Package | Description |
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htsjdk.samtools |
Modifier and Type | Method and Description |
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SAMFileHeader.SortOrder |
SAMFileHeader.getSortOrder() |
protected SAMFileHeader.SortOrder |
SAMFileWriterImpl.getSortOrder()
Must be called after calling setHeader().
|
static SAMFileHeader.SortOrder |
SAMFileHeader.SortOrder.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
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static SAMFileHeader.SortOrder[] |
SAMFileHeader.SortOrder.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
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SAMRecordIterator |
CRAMFileReader.IntervalIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SamReader.AssertingIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SRAIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
CRAMIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SAMRecordIterator.assertSorted(SAMFileHeader.SortOrder sortOrder)
Establishes that records returned by this iterator are expected to
be in the specified sort order.
|
void |
SAMFileHeader.setSortOrder(SAMFileHeader.SortOrder so) |
void |
SAMFileWriterImpl.setSortOrder(SAMFileHeader.SortOrder sortOrder,
boolean presorted)
Must be called before calling setHeader().
|
Constructor and Description |
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SamFileHeaderMerger(java.util.Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder)
Deprecated.
replaced by SamFileHeaderMerger(Collection
|
SamFileHeaderMerger(java.util.Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder,
boolean mergeDictionaries)
Deprecated.
replaced by SamFileHeaderMerger(Collection
|
SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder,
java.util.Collection<SAMFileHeader> headers,
boolean mergeDictionaries)
Create SAMFileHeader with additional information..
|
SAMRecordSetBuilder(boolean sortForMe,
SAMFileHeader.SortOrder sortOrder)
Construct a new SAMRecordSetBuilder.
|
SAMRecordSetBuilder(boolean sortForMe,
SAMFileHeader.SortOrder sortOrder,
boolean addReadGroup) |
SAMRecordSetBuilder(boolean sortForMe,
SAMFileHeader.SortOrder sortOrder,
boolean addReadGroup,
int defaultChromosomeLength) |
SAMRecordSetBuilder(boolean sortForMe,
SAMFileHeader.SortOrder sortOrder,
boolean addReadGroup,
int defaultChromosomeLength,
DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy) |
SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder) |