of the mate's CIGAR.
static java.util.List<SAMValidationError>	validateMateCigar(SAMRecord rec, long recordNumber) Run all validations of the mate's CIGAR.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_PHRED_SCORE

public static final int MAX_PHRED_SCORE

See Also:

Constant Field Values

Constructor Detail

SAMUtils

public SAMUtils()

Method Detail

compressedBasesToBytes

public static byte[] compressedBasesToBytes(int length,
                            byte[] compressedBases,
                            int compressedOffset)

Convert from a byte array with basese stored in nybbles, with =, A, C, G, T represented as 0, 1, 2, 4, 8, 15, to a a byte array containing =AaCcGgTtNn represented as ASCII.

Parameters:

length - Number of bases (not bytes) to convert.

compressedBases - Bases represented as nybbles, in BAM binary format.

compressedOffset - Byte offset in compressedBases to start.

Returns:

New byte array with bases as ASCII bytes.

phredToFastq

public static java.lang.String phredToFastq(byte[] data)

Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.

Equivalent to phredToFastq(data, 0, data.length)

Parameters:

data - Array of bytes in which each byte is a binar phred score.

Returns:

String with ASCII representation of those quality scores.

phredToFastq

public static java.lang.String phredToFastq(byte[] buffer,
                            int offset,
                            int length)

Convert an array of bytes, in which each byte is a binary phred quality score, to printable ASCII representation of the quality scores, ala FASTQ format.

Parameters:

buffer - Array of bytes in which each byte is a binar phred score.

offset - Where in buffer to start conversion.

length - How many bytes of buffer to convert.

Returns:

String with ASCII representation of those quality scores.

phredToFastq

public static char phredToFastq(int phredScore)

Convert a single binary phred score to printable ASCII representation, ala FASTQ format.

Parameters:

phredScore - binary phred score.

Returns:

Printable ASCII representation of phred score.

fastqToPhred

public static byte[] fastqToPhred(java.lang.String fastq)

Convert a string with phred scores in printable ASCII FASTQ format to an array of binary phred scores.

Parameters:

fastq - Phred scores in FASTQ printable ASCII format.

Returns:

byte array of binary phred scores in which each byte corresponds to a character in the input string.

fastqToPhred

public static void fastqToPhred(byte[] fastq)

Converts printable qualities in Sanger fastq format to binary phred scores.

fastqToPhred

public static int fastqToPhred(char ch)

Convert a single printable ASCII FASTQ format phred score to binary phred score.

Parameters:

ch - Printable ASCII FASTQ format phred score.

Returns:

Binary phred score.

processValidationErrors

public static void processValidationErrors(java.util.List<SAMValidationError> validationErrors,
                           long samRecordIndex,
                           ValidationStringency validationStringency)

Handle a list of validation errors according to the validation stringency.

Parameters:

validationErrors - List of errors to report, or null if there are no errors.

samRecordIndex - Record number of the SAMRecord corresponding to the validation errors, or -1 if the record number is not known.

validationStringency - If STRICT, throw a SAMFormatException. If LENIENT, print the validation errors to stderr. If SILENT, do nothing.

processValidationError

public static void processValidationError(SAMValidationError validationError,
                          ValidationStringency validationStringency)

calculateReadGroupRecordChecksum

public static java.lang.String calculateReadGroupRecordChecksum(java.io.File input,
                                                java.io.File referenceFasta)

Calculate a hash code from identifying information in the RG (read group) records in a SAM file's header. This hash code changes any time read groups are added or removed. Comparing one file's hash code to another's tells you if the read groups in the BAM files are different.

chainSAMProgramRecord

public static void chainSAMProgramRecord(SAMFileHeader header,
                         SAMProgramRecord program)

Chains program in front of the first "head" item in the list of SAMProgramRecords in header. This method should not be used when there are multiple chains of program groups in a header, only when it can safely be assumed that there is only one chain. It correctly handles the case where program has already been added to the header, so it can be used whether creating a SAMProgramRecord with a constructor or when calling SAMFileHeader.createProgramRecord().

makeReadUnmapped

public static void makeReadUnmapped(SAMRecord rec)

cigarMapsNoBasesToRef

public static boolean cigarMapsNoBasesToRef(Cigar cigar)

Determines if a cigar has any element that both consumes read bases and consumes reference bases (e.g. is not all soft-clipped)

recordMapsEntirelyBeyondEndOfReference

public static boolean recordMapsEntirelyBeyondEndOfReference(SAMRecord record)

Tests if the provided record is mapped entirely beyond the end of the reference (i.e., the alignment start is greater than the length of the sequence to which the record is mapped).

compareMapqs

public static int compareMapqs(int mapq1,
               int mapq2)

Returns:

negative if mapq1 < mapq2, etc. Note that MAPQ(0) < MAPQ(255) < MAPQ(1)

combineMapqs

public static int combineMapqs(int m1,
               int m2)

Hokey algorithm for combining two MAPQs into values that are comparable, being cognizant of the fact that in MAPQ world, 1 > 255 > 0. In this algorithm, 255 is treated as if it were 0.01, so that CombinedMapq(1,0) > CombinedMapq(255, 255) > CombinedMapq(0, 0). The return value should not be used for anything other than comparing to the return value of other invocations of this method.

findVirtualOffsetOfFirstRecordInBam

public static long findVirtualOffsetOfFirstRecordInBam(java.io.File bamFile)

Returns the virtual file offset of the first record in a BAM file - i.e. the virtual file offset after skipping over the text header and the sequence records.

getAlignmentBlocks

public static java.util.List<AlignmentBlock> getAlignmentBlocks(Cigar cigar,
                                                int alignmentStart,
                                                java.lang.String cigarTypeName)

Given a Cigar, Returns blocks of the sequence that have been aligned directly to the reference sequence. Note that clipped portions, and inserted and deleted bases (vs. the reference) are not represented in the alignment blocks.

