htsjdk.samtools

Class SamFileHeaderMerger

java.lang.Object

htsjdk.samtools.SamFileHeaderMerger

public class SamFileHeaderMerger
extends java.lang.Object

Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups clash across input headers.

Constructor Summary

Constructors

Constructor and Description
SamFileHeaderMerger(java.util.Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder) Deprecated. replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
SamFileHeaderMerger(java.util.Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder, boolean mergeDictionaries) Deprecated. replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder, java.util.Collection<SAMFileHeader> headers, boolean mergeDictionaries) Create SAMFileHeader with additional information..

Method Summary

Modifier and Type	Method and Description
java.util.Collection<SAMFileHeader>	getHeaders() Returns the collection of readers that this header merger is working with.
SAMFileHeader	getMergedHeader() Returns the merged header that should be written to any output merged file.
java.lang.Integer	getMergedSequenceIndex(SAMFileHeader header, java.lang.Integer oldReferenceSequenceIndex) Another mechanism for getting the new sequence index, for situations in which the reader is not available.
java.lang.Integer	getMergedSequenceIndex(SamReader reader, java.lang.Integer oldReferenceSequenceIndex) Deprecated. replaced by getMergedSequenceIndex(SAMFileHeader, Integer)
java.lang.String	getProgramGroupId(SAMFileHeader header, java.lang.String originalProgramGroupId)
java.lang.String	getProgramGroupId(SamReader reader, java.lang.String originalProgramGroupId) Deprecated. replaced by getProgramGroupId(SAMFileHeader, String)
java.util.Collection<SamReader>	getReaders() Deprecated. replaced by getHeaders()
java.lang.String	getReadGroupId(SAMFileHeader header, java.lang.String originalReadGroupId) Returns the read group id that should be used for the input read and RG id.
java.lang.String	getReadGroupId(SamReader reader, java.lang.String originalReadGroupId) Deprecated. replaced by getReadGroupId(SAMFileHeader, String)
boolean	hasMergedSequenceDictionary()
boolean	hasProgramGroupCollisions() Returns true if there are program group duplicates within the merged headers.
boolean	hasReadGroupCollisions() Returns true if there are read group duplicates within the merged headers.
static java.lang.String	positiveFourDigitBase36Str(int leftOver) Convert an integer to base36, protected solely for testing

Methods inherited from class java.lang.Object

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

Constructor Detail

SamFileHeaderMerger

@Deprecated
public SamFileHeaderMerger(java.util.Collection<SamReader> readers,
                                       SAMFileHeader.SortOrder sortOrder)

Deprecated. replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)

Create SAMFileHeader with additional information. Required that sequence dictionaries agree.

Parameters:

readers - sam file readers to combine

sortOrder - sort order new header should have

SamFileHeaderMerger

@Deprecated
public SamFileHeaderMerger(java.util.Collection<SamReader> readers,
                                       SAMFileHeader.SortOrder sortOrder,
                                       boolean mergeDictionaries)

Deprecated. replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)

Create SAMFileHeader with additional information.

Parameters:

readers - sam file readers to combine

sortOrder - sort order new header should have

mergeDictionaries - If true, merge sequence dictionaries in new header. If false, require that all input sequence dictionaries be identical.

SamFileHeaderMerger

public SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder,
                           java.util.Collection<SAMFileHeader> headers,
                           boolean mergeDictionaries)

Create SAMFileHeader with additional information.. This is the preferred constructor.

Parameters:

sortOrder - sort order new header should have

headers - sam file headers to combine

mergeDictionaries - If true, merge sequence dictionaries in new header. If false, require that all input sequence dictionaries be identical.

Method Detail

positiveFourDigitBase36Str

public static java.lang.String positiveFourDigitBase36Str(int leftOver)

Convert an integer to base36, protected solely for testing

Parameters:

leftOver - Both the initial value and the running quotient

Returns:

A four digit string composed of base 36 symbols

getReadGroupId

@Deprecated
public java.lang.String getReadGroupId(SamReader reader,
                                                   java.lang.String originalReadGroupId)

Deprecated. replaced by getReadGroupId(SAMFileHeader, String)

Returns the read group id that should be used for the input read and RG id.

getReadGroupId

public java.lang.String getReadGroupId(SAMFileHeader header,
                                       java.lang.String originalReadGroupId)

Returns the read group id that should be used for the input read and RG id.

getProgramGroupId

@Deprecated
public java.lang.String getProgramGroupId(SamReader reader,
                                                      java.lang.String originalProgramGroupId)

Deprecated. replaced by getProgramGroupId(SAMFileHeader, String)

Parameters:

reader - one of the input files

originalProgramGroupId - a program group ID from the above input file

Returns:

new ID from the merged list of program groups in the output file

getProgramGroupId

public java.lang.String getProgramGroupId(SAMFileHeader header,
                                          java.lang.String originalProgramGroupId)

Parameters:

header - one of the input headers

originalProgramGroupId - a program group ID from the above input file

Returns:

new ID from the merged list of program groups in the output file

hasReadGroupCollisions

public boolean hasReadGroupCollisions()

Returns true if there are read group duplicates within the merged headers.

hasProgramGroupCollisions

public boolean hasProgramGroupCollisions()

Returns true if there are program group duplicates within the merged headers.

hasMergedSequenceDictionary

public boolean hasMergedSequenceDictionary()

Returns:

if we've merged the sequence dictionaries, return true

getMergedHeader

public SAMFileHeader getMergedHeader()

Returns the merged header that should be written to any output merged file.

getReaders

@Deprecated
public java.util.Collection<SamReader> getReaders()

Deprecated. replaced by getHeaders()

Returns the collection of readers that this header merger is working with. May return null.

getHeaders

public java.util.Collection<SAMFileHeader> getHeaders()

Returns the collection of readers that this header merger is working with.

getMergedSequenceIndex

@Deprecated
public java.lang.Integer getMergedSequenceIndex(SamReader reader,
                                                            java.lang.Integer oldReferenceSequenceIndex)

Deprecated. replaced by getMergedSequenceIndex(SAMFileHeader, Integer)

returns the new mapping for a specified reader, given it's old sequence index

Parameters:

reader - the reader

oldReferenceSequenceIndex - the old sequence (also called reference) index

Returns:

the new index value

getMergedSequenceIndex

public java.lang.Integer getMergedSequenceIndex(SAMFileHeader header,
                                                java.lang.Integer oldReferenceSequenceIndex)

Another mechanism for getting the new sequence index, for situations in which the reader is not available. Note that if the SAMRecord has already had its header replaced with the merged header, this won't work.

Parameters:

header - The original header for the input record in question.

oldReferenceSequenceIndex - The original sequence index.

Returns:

the new index value that is compatible with the merged sequence index.