picard.sam

Class AbstractAlignmentMerger

java.lang.Object

picard.sam.AbstractAlignmentMerger

Direct Known Subclasses:

SamAlignmentMerger

public abstract class AbstractAlignmentMerger
extends java.lang.Object

Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.

The order of processing is as follows:

1. Get records from the unmapped bam and the alignment data 2. Merge the alignment information and public tags ONLY from the aligned SAMRecords 3. Do additional modifications -- handle clipping, trimming, etc. 4. Fix up mate information on paired reads 5. Do a final calculation of the NM and UQ tags (coordinate sorted only) 6. Write the records to the output file.

Concrete subclasses which extend AbstractAlignmentMerger should implement getQueryNameSortedAlignedRecords. If these records are not in queryname order, mergeAlignment will throw an IllegalStateException.

Subclasses may optionally implement ignoreAlignment(), which can be used to skip over certain alignments.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractAlignmentMerger.UnmappingReadStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_RECORDS_IN_RAM
protected java.io.File	referenceFasta

Constructor Summary

Constructors

Constructor and Description
AbstractAlignmentMerger(java.io.File unmappedBamFile, java.io.File targetBamFile, java.io.File referenceFasta, boolean clipAdapters, boolean bisulfiteSequence, boolean alignedReadsOnly, htsjdk.samtools.SAMProgramRecord programRecord, java.util.List<java.lang.String> attributesToRetain, java.util.List<java.lang.String> attributesToRemove, java.lang.Integer read1BasesTrimmed, java.lang.Integer read2BasesTrimmed, java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, htsjdk.samtools.SAMFileHeader.SortOrder sortOrder, PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy, boolean addMateCigar, boolean unmapContaminantReads) constructor with a default setting for unmappingReadsStrategy.
AbstractAlignmentMerger(java.io.File unmappedBamFile, java.io.File targetBamFile, java.io.File referenceFasta, boolean clipAdapters, boolean bisulfiteSequence, boolean alignedReadsOnly, htsjdk.samtools.SAMProgramRecord programRecord, java.util.List<java.lang.String> attributesToRetain, java.util.List<java.lang.String> attributesToRemove, java.lang.Integer read1BasesTrimmed, java.lang.Integer read2BasesTrimmed, java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, htsjdk.samtools.SAMFileHeader.SortOrder sortOrder, PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy, boolean addMateCigar, boolean unmapContaminantReads, AbstractAlignmentMerger.UnmappingReadStrategy unmappingReadsStrategy) Constructor

Method Summary

Modifier and Type	Method and Description
protected static void	clipForOverlappingReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2) Checks to see whether the ends of the reads overlap and soft clips reads them if necessary.
void	close()
static void	createNewCigarsIfMapsOffEndOfReference(htsjdk.samtools.SAMRecord rec) Soft-clip an alignment that hangs off the end of its reference sequence.
static void	fixNmMdAndUq(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequenceFileWalker refSeqWalker, boolean isBisulfiteSequence) Calculates and sets the NM, MD, and and UQ tags from the record and the reference
static void	fixUq(htsjdk.samtools.SAMRecord record, htsjdk.samtools.reference.ReferenceSequenceFileWalker refSeqWalker, boolean isBisulfiteSequence) Calculates and sets UQ tag from the record and the reference
java.util.Set<java.lang.String>	getAttributesToReverse() Gets the set of attributes to be reversed on reads marked as negative strand.
java.util.Set<java.lang.String>	getAttributesToReverseComplement() Gets the set of attributes to be reverse complemented on reads marked as negative strand.
protected abstract htsjdk.samtools.SAMSequenceDictionary	getDictionaryForMergedBam()
protected htsjdk.samtools.SAMFileHeader	getHeader()
protected htsjdk.samtools.SAMProgramRecord	getProgramRecord()
protected abstract htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord>	getQuerynameSortedAlignedRecords()
protected boolean	ignoreAlignment(htsjdk.samtools.SAMRecord sam)
boolean	isClipOverlappingReads()
protected boolean	isContaminant(picard.sam.HitsForInsert hits)
boolean	isKeepAlignerProperPairFlags()
protected boolean	isReservedTag(java.lang.String tag)
void	mergeAlignment(java.io.File referenceFasta) Merges the alignment data with the non-aligned records from the source BAM file.
protected void	resetRefSeqFileWalker()
void	setAddPGTagToReads(boolean addPGTagToReads) Set addPGTagToReads.
void	setAttributesToReverse(java.util.Set<java.lang.String> attributesToReverse) Sets the set of attributes to be reversed on reads marked as negative strand.
void	setAttributesToReverseComplement(java.util.Set<java.lang.String> attributesToReverseComplement) Sets the set of attributes to be reverse complemented on reads marked as negative strand.
void	setClipOverlappingReads(boolean clipOverlappingReads)
void	setIncludeSecondaryAlignments(boolean includeSecondaryAlignments)
void	setKeepAlignerProperPairFlags(boolean keepAlignerProperPairFlags) If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
void	setMaxRecordsInRam(int maxRecordsInRam) Allows the caller to override the maximum records in RAM.
protected void	setProgramRecord(htsjdk.samtools.SAMProgramRecord pg)
protected void	setValuesFromAlignment(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.SAMRecord alignment, boolean needsSafeReverseComplement) Sets the values from the alignment record on the unaligned BAM record.
protected void	updateCigarForTrimmedOrClippedBases(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.SAMRecord alignment)