Parameters:

cigar - The cigar containing the alignment information

alignmentStart - The start (1-based) of the alignment

cigarTypeName - The type of cigar passed - for error logging.

Returns:

List of alignment blocks

getUnclippedStart

public static int getUnclippedStart(int alignmentStart,
                    Cigar cigar)

Parameters:

alignmentStart - The start (1-based) of the alignment

cigar - The cigar containing the alignment information

Returns:

the alignment start (1-based, inclusive) adjusted for clipped bases. For example if the read has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped) then this method will return 96.

Invalid to call on an unmapped read. Invalid to call with cigar = null

getUnclippedEnd

public static int getUnclippedEnd(int alignmentEnd,
                  Cigar cigar)

Parameters:

alignmentEnd - The end (1-based) of the alignment

cigar - The cigar containing the alignment information

Returns:

the alignment end (1-based, inclusive) adjusted for clipped bases. For example if the read has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped) then this method will return 107.

Invalid to call on an unmapped read. Invalid to call with cigar = null

getMateCigarString

public static java.lang.String getMateCigarString(SAMRecord rec)

Returns the Mate Cigar String as stored in the attribute 'MC'.

Parameters:

rec - the SAM record

Returns:

Mate Cigar String, or null if there is none.

getMateCigar

public static Cigar getMateCigar(SAMRecord rec,
                 boolean withValidation)

Returns the Mate Cigar or null if there is none.

Parameters:

rec - the SAM record

withValidation - true if we are to validate the mate cigar before returning, false otherwise.

Returns:

Cigar object for the read's mate, or null if there is none.

getMateCigar

public static Cigar getMateCigar(SAMRecord rec)

Returns the Mate Cigar or null if there is none. No validation is done on the returned cigar.

Parameters:

rec - the SAM record

Returns:

Cigar object for the read's mate, or null if there is none.

getMateCigarLength

public static int getMateCigarLength(SAMRecord rec)

Parameters:

rec - the SAM record

Returns:

number of cigar elements (number + operator) in the mate cigar string.

getMateAlignmentEnd

public static int getMateAlignmentEnd(SAMRecord rec)

This method uses the MateCigar value as determined from the attribute MC. It must be non-null.

Parameters:

rec - the SAM record

Returns:

1-based inclusive rightmost position of the clipped mate sequence, or 0 read if unmapped.

getMateUnclippedStart

public static int getMateUnclippedStart(SAMRecord rec)

Parameters:

rec - the SAM record

Returns:

the mate alignment start (1-based, inclusive) adjusted for clipped bases. For example if the mate has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped) then this method will return 96.

Invalid to call on an unmapped read.

getMateUnclippedEnd

public static int getMateUnclippedEnd(SAMRecord rec)

Parameters:

rec - the SAM record

Returns:

the mate alignment end (1-based, inclusive) adjusted for clipped bases. For example if the mate has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped) then this method will return 107.

Invalid to call on an unmapped read.

getMateAlignmentBlocks

public static java.util.List<AlignmentBlock> getMateAlignmentBlocks(SAMRecord rec)

Parameters:

rec - the SAM record Returns blocks of the mate sequence that have been aligned directly to the reference sequence. Note that clipped portions of the mate and inserted and deleted bases (vs. the reference) are not represented in the alignment blocks.

validateCigar

public static java.util.List<SAMValidationError> validateCigar(SAMRecord rec,
                                               Cigar cigar,
                                               java.lang.Integer referenceIndex,
                                               java.util.List<AlignmentBlock> alignmentBlocks,
                                               long recordNumber,
                                               java.lang.String cigarTypeName)

Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.

Parameters:

rec - the SAM record

cigar - The cigar containing the alignment information

referenceIndex - The reference index

alignmentBlocks - The alignment blocks (parsed from the cigar)

recordNumber - For error reporting. -1 if not known.

cigarTypeName - For error reporting. "Read CIGAR" or "Mate Cigar"

Returns:

List of errors, or null if no errors.

validateMateCigar

public static java.util.List<SAMValidationError> validateMateCigar(SAMRecord rec,
                                                   long recordNumber)

Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.

Parameters:

rec - the SAM record

recordNumber - For error reporting. -1 if not known.

Returns:

List of errors, or null if no errors.

hasMateCigar

public static boolean hasMateCigar(SAMRecord rec)

Checks to see if it is valid for this record to have a mate CIGAR (MC) and then if there is a mate CIGAR available. This is done by checking that this record is paired, its mate is mapped, and that it returns a non-null mate CIGAR.

Parameters:

rec -

Returns:

getCanonicalRecordName

public static java.lang.String getCanonicalRecordName(SAMRecord record)

Returns a string that is the the read group ID and read name separated by a colon. This is meant to cannonically identify a given record within a set of records.

Parameters:

record -

Returns: