Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.digest | |
htsjdk.samtools.cram.lossy | |
htsjdk.samtools.filter | |
htsjdk.samtools.sra | |
htsjdk.samtools.util |
Modifier and Type | Class and Description |
---|---|
class |
BAMRecord
Wrapper class for binary BAM records.
|
Modifier and Type | Method and Description |
---|---|
SAMRecord |
SAMRecordSetBuilder.addFrag(java.lang.String name,
int contig,
int start,
boolean negativeStrand)
Adds a skeletal fragment (non-PE) record to the set using the provided
contig start and strand information.
|
SAMRecord |
SAMRecordSetBuilder.addFrag(java.lang.String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
java.lang.String cigar,
java.lang.String qualityString,
int defaultQuality)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
SAMRecord |
SAMRecordSetBuilder.addFrag(java.lang.String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
java.lang.String cigar,
java.lang.String qualityString,
int defaultQuality,
boolean isSecondary)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
SAMRecord |
SAMRecordSetBuilder.addFrag(java.lang.String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
java.lang.String cigar,
java.lang.String qualityString,
int defaultQuality,
boolean isSecondary,
boolean isSupplementary)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
static SAMRecord |
SAMUtils.clipOverlappingAlignedBases(SAMRecord record,
boolean noSideEffects)
Returns a (possibly new) record that has been clipped if isa mapped paired and has overlapping bases with its mate.
|
static SAMRecord |
SAMUtils.clipOverlappingAlignedBases(SAMRecord record,
int numOverlappingBasesToClip,
boolean noSideEffects)
Returns a (possibly new) SAMRecord with the given number of bases soft-clipped at the end of the read if is a mapped
paired and has overlapping bases with its mate.
|
SAMRecord |
DefaultSAMRecordFactory.createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled in
|
SAMRecord |
SAMRecordFactory.createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled in
|
SAMRecord |
BAMRecordCodec.decode()
Read the next record from the input stream and convert into a java object.
|
SAMRecord |
SAMRecord.deepCopy()
Returns a deep copy of the SAM record, with the following exceptions:
- The header field, which shares the reference with the original record
- The file source field, which will always always be set to null in the copy
Note that some fields, i.e.
|
SAMRecord |
NotPrimarySkippingIterator.getCurrent() |
SAMRecord |
SecondaryOrSupplementarySkippingIterator.getCurrent() |
SAMRecord |
SAMSortOrderChecker.getPreviousRecord() |
SAMRecord |
DuplicateSet.getRepresentative()
Gets the representative record according to the duplicate comparator.
|
SAMRecord |
SamPairUtil.SetMateInfoIterator.next() |
SAMRecord |
CRAMFileReader.IntervalIterator.next() |
SAMRecord |
SamReader.AssertingIterator.next() |
SAMRecord |
CRAMIterator.next() |
SAMRecord |
MergingSamRecordIterator.next()
Returns the next record from the top most iterator during merging.
|
SAMRecord |
SRAIterator.next()
Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from
one of them.
|
static SAMRecord |
SamPairUtil.obtainAssertedMate(java.util.Iterator<SAMRecord> samRecordIterator,
SAMRecord firstOfPair)
Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord
(assumed to be in the next element of the specified samRecordIterator)
|
SAMRecord |
SAMLineParser.parseLine(java.lang.String line)
Parse a SAM line.
|
SAMRecord |
SAMLineParser.parseLine(java.lang.String line,
int lineNumber)
Parse a SAM line.
|
SAMRecord |
SamPairUtil.SetMateInfoIterator.peek() |
SAMRecord |
SamReader.queryMate(SAMRecord rec)
Fetch the mate for the given read.
|
SAMRecord |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryMate(SAMRecord rec)
Wraps the boilerplate code for querying a record's mate, which is common across many implementations.
|
SAMRecord |
SAMFileReader.queryMate(SAMRecord rec)
Deprecated.