Methods inherited from class java.lang.Object

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

Field Detail

MAX_RECORDS_IN_RAM

public static final int MAX_RECORDS_IN_RAM

See Also:

Constant Field Values

referenceFasta

protected final java.io.File referenceFasta

Constructor Detail

AbstractAlignmentMerger

public AbstractAlignmentMerger(java.io.File unmappedBamFile,
                               java.io.File targetBamFile,
                               java.io.File referenceFasta,
                               boolean clipAdapters,
                               boolean bisulfiteSequence,
                               boolean alignedReadsOnly,
                               htsjdk.samtools.SAMProgramRecord programRecord,
                               java.util.List<java.lang.String> attributesToRetain,
                               java.util.List<java.lang.String> attributesToRemove,
                               java.lang.Integer read1BasesTrimmed,
                               java.lang.Integer read2BasesTrimmed,
                               java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations,
                               htsjdk.samtools.SAMFileHeader.SortOrder sortOrder,
                               PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
                               boolean addMateCigar,
                               boolean unmapContaminantReads)

constructor with a default setting for unmappingReadsStrategy. see full constructor for parameters

AbstractAlignmentMerger

public AbstractAlignmentMerger(java.io.File unmappedBamFile,
                               java.io.File targetBamFile,
                               java.io.File referenceFasta,
                               boolean clipAdapters,
                               boolean bisulfiteSequence,
                               boolean alignedReadsOnly,
                               htsjdk.samtools.SAMProgramRecord programRecord,
                               java.util.List<java.lang.String> attributesToRetain,
                               java.util.List<java.lang.String> attributesToRemove,
                               java.lang.Integer read1BasesTrimmed,
                               java.lang.Integer read2BasesTrimmed,
                               java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations,
                               htsjdk.samtools.SAMFileHeader.SortOrder sortOrder,
                               PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
                               boolean addMateCigar,
                               boolean unmapContaminantReads,
                               AbstractAlignmentMerger.UnmappingReadStrategy unmappingReadsStrategy)

Constructor

Parameters:

unmappedBamFile - The BAM file that was used as the input to the aligner, which will include info on all the reads that did not map. Required.

targetBamFile - The file to which to write the merged SAM records. Required.

referenceFasta - The reference sequence for the map files. Required.

clipAdapters - Whether adapters marked in unmapped BAM file should be marked as soft clipped in the merged bam. Required.

bisulfiteSequence - Whether the reads are bisulfite sequence (used when calculating the NM and UQ tags). Required.

alignedReadsOnly - Whether to output only those reads that have alignment data

programRecord - Program record for target file SAMRecords created.

attributesToRetain - private attributes from the alignment record that should be included when merging. This overrides the exclusion of attributes whose tags start with the reserved characters of X, Y, and Z

attributesToRemove - attributes from the alignment record that should be removed when merging. This overrides attributesToRetain if they share common tags.

read1BasesTrimmed - The number of bases trimmed from start of read 1 prior to alignment. Optional.

read2BasesTrimmed - The number of bases trimmed from start of read 2 prior to alignment. Optional.

expectedOrientations - A List of SamPairUtil.PairOrientations that are expected for aligned pairs. Used to determine the properPair flag.

sortOrder - The order in which the merged records should be output. If null, output will be coordinate-sorted

primaryAlignmentSelectionStrategy - What to do when there are multiple primary alignments, or multiple alignments but none primary, for a read or read pair.

addMateCigar - True if we are to add or maintain the mate CIGAR (MC) tag, false if we are to remove or not include.

unmapContaminantReads - If true, identify reads having the signature of cross-species contamination (i.e. mostly clipped bases), and mark them as unmapped.

unmappingReadsStrategy - An enum describing how to deal with reads whose mapping information are being removed (currently this happens due to cross-species contamination). Ignored unless unmapContaminantReads is true.

