org.broadinstitute.hellbender.utils.read

Class ArtificialReadUtils

java.lang.Object

org.broadinstitute.hellbender.utils.read.ArtificialReadUtils

public final class ArtificialReadUtils
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_READ_LENGTH
static java.lang.String	READ_GROUP_ID

Constructor Summary

Constructors

Constructor and Description
ArtificialReadUtils()

Method Summary

Modifier and Type	Method and Description
static GATKRead	createArtificialRead(byte[] bases, byte[] qual, java.lang.String cigar)
static GATKRead	createArtificialRead(htsjdk.samtools.Cigar cigar)
static GATKRead	createArtificialRead(htsjdk.samtools.Cigar cigar, java.lang.String name)
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, byte[] bases, byte[] qual, java.lang.String cigar) Create an artificial GATKRead with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.Cigar cigar)
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String cigarString)
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual) Create an artificial GATKRead based on the parameters.
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual, java.lang.String cigar) Create an artificial GATKRead based on the parameters
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, int length) Create an artificial GATKRead based on the parameters.
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String name, java.lang.String contig, int alignmentStart, byte[] bases, byte[] qual) Create an artificial GATKRead based on the parameters.
static GATKRead	createArtificialRead(htsjdk.samtools.SAMFileHeader header, java.lang.String name, java.lang.String contig, int alignmentStart, byte[] bases, byte[] qual, java.lang.String cigar) Create an artificial GATKRead based on the parameters
static GATKRead	createArtificialRead(java.lang.String cigarString)
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeader() Creates an artificial SAM header with standard test parameters
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeader(int numberOfChromosomes, int startingChromosome, int chromosomeSize) Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeader(htsjdk.samtools.SAMSequenceDictionary dict) Creates an artificial SAM header based on the sequence dictionary dict
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeaderWithGroups(int numberOfChromosomes, int startingChromosome, int chromosomeSize, int groupCount) Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds read groups.
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeaderWithPrograms(int numberOfChromosomes, int startingChromosome, int chromosomeSize, int programCount) Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds program records.
static htsjdk.samtools.SAMFileHeader	createArtificialSamHeaderWithReadGroup(htsjdk.samtools.SAMReadGroupRecord readGroup) Creates an artificial SAM header with standard test parameters and a Read Group
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(byte[] bases, byte[] qual, java.lang.String cigar)
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.Cigar cigar)
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, byte[] bases, byte[] qual, java.lang.String cigar) Create an artificial SAMRecord with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.Cigar cigar)
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.Cigar cigar, java.lang.String name)
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual) Create an artificial SAMRecord based on the parameters.
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual, java.lang.String cigar) Create an artificial SAMRecord based on the parameters
static htsjdk.samtools.SAMRecord	createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, int length) Create an artificial SAMRecord based on the parameters.
static GATKRead	createArtificialUnmappedRead(htsjdk.samtools.SAMFileHeader header, byte[] bases, byte[] qual)
static GATKRead	createArtificialUnmappedReadWithAssignedPosition(htsjdk.samtools.SAMFileHeader header, java.lang.String contig, int alignmentStart, byte[] bases, byte[] qual)
static GATKRead	createHeaderlessSamBackedRead(java.lang.String name, java.lang.String contig, int start, int length) Creates an artificial GATKRead backed by a SAMRecord with no header.
static java.util.Collection<GATKRead>	createIdenticalArtificialReads(int size, htsjdk.samtools.SAMFileHeader header, java.lang.String name, int refIndex, int alignmentStart, int length) Create a collection of identical artificial reads based on the parameters.
static PileupElement	createNonIndelPileupElement(int offsetIntoRead, htsjdk.variant.variantcontext.Allele newAllele, int lengthOfRead) See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing base-by-base replacement.
static java.util.List<GATKRead>	createPair(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative)
static java.util.List<GATKRead>	createPair(htsjdk.samtools.SAMFileHeader header, java.lang.String name, int readLen, int refIndex, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative)
static GATKRead	createRandomRead(int length)
static GATKRead	createRandomRead(int length, boolean allowNs)
static GATKRead	createRandomRead(htsjdk.samtools.SAMFileHeader header, int length)
static GATKRead	createRandomRead(htsjdk.samtools.SAMFileHeader header, int length, boolean allowNs)
static byte[]	createRandomReadBases(int length, boolean allowNs) Create random read qualities
static byte[]	createRandomReadQuals(int length) Create random read qualities
static GATKRead	createSamBackedRead(java.lang.String name, int start, int length) Creates an artificial GATKRead backed by a SAMRecord.
static GATKRead	createSamBackedRead(java.lang.String name, java.lang.String contig, int start, int length) Creates an artificial GATKRead backed by a SAMRecord.
static PileupElement	createSplicedDeletionPileupElement(int offsetIntoRead, htsjdk.variant.variantcontext.Allele referenceAllele, int lengthOfRead) See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing the specified deletion.
static PileupElement	createSplicedInsertionPileupElement(int offsetIntoRead, htsjdk.variant.variantcontext.Allele insertionAllele, int lengthOfRead) Create a pileupElement with the given insertion added to the bases.
static GATKRead	createUniqueArtificialRead(htsjdk.samtools.Cigar cigar) Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
static GATKRead	createUniqueArtificialRead(java.lang.String cigarString) Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
static htsjdk.samtools.SAMRecord	createUniqueArtificialSAMRecord(htsjdk.samtools.Cigar cigar) Makes a new read with a name that is unique (so that it will return false to equals(otherRead)
static ArtificialReadQueryIterator	mappedAndUnmappedReadIterator(int startingChr, int endingChr, int readCount, int unmappedReadCount) create an iterator containing the specified read piles
static ArtificialReadQueryIterator	mappedReadIterator(int startingChr, int endingChr, int readCount) create an iterator containing the specified read piles