Fetch the mate for the given read.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<SAMRecord> |
SAMRecordSetBuilder.addPair(java.lang.String name,
int contig,
int start1,
int start2,
boolean record1Unmapped,
boolean record2Unmapped,
java.lang.String cigar1,
java.lang.String cigar2,
boolean strand1,
boolean strand2,
boolean record1NonPrimary,
boolean record2NonPrimary,
int defaultQuality)
Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
|
java.util.List<SAMRecord> |
SAMRecordSetBuilder.addPair(java.lang.String name,
int contig,
int start1,
int start2,
boolean record1Unmapped,
boolean record2Unmapped,
java.lang.String cigar1,
java.lang.String cigar2,
boolean strand1,
boolean strand2,
int defaultQuality)
Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
|
java.util.List<SAMRecord> |
SAMRecordSetBuilder.addPair(java.lang.String name,
int contig1,
int contig2,
int start1,
int start2,
boolean record1Unmapped,
boolean record2Unmapped,
java.lang.String cigar1,
java.lang.String cigar2,
boolean strand1,
boolean strand2,
boolean record1NonPrimary,
boolean record2NonPrimary,
int defaultQuality)
Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
|
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.getIterator() |
CloseableIterator<SAMRecord> |
SRAFileReader.getIterator() |
CloseableIterator<SAMRecord> |
CRAMFileReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SRAFileReader.getIterator(SAMFileSpan chunks) |
java.util.List<SAMRecord> |
DuplicateSet.getRecords()
Gets the list of records from this set.
|
java.util.Collection<SAMRecord> |
SAMRecordSetBuilder.getRecords()
Returns the accumulated list of sam records.
|
java.util.List<SAMRecord> |
DuplicateSet.getRecords(boolean sort)
Gets the list of records from this set.
|
CloseableIterator<SAMRecord> |
SAMRecordSetBuilder.iterator()
Returns a CloseableIterator over the collection of SAMRecords.
|
CloseableIterator<SAMRecord> |
CRAMFileReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
SRAFileReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
CRAMFileReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
SRAFileReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
CRAMFileReader.queryUnmapped() |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.queryUnmapped() |
CloseableIterator<SAMRecord> |
SRAFileReader.queryUnmapped() |
Modifier and Type | Method and Description |
---|---|
int |
DuplicateSet.add(SAMRecord record)
Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set.
|
void |
SAMFileWriter.addAlignment(SAMRecord alignment) |
void |
SAMFileWriterImpl.addAlignment(SAMRecord alignment)
Add an alignment record to be emitted by the writer.
|
void |
SAMRecordSetBuilder.addRecord(SAMRecord record)
The record should already have the DS and MC tags computed
|
static void |
SamPairUtil.assertMate(SAMRecord firstOfPair,
SAMRecord secondOfPair) |
void |
SAMTestUtil.assertPairValid(SAMRecord firstEnd,
SAMRecord secondEnd)
Basic sanity check for a pair of SAMRecords.
|
void |
SAMTestUtil.assertReadValid(SAMRecord read)
Basic sanity check for a SAMRecord.
|
static SAMRecord |
SAMUtils.clipOverlappingAlignedBases(SAMRecord record,
boolean noSideEffects)
Returns a (possibly new) record that has been clipped if isa mapped paired and has overlapping bases with its mate.
|
static SAMRecord |
SAMUtils.clipOverlappingAlignedBases(SAMRecord record,
int numOverlappingBasesToClip,
boolean noSideEffects)
Returns a (possibly new) SAMRecord with the given number of bases soft-clipped at the end of the read if is a mapped
paired and has overlapping bases with its mate.
|
int |
SAMRecordCoordinateComparator.compare(SAMRecord samRecord1,
SAMRecord samRecord2) |
int |
SAMRecordDuplicateComparator.compare(SAMRecord samRecord1,
SAMRecord samRecord2)
Most stringent comparison.
|
int |
SAMRecordQueryNameComparator.compare(SAMRecord samRecord1,
SAMRecord samRecord2) |
int |
SAMRecordQueryHashComparator.compare(SAMRecord lhs,
SAMRecord rhs)
Compares two records based on an integer hash of their read name's.
|
static int |
DuplicateScoringStrategy.compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
Compare two records based on their duplicate scores.