Method Detail

getDictionaryForMergedBam

protected abstract htsjdk.samtools.SAMSequenceDictionary getDictionaryForMergedBam()

getQuerynameSortedAlignedRecords

protected abstract htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord> getQuerynameSortedAlignedRecords()

ignoreAlignment

protected boolean ignoreAlignment(htsjdk.samtools.SAMRecord sam)

isContaminant

protected boolean isContaminant(picard.sam.HitsForInsert hits)

getAttributesToReverse

public java.util.Set<java.lang.String> getAttributesToReverse()

Gets the set of attributes to be reversed on reads marked as negative strand.

setAttributesToReverse

public void setAttributesToReverse(java.util.Set<java.lang.String> attributesToReverse)

Sets the set of attributes to be reversed on reads marked as negative strand.

getAttributesToReverseComplement

public java.util.Set<java.lang.String> getAttributesToReverseComplement()

Gets the set of attributes to be reverse complemented on reads marked as negative strand.

setAttributesToReverseComplement

public void setAttributesToReverseComplement(java.util.Set<java.lang.String> attributesToReverseComplement)

Sets the set of attributes to be reverse complemented on reads marked as negative strand.

setMaxRecordsInRam

public void setMaxRecordsInRam(int maxRecordsInRam)

Allows the caller to override the maximum records in RAM.

setAddPGTagToReads

public void setAddPGTagToReads(boolean addPGTagToReads)

Set addPGTagToReads. If true, the PG will be added to reads when applicable. If false, the PG tag will not be added. Default is true

mergeAlignment

public void mergeAlignment(java.io.File referenceFasta)

Merges the alignment data with the non-aligned records from the source BAM file.

fixNmMdAndUq

public static void fixNmMdAndUq(htsjdk.samtools.SAMRecord record,
                                htsjdk.samtools.reference.ReferenceSequenceFileWalker refSeqWalker,
                                boolean isBisulfiteSequence)

Calculates and sets the NM, MD, and and UQ tags from the record and the reference

Parameters:

record - the record to be fixed

refSeqWalker - a ReferenceSequenceWalker that will be used to traverse the reference

isBisulfiteSequence - a flag indicating whether the sequence came from bisulfite-sequencing which would imply a different calculation of the NM tag. No return value, modifies the provided record.

fixUq

public static void fixUq(htsjdk.samtools.SAMRecord record,
                         htsjdk.samtools.reference.ReferenceSequenceFileWalker refSeqWalker,
                         boolean isBisulfiteSequence)

Calculates and sets UQ tag from the record and the reference

Parameters:

record - the record to be fixed

refSeqWalker - a ReferenceSequenceWalker that will be used to traverse the reference

isBisulfiteSequence - a flag indicating whether the sequence came from bisulfite-sequencing. No return value, modifies the provided record.

clipForOverlappingReads

protected static void clipForOverlappingReads(htsjdk.samtools.SAMRecord read1,
                                              htsjdk.samtools.SAMRecord read2)

Checks to see whether the ends of the reads overlap and soft clips reads them if necessary.

setValuesFromAlignment

protected void setValuesFromAlignment(htsjdk.samtools.SAMRecord rec,
                                      htsjdk.samtools.SAMRecord alignment,
                                      boolean needsSafeReverseComplement)

Sets the values from the alignment record on the unaligned BAM record. This preserves all data from the unaligned record (ReadGroup, NoiseRead status, etc) and adds all the alignment info

Parameters:

rec - The unaligned read record

alignment - The alignment record

createNewCigarsIfMapsOffEndOfReference

public static void createNewCigarsIfMapsOffEndOfReference(htsjdk.samtools.SAMRecord rec)

Soft-clip an alignment that hangs off the end of its reference sequence. Checks both the read and its mate, if available.

Parameters:

rec -

updateCigarForTrimmedOrClippedBases

protected void updateCigarForTrimmedOrClippedBases(htsjdk.samtools.SAMRecord rec,
                                                   htsjdk.samtools.SAMRecord alignment)

getProgramRecord

protected htsjdk.samtools.SAMProgramRecord getProgramRecord()

setProgramRecord

protected void setProgramRecord(htsjdk.samtools.SAMProgramRecord pg)

isReservedTag

protected boolean isReservedTag(java.lang.String tag)

getHeader

protected htsjdk.samtools.SAMFileHeader getHeader()

resetRefSeqFileWalker

protected void resetRefSeqFileWalker()

isClipOverlappingReads

public boolean isClipOverlappingReads()

setClipOverlappingReads

public void setClipOverlappingReads(boolean clipOverlappingReads)

isKeepAlignerProperPairFlags

public boolean isKeepAlignerProperPairFlags()

setKeepAlignerProperPairFlags

public void setKeepAlignerProperPairFlags(boolean keepAlignerProperPairFlags)

If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.

setIncludeSecondaryAlignments

public void setIncludeSecondaryAlignments(boolean includeSecondaryAlignments)

close

public void close()