Package htsjdk.samtools
Class SAMRecordSetBuilder
- java.lang.Object
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- htsjdk.samtools.SAMRecordSetBuilder
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public class SAMRecordSetBuilder extends Object implements Iterable<SAMRecord>
Factory class for creating SAMRecords for testing purposes. Various methods can be called to add new SAM records (or pairs of records) to a list which can then be returned at any point. The records must reference human chromosomes (excluding randoms etc.). Although this is a class for testing, it is in the src tree because it is included in the sam jarfile.
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_CHROMOSOME_LENGTH
static DuplicateScoringStrategy.ScoringStrategy
DEFAULT_DUPLICATE_SCORING_STRATEGY
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Constructor Summary
Constructors Constructor Description SAMRecordSetBuilder()
Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description SAMRecord
addFrag(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
addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, 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
addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, 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
addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, 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.void
addPair(String name, int contig, int start1, int start2)
Adds a skeletal pair of records to the set using the provided contig starts.List<SAMRecord>
addPair(String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, 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.List<SAMRecord>
addPair(String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, String cigar2, boolean strand1, boolean strand2, int defaultQuality)
Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.List<SAMRecord>
addPair(String name, int contig1, int contig2, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, 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.void
addRecord(SAMRecord record)
The record should already have the DS and MC tags computedvoid
addUnmappedFragment(String name)
Adds an unmapped fragment read to the builder.void
addUnmappedPair(String name)
Adds a pair with both ends unmapped to the builder.SAMFileHeader
getHeader()
Collection<SAMRecord>
getRecords()
Returns the accumulated list of sam records.SamReader
getSamReader()
Creates samFileReader from the data in instance of this classCloseableIterator<SAMRecord>
iterator()
Returns a CloseableIterator over the collection of SAMRecords.static SAMFileHeader
makeDefaultHeader(SAMFileHeader.SortOrder sortOrder, int contigLength, boolean addReadGroup)
creates a simple headervoid
setHeader(SAMFileHeader header)
void
setProgramRecord(SAMProgramRecord programRecord)
Adds the given program record to the header, and assigns the PG tag to any SAMRecords created after it has been added.void
setRandomSeed(long seed)
Set the seed of the random number generator for cases in which repeatable result is desired.void
setReadGroup(SAMReadGroupRecord readGroup)
void
setReadLength(int readLength)
void
setUnmappedHasBasesAndQualities(boolean value)
void
setUseBamFile(boolean useBamFile)
Determine whether the class will use a bam (default) or a sam file to hold the records when providing a reader to them.void
setUseNmFlag(boolean useNmFlag)
int
size()
static void
writeRandomReference(SAMFileHeader header, Path fasta)
Writes a random (but deterministic) reference file given aSAMFileHeader
output file is expected to have a non-compressed fasta suffix.void
writeRandomReference(Path fasta)
Writes a random (but deterministic) reference file given aSAMFileHeader
output file is expected to have a non-compressed fasta suffix.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Detail
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DEFAULT_CHROMOSOME_LENGTH
public static final int DEFAULT_CHROMOSOME_LENGTH
- See Also:
- Constant Field Values
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DEFAULT_DUPLICATE_SCORING_STRATEGY
public static final DuplicateScoringStrategy.ScoringStrategy DEFAULT_DUPLICATE_SCORING_STRATEGY
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Constructor Detail
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SAMRecordSetBuilder
public SAMRecordSetBuilder()
Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.
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SAMRecordSetBuilder
public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder)
Construct a new SAMRecordSetBuilder.- Parameters:
sortOrder
- If sortForMe, defines the sort order.sortForMe
- If true, keep the records created in sorted order.
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SAMRecordSetBuilder
public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup)
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SAMRecordSetBuilder
public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength)
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SAMRecordSetBuilder
public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength, DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)
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Method Detail
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setUseBamFile
public void setUseBamFile(boolean useBamFile)
Determine whether the class will use a bam (default) or a sam file to hold the records when providing a reader to them.- Parameters:
useBamFile
- if true will use a BAM file, otherwise it will use a SAM file to hold the records.