|
static int |
DuplicateScoringStrategy.compare(SAMRecord rec1,
SAMRecord rec2,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar)
Compare two records based on their duplicate scores.
|
static short |
DuplicateScoringStrategy.computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
Returns the duplicate score computed from the given fragment.
|
static short |
DuplicateScoringStrategy.computeDuplicateScore(SAMRecord record,
DuplicateScoringStrategy.ScoringStrategy scoringStrategy,
boolean assumeMateCigar)
Returns the duplicate score computed from the given fragment.
|
static int |
SamPairUtil.computeInsertSize(SAMRecord firstEnd,
SAMRecord secondEnd)
Compute SAMRecord insert size
|
int |
SAMRecordDuplicateComparator.duplicateSetCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary.
|
void |
BAMRecordCodec.encode(SAMRecord alignment)
Write object to OutputStream.
|
int |
SAMRecordCoordinateComparator.fileOrderCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent compare method than the regular compare.
|
int |
SAMRecordDuplicateComparator.fileOrderCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.
|
int |
SAMRecordComparator.fileOrderCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent compare method than the regular compare.
|
int |
SAMRecordQueryNameComparator.fileOrderCompare(SAMRecord samRecord1,
SAMRecord samRecord2)
Less stringent compare method than the regular compare.
|
int |
SAMRecordQueryHashComparator.fileOrderCompare(SAMRecord lhs,
SAMRecord rhs)
Compares two records based on an integer hash of their read names.
|
static java.lang.String |
SAMUtils.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> |
SAMUtils.getMateAlignmentBlocks(SAMRecord rec) |
static int |
SAMUtils.getMateAlignmentEnd(SAMRecord rec)
This method uses the MateCigar value as determined from the attribute MC.
|
static Cigar |
SAMUtils.getMateCigar(SAMRecord rec)
Returns the Mate Cigar or null if there is none.
|
static Cigar |
SAMUtils.getMateCigar(SAMRecord rec,
boolean withValidation)
Returns the Mate Cigar or null if there is none.
|
static int |
SAMUtils.getMateCigarLength(SAMRecord rec) |
static java.lang.String |
SAMUtils.getMateCigarString(SAMRecord rec)
Returns the Mate Cigar String as stored in the attribute 'MC'.
|
static int |
SAMUtils.getMateUnclippedEnd(SAMRecord rec) |
static int |
SAMUtils.getMateUnclippedStart(SAMRecord rec) |
static int |
SAMUtils.getNumOverlappingAlignedBasesToClip(SAMRecord rec)
Returns the number of bases that need to be clipped due to overlapping pairs.
|
static SamPairUtil.PairOrientation |
SamPairUtil.getPairOrientation(SAMRecord r)
Computes the pair orientation of the given SAMRecord.
|
static int |
SAMRecord.getReadPositionAtReferencePosition(SAMRecord rec,
int pos,
boolean returnLastBaseIfDeleted) |
static int |
SAMRecord.getReferencePositionAtReadPosition(SAMRecord rec,
int offset) |
java.lang.String |
SAMSortOrderChecker.getSortKey(SAMRecord rec)
Return the sort key used for the given sort order.
|
static boolean |
SAMUtils.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 boolean |
SAMUtils.hasOriginalMappingInformation(SAMRecord rec)
See if any tags pertaining to original mapping information have been set.
|
static boolean |
SamPairUtil.isProperPair(SAMRecord firstEnd,
SAMRecord secondEnd,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations) |
boolean |
SAMSortOrderChecker.isSorted(SAMRecord rec)
Check if given SAMRecord violates sort order relative to previous SAMRecord.
|
static void |
SAMUtils.makeReadUnmapped(SAMRecord rec)
Strip mapping information from a SAMRecord.
|
static void |
SAMUtils.makeReadUnmappedWithOriginalTags(SAMRecord rec)
Strip mapping information from a SAMRecord, but preserve it in the 'O' tags if it isn't already set.
