public class SamFileHeaderMerger extends Object
Constructor and Description |
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SamFileHeaderMerger(Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder)
Deprecated.
replaced by SamFileHeaderMerger(Collection
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SamFileHeaderMerger(Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder,
boolean mergeDictionaries)
Deprecated.
replaced by SamFileHeaderMerger(Collection
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SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder,
Collection<SAMFileHeader> headers,
boolean mergeDictionaries)
Create SAMFileHeader with additional information..
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Modifier and Type | Method and Description |
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Collection<SAMFileHeader> |
getHeaders()
Returns the collection of readers that this header merger is working with.
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SAMFileHeader |
getMergedHeader()
Returns the merged header that should be written to any output merged file.
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Integer |
getMergedSequenceIndex(SAMFileHeader header,
Integer oldReferenceSequenceIndex)
Another mechanism for getting the new sequence index, for situations in which the reader is not available.
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Integer |
getMergedSequenceIndex(SamReader reader,
Integer oldReferenceSequenceIndex)
Deprecated.
replaced by getMergedSequenceIndex(SAMFileHeader, Integer)
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String |
getProgramGroupId(SAMFileHeader header,
String originalProgramGroupId) |
String |
getProgramGroupId(SamReader reader,
String originalProgramGroupId)
Deprecated.
replaced by getProgramGroupId(SAMFileHeader, String)
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Collection<SamReader> |
getReaders()
Deprecated.
replaced by getHeaders()
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String |
getReadGroupId(SAMFileHeader header,
String originalReadGroupId)
Returns the read group id that should be used for the input read and RG id.
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String |
getReadGroupId(SamReader reader,
String originalReadGroupId)
Deprecated.
replaced by getReadGroupId(SAMFileHeader, String)
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boolean |
hasMergedSequenceDictionary() |
boolean |
hasProgramGroupCollisions()
Returns true if there are program group duplicates within the merged headers.
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boolean |
hasReadGroupCollisions()
Returns true if there are read group duplicates within the merged headers.
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static String |
positiveFourDigitBase36Str(int leftOver)
Convert an integer to base36, protected solely for testing
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public SamFileHeaderMerger(Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder)
readers
- sam file readers to combinesortOrder
- sort order new header should havepublic SamFileHeaderMerger(Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder, boolean mergeDictionaries)
readers
- sam file readers to combinesortOrder
- sort order new header should havemergeDictionaries
- If true, merge sequence dictionaries in new header. If false, require that
all input sequence dictionaries be identical.public SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder, Collection<SAMFileHeader> headers, boolean mergeDictionaries)
sortOrder
- sort order new header should haveheaders
- sam file headers to combinemergeDictionaries
- If true, merge sequence dictionaries in new header. If false, require that
all input sequence dictionaries be identical.public static String positiveFourDigitBase36Str(int leftOver)
leftOver
- Both the initial value and the running quotientpublic String getReadGroupId(SamReader reader, String originalReadGroupId)
public String getReadGroupId(SAMFileHeader header, String originalReadGroupId)
public String getProgramGroupId(SamReader reader, String originalProgramGroupId)
reader
- one of the input filesoriginalProgramGroupId
- a program group ID from the above input filepublic String getProgramGroupId(SAMFileHeader header, String originalProgramGroupId)
header
- one of the input headersoriginalProgramGroupId
- a program group ID from the above input filepublic boolean hasReadGroupCollisions()
public boolean hasProgramGroupCollisions()
public boolean hasMergedSequenceDictionary()
public SAMFileHeader getMergedHeader()
public Collection<SamReader> getReaders()
public Collection<SAMFileHeader> getHeaders()
public Integer getMergedSequenceIndex(SamReader reader, Integer oldReferenceSequenceIndex)
reader
- the readeroldReferenceSequenceIndex
- the old sequence (also called reference) indexpublic Integer getMergedSequenceIndex(SAMFileHeader header, Integer oldReferenceSequenceIndex)
header
- The original header for the input record in question.oldReferenceSequenceIndex
- The original sequence index.