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setUnmappedHasBasesAndQualities
public void setUnmappedHasBasesAndQualities(boolean value)
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size
public int size()
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setRandomSeed
public void setRandomSeed(long seed)
Set the seed of the random number generator for cases in which repeatable result is desired.
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setProgramRecord
public void setProgramRecord(SAMProgramRecord programRecord)
Adds the given program record to the header, and assigns the PG tag to any SAMRecords created after it has been added. May be called multiple times in order to assign different PG IDs to different SAMRecords. programRecord may be null to stop assignment of PG tag. It is up to the caller to ensure that program record IDs do not collide.
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setUseNmFlag
public void setUseNmFlag(boolean useNmFlag)
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setReadGroup
public void setReadGroup(SAMReadGroupRecord readGroup)
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getRecords
public Collection<SAMRecord> getRecords()
Returns the accumulated list of sam records.
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setHeader
public void setHeader(SAMFileHeader header)
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addRecord
public void addRecord(SAMRecord record)
The record should already have the DS and MC tags computed
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iterator
public CloseableIterator<SAMRecord> iterator()
Returns a CloseableIterator over the collection of SAMRecords.
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addFrag
public SAMRecord addFrag(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.
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addFrag
public SAMRecord addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, String qualityString, int defaultQuality) throws SAMException
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.- Throws:
SAMException
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addFrag
public SAMRecord addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, String qualityString, int defaultQuality, boolean isSecondary) throws SAMException
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.- Throws:
SAMException
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addFrag
public SAMRecord addFrag(String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, String cigar, String qualityString, int defaultQuality, boolean isSecondary, boolean isSupplementary) throws SAMException
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.- Throws:
SAMException
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addUnmappedFragment
public void addUnmappedFragment(String name)
Adds an unmapped fragment read to the builder.
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addPair
public void addPair(String name, int contig, int start1, int start2)
Adds a skeletal pair of records to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.
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addPair
public List<SAMRecord> addPair(String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, String cigar2, boolean strand1, boolean strand2, int defaultQuality)
Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.
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addPair
public List<SAMRecord> addPair(String name, int contig1, int contig2, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, 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. The pair is assumed to be a well formed pair sitting on a single contig.
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addPair
public List<SAMRecord> addPair(String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, String cigar1, 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. The pair is assumed to be a well formed pair sitting on a single contig.
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addUnmappedPair
public void addUnmappedPair(String name)
Adds a pair with both ends unmapped to the builder.
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getSamReader
public SamReader getSamReader()
Creates samFileReader from the data in instance of this class- Returns:
- SamReader
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getHeader
public SAMFileHeader getHeader()
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setReadLength
public void setReadLength(int readLength)
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makeDefaultHeader
public static SAMFileHeader makeDefaultHeader(SAMFileHeader.SortOrder sortOrder, int contigLength, boolean addReadGroup)
creates a simple header- Parameters:
sortOrder
- Use this sort order in the headercontigLength
- length of the other contigs- Returns:
- newly formed header
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writeRandomReference
public void writeRandomReference(Path fasta) throws IOException
Writes a random (but deterministic) reference file given aSAMFileHeader
output file is expected to have a non-compressed fasta suffix. Method will also write .dict and .fai files next to the reference file. files next to the provided. Will use the currentSAMFileHeader
to model the reference on.- Parameters:
fasta
- Path to output reference where it will be written. No checks will be performed regarding the writability, or existence of the files prior to writing.- Throws:
IOException
- In case of problem during writing the files.
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writeRandomReference
public static void writeRandomReference(SAMFileHeader header, Path fasta) throws IOException
Writes a random (but deterministic) reference file given aSAMFileHeader
output file is expected to have a non-compressed fasta suffix. Method will also write .dict and .fai files next to the reference file. files next to the provided- Parameters:
header
- Header file to base the reference on. Length and names of sequences will be taken from here, as will the order of the contigs in the reference.fasta
- Path to output reference where it will be written. No checks will be performed regarding the writability, or existence of the files prior to writing.- Throws:
IOException
- In case of problem during writing the files.
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