|
static SAMRecord |
SamPairUtil.obtainAssertedMate(java.util.Iterator<SAMRecord> samRecordIterator,
SAMRecord firstOfPair)
Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord
(assumed to be in the next element of the specified samRecordIterator)
|
void |
BAMIndexer.processAlignment(SAMRecord rec)
Record any index information for a given BAM record.
|
SAMRecord |
SamReader.queryMate(SAMRecord rec)
Fetch the mate for the given read.
|
SAMRecord |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryMate(SAMRecord rec)
Wraps the boilerplate code for querying a record's mate, which is common across many implementations.
|
SAMRecord |
SAMFileReader.queryMate(SAMRecord rec)
Deprecated.
Fetch the mate for the given read.
|
static boolean |
SAMUtils.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 void |
SAMRecordUtil.reverseComplement(SAMRecord rec)
Reverse-complement all known sequence and base quality attributes of the SAMRecord.
|
static void |
SamPairUtil.setMateInfo(SAMRecord rec1,
SAMRecord rec2,
boolean setMateCigar)
Write the mate info for two SAMRecords
|
static void |
SamPairUtil.setMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header)
Write the mate info for two SAMRecords.
|
static void |
SamPairUtil.setMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
boolean setMateCigar)
Deprecated.
|
static void |
SamPairUtil.setMateInformationOnSupplementalAlignment(SAMRecord supplemental,
SAMRecord matePrimary)
Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
|
static void |
SamPairUtil.setMateInformationOnSupplementalAlignment(SAMRecord supplemental,
SAMRecord matePrimary,
boolean setMateCigar)
Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
|
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> exepectedOrientations)
This method will clear any mate cigar already present.
|
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> exepectedOrientations,
boolean addMateCigar) |
static void |
SamPairUtil.setProperPairFlags(SAMRecord rec1,
SAMRecord rec2,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations) |
protected boolean |
CRAMContainerStreamWriter.shouldFlushContainer(SAMRecord nextRecord)
Decide if the current container should be completed and flushed.
|
static java.util.List<SAMValidationError> |
SAMUtils.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> |
SAMUtils.validateMateCigar(SAMRecord rec,
long recordNumber)
Run all validations of the mate's CIGAR.
|
void |
SAMTextWriter.writeAlignment(SAMRecord alignment)
Write the record.
|
void |
CRAMContainerStreamWriter.writeAlignment(SAMRecord alignment)
Write an alignment record.
|
protected abstract void |
SAMFileWriterImpl.writeAlignment(SAMRecord alignment)
Writes the record to disk.
|
protected void |
CRAMFileWriter.writeAlignment(SAMRecord alignment)
Write an alignment record.
|
Modifier and Type | Method and Description |
---|---|
static DownsamplingIterator |
DownsamplingIteratorFactory.make(java.util.Iterator<SAMRecord> iterator,
DownsamplingIteratorFactory.Strategy strategy,
double proportion,
double accuracy,
int seed)
Creates a new DownsamplingIterator using the supplied Strategy that attempts to read from the provided iterator and return
approximately proportion of the records read.
|
static SAMRecord |
SamPairUtil.obtainAssertedMate(java.util.Iterator<SAMRecord> samRecordIterator,
SAMRecord firstOfPair)
Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord
(assumed to be in the next element of the specified samRecordIterator)
|
Constructor and Description |
---|
AssertingIterator(CloseableIterator<SAMRecord> iterator) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header,
boolean preSorted) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header,
boolean preSorted,
SAMRecordDuplicateComparator comparator)
Allows the user of this iterator to skip the sorting of the input if the input is already sorted.
|
IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval) |
IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval,
boolean overlap) |
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted)
Add a set of SAM file iterators to the merging iterator.
|
NotPrimarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) |
SecondaryOrSupplementarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) |
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator)
By default, the mate cigar tag is set
|
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator,
boolean setMateCigar) |
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator,
boolean setMateCigar,
boolean ignoreMissingMates) |
Modifier and Type | Method and Description |
---|---|
SAMRecord |
Cram2SamRecordFactory.create(CramCompressionRecord cramRecord) |
Modifier and Type | Method and Description |
---|---|
CramCompressionRecord |
Sam2CramRecordFactory.createCramRecord(SAMRecord record)
Create a CramCompressionRecord.
