Package htsjdk.samtools

Class SAMRecordSetBuilder

java.lang.Object
htsjdk.samtools.SAMRecordSetBuilder
All Implemented Interfaces:
Iterable<SAMRecord>
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.

  • Field Details

  • Constructor Details

    • SAMRecordSetBuilder

      public SAMRecordSetBuilder()
      Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.

    • 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.

    • SAMRecordSetBuilder

      public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup)

    • SAMRecordSetBuilder

      public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength)

    • SAMRecordSetBuilder

      public SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength, DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)

  • Method Details

    • 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.

    • setUnmappedHasBasesAndQualities

      public void setUnmappedHasBasesAndQualities(boolean value)

    • size

      public int size()

    • setRandomSeed

      public void setRandomSeed(long seed)
      Set the seed of the random number generator for cases in which repeatable result is desired.

    • 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.

    • setUseNmFlag

      public void setUseNmFlag(boolean useNmFlag)

    • setReadGroup

      public void setReadGroup(SAMReadGroupRecord readGroup)

    • getRecords

      public Collection<SAMRecord> getRecords()
      Returns the accumulated list of sam records.

    • setHeader

      public void setHeader(SAMFileHeader header)

    • addRecord

      public void addRecord(SAMRecord record)
      The record should already have the DS and MC tags computed

    • iterator

      public CloseableIterator<SAMRecord> iterator()
      Returns a CloseableIterator over the collection of SAMRecords.
      Specified by:
      iterator in interface Iterable<SAMRecord>

    • 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.

    • 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

    • 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

    • 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

    • addUnmappedFragment

      public void addUnmappedFragment(String name)
      Adds an unmapped fragment read to the builder.

    • 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.

    • 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.

    • 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.

    • 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.

    • addUnmappedPair

      public void addUnmappedPair(String name)
      Adds a pair with both ends unmapped to the builder.

    • getSamReader

      public SamReader getSamReader()
      Creates samFileReader from the data in instance of this class
      Returns:
      SamReader

    • getHeader

      public SAMFileHeader getHeader()

    • setReadLength

      public void setReadLength(int readLength)

    • makeDefaultHeader

      public static SAMFileHeader makeDefaultHeader(SAMFileHeader.SortOrder sortOrder, int contigLength, boolean addReadGroup)
      creates a simple header
      Parameters:
      sortOrder - Use this sort order in the header
      contigLength - length of the other contigs
      Returns:
      newly formed header

    • writeRandomReference

      public void writeRandomReference(Path fasta) throws IOException
      Writes a random (but deterministic) reference file given a SAMFileHeader 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 current SAMFileHeader 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.

    • writeRandomReference

      public static void writeRandomReference(SAMFileHeader header, Path fasta) throws IOException
      Writes a random (but deterministic) reference file given a SAMFileHeader 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.