|
Modifier and Type | Method and Description |
---|---|
void |
ContentDigests.addSAMRecords(java.lang.Iterable<SAMRecord> records) |
Modifier and Type | Method and Description |
---|---|
void |
QualityScorePreservation.addQualityScores(SAMRecord samRecord,
CramCompressionRecord cramRecord,
ReferenceTracks referenceTracks) |
Modifier and Type | Method and Description |
---|---|
SAMRecord |
FilteringIterator.next()
Returns the next element in the iteration.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SecondaryOrSupplementaryFilter.filterOut(SAMRecord record) |
boolean |
WholeReadClippedFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
IntervalFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
MappingQualityFilter.filterOut(SAMRecord record) |
boolean |
JavascriptSamRecordFilter.filterOut(SAMRecord record)
read is filtered out if the javascript program returns false
|
boolean |
InsertSizeFilter.filterOut(SAMRecord rec) |
boolean |
SecondaryAlignmentFilter.filterOut(SAMRecord record)
Returns true if the read is marked as secondary.
|
boolean |
TagFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
ReadNameFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
OverclippedReadFilter.filterOut(SAMRecord record) |
boolean |
SamRecordFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
NotPrimaryAlignmentFilter.filterOut(SAMRecord record) |
boolean |
SolexaNoiseFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
FailsVendorReadQualityFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
AggregateFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
AlignedFilter.filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filter
|
boolean |
DuplicateReadFilter.filterOut(SAMRecord record) |
boolean |
SecondaryOrSupplementaryFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
WholeReadClippedFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a paired of SAMRecord matches this filter
|
boolean |
IntervalFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
MappingQualityFilter.filterOut(SAMRecord first,
SAMRecord second) |
boolean |
JavascriptSamRecordFilter.filterOut(SAMRecord first,
SAMRecord second)
return true of both records are filteredOut (AND)
|
boolean |
InsertSizeFilter.filterOut(SAMRecord r1,
SAMRecord r2) |
boolean |
SecondaryAlignmentFilter.filterOut(SAMRecord first,
SAMRecord second)
Returns true if either read is marked as secondary.
|
boolean |
TagFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a paired of SAMRecord matches this filter
|
boolean |
ReadNameFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecords matches this filter
|
boolean |
OverclippedReadFilter.filterOut(SAMRecord first,
SAMRecord second) |
boolean |
SamRecordFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecords matches this filter
|
boolean |
NotPrimaryAlignmentFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
SolexaNoiseFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
FailsVendorReadQualityFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
AggregateFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
AlignedFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
boolean |
DuplicateReadFilter.filterOut(SAMRecord first,
SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
|
Constructor and Description |
---|
FilteringIterator(java.util.Iterator<SAMRecord> iterator,
SamRecordFilter filter)
Constructor
|
FilteringIterator(java.util.Iterator<SAMRecord> iterator,
SamRecordFilter filter,
boolean filterByPair)
Constructor
|
Modifier and Type | Class and Description |
---|---|
class |
SRALazyRecord
Extends SAMRecord so that any of the fields will be loaded only when needed.
|
Modifier and Type | Method and Description |
---|---|
SAMRecord |
SRAAlignmentIterator.next() |
SAMRecord |
SRAUnalignmentIterator.next() |
Modifier and Type | Method and Description |
---|---|
SAMRecord |
SamLocusIterator.RecordAndOffset.getRecord() |
SAMRecord |
SamRecordWithOrdinal.getRecord() |
Modifier and Type | Method and Description |
---|---|
CloseableIterator<SAMRecord> |
SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamReader samReader,
java.util.List<Interval> uniqueIntervals,
boolean useIndex) |
Modifier and Type | Method and Description |
---|---|
void |
QualityEncodingDetector.add(SAMRecord samRecord) |
void |
QualityEncodingDetector.add(SAMRecord samRecord,
boolean useOriginalQualities)
Adds the provided record's qualities to the detector.
|
void |
SamLocusIterator.LocusInfo.add(SAMRecord read,
int position)
Accumulate info for one read at the locus.
|
static void |
SequenceUtil.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 |
SequenceUtil.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 |
SequenceUtil.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 |
SequenceUtil.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 |
SequenceUtil.calculateSamNmTag(SAMRecord read,
char[] referenceBases,
int referenceOffset)
Deprecated.
|
static int |
SequenceUtil.calculateSamNmTagFromCigar(SAMRecord record)
Attempts to calculate the predefined NM tag from the SAM spec using the cigar string alone.
|
static int |
SequenceUtil.countDeletedBases(SAMRecord read) |
static int |
SequenceUtil.countInsertedBases(SAMRecord read) |
static int |
SequenceUtil.countMismatches(SAMRecord read,
byte[] referenceBases)
Calculates the number of mismatches between the read and the reference sequence provided.
|
static int |
SequenceUtil.countMismatches(SAMRecord read,
byte[] referenceBases,
boolean bisulfiteSequence)
Calculates the number of mismatches between the read and the reference sequence provided.
|
static int |
SequenceUtil.countMismatches(SAMRecord read,
byte[] referenceBases,
int referenceOffset)
Calculates the number of mismatches between the read and the reference sequence provided.
|
static int |
SequenceUtil.countMismatches(SAMRecord read,
byte[] referenceBases,
int referenceOffset,
boolean bisulfiteSequence)
Calculates the number of mismatches between the read and the reference sequence provided.
|
static int |
SequenceUtil.countMismatches(SAMRecord read,
byte[] referenceBases,
int referenceOffset,
boolean bisulfiteSequence,
boolean matchAmbiguousRef) |
static byte[] |
SequenceUtil.makeReferenceFromAlignment(SAMRecord rec,
boolean includeReferenceBasesForDeletions)
Produce reference bases from an aligned SAMRecord with MD string and Cigar.
|
boolean |
AbstractProgressLogger.record(SAMRecord... recs)
Records multiple SAMRecords and triggers logging if necessary.
|
boolean |
ProgressLoggerInterface.record(SAMRecord... recs) |
boolean |
AbstractProgressLogger.record(SAMRecord rec)
Records that a given record has been processed and triggers logging if necessary.
|
boolean |
ProgressLoggerInterface.record(SAMRecord rec) |
void |
SamRecordWithOrdinal.setRecord(SAMRecord record) |
static void |
CigarUtil.softClip3PrimeEndOfRead(SAMRecord rec,
int clipFrom)
Adds a soft-clip, based on
clipFrom , to the SAM record's existing cigar
and, for negative strands, also adjusts the SAM record's start position. |
static double |
QualityUtil.sumOfErrorProbabilities(SAMRecord rec)
Calculates the sum of error probabilities for all read bases in the SAM record.
|
static int |
SequenceUtil.sumQualitiesOfMismatches(SAMRecord read,
byte[] referenceBases)
Calculates the sum of qualities for mismatched bases in the read.
|
static int |
SequenceUtil.sumQualitiesOfMismatches(SAMRecord read,
byte[] referenceBases,
int referenceOffset)
Calculates the sum of qualities for mismatched bases in the read.
|
static int |
SequenceUtil.sumQualitiesOfMismatches(SAMRecord read,
byte[] referenceBases,
int referenceOffset,
boolean bisulfiteSequence)
Calculates the sum of qualities for mismatched bases in the read.
|
static int |
SequenceUtil.sumQualitiesOfMismatches(SAMRecord read,
char[] referenceBases,
int referenceOffset)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
long |
QualityEncodingDetector.add(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
long |
QualityEncodingDetector.add(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Adds the provided iterator's records (optionally using the original qualities) to the detector.
|
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Reads through the records in the provided SAM reader and uses their quality scores to determine the quality
format used in the SAM.
|
Constructor and Description |
---|
RecordAndOffset(SAMRecord record,
int offset) |
SamRecordWithOrdinal(SAMRecord record,
long recordOrdinal) |