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_READ_LENGTH

public static final int DEFAULT_READ_LENGTH

See Also:

Constant Field Values

READ_GROUP_ID

public static final java.lang.String READ_GROUP_ID

See Also:

Constant Field Values

Constructor Detail

ArtificialReadUtils

public ArtificialReadUtils()

Method Detail

createArtificialSamHeader

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeader(int numberOfChromosomes,
                                                                      int startingChromosome,
                                                                      int chromosomeSize)

Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc

Parameters:

numberOfChromosomes - the number of chromosomes to create

startingChromosome - the starting number for the chromosome (most likely set to 1)

chromosomeSize - the length of each chromosome

Returns:

createArtificialSamHeaderWithGroups

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeaderWithGroups(int numberOfChromosomes,
                                                                                int startingChromosome,
                                                                                int chromosomeSize,
                                                                                int groupCount)

Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds read groups.

Parameters:

numberOfChromosomes - the number of chromosomes to create

startingChromosome - the starting number for the chromosome (most likely set to 1)

chromosomeSize - the length of each chromosome

groupCount - the number of groups to make

createArtificialSamHeaderWithPrograms

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeaderWithPrograms(int numberOfChromosomes,
                                                                                  int startingChromosome,
                                                                                  int chromosomeSize,
                                                                                  int programCount)

Creates an artificial SAM header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc It also adds program records.

Parameters:

numberOfChromosomes - the number of chromosomes to create

startingChromosome - the starting number for the chromosome (most likely set to 1)

chromosomeSize - the length of each chromosome

programCount - the number of programs to make

Returns:

createArtificialSamHeader

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeader()

Creates an artificial SAM header with standard test parameters

Returns:

the SAM header

createArtificialSamHeaderWithReadGroup

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeaderWithReadGroup(htsjdk.samtools.SAMReadGroupRecord readGroup)

Creates an artificial SAM header with standard test parameters and a Read Group

Parameters:

readGroup - read group

Returns:

the SAM header

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String name,
                                            int refIndex,
                                            int alignmentStart,
                                            int length)

Create an artificial GATKRead based on the parameters. The cigar string will be *M, where * is the length of the read

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

length - the length of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String name,
                                            int refIndex,
                                            int alignmentStart,
                                            byte[] bases,
                                            byte[] qual)

Create an artificial GATKRead based on the parameters. The cigar string will be *M, where * is the length of the read

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String name,
                                            java.lang.String contig,
                                            int alignmentStart,
                                            byte[] bases,
                                            byte[] qual)

Create an artificial GATKRead based on the parameters. The cigar string will be *M, where * is the length of the read

Parameters:

header - the SAM header to associate the read with

name - the name of the read

contig - the contig to which the read is aligned

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String name,
                                            int refIndex,
                                            int alignmentStart,
                                            byte[] bases,
                                            byte[] qual,
                                            java.lang.String cigar)

Create an artificial GATKRead based on the parameters

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

cigar - the cigar string of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String name,
                                            java.lang.String contig,
                                            int alignmentStart,
                                            byte[] bases,
                                            byte[] qual,
                                            java.lang.String cigar)

Create an artificial GATKRead based on the parameters

Parameters:

header - the SAM header to associate the read with

name - the name of the read

contig - the contig to which the read is aligned

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

cigar - the cigar string of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            byte[] bases,
                                            byte[] qual,
                                            java.lang.String cigar)

Create an artificial GATKRead with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000

Parameters:

header - SAM header for the read

bases - the sequence of the read

qual - the qualities of the read

cigar - the cigar string of the read

Returns:

the artificial GATKRead

createArtificialRead

public static GATKRead createArtificialRead(byte[] bases,
                                            byte[] qual,
                                            java.lang.String cigar)

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            java.lang.String cigarString)

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.SAMFileHeader header,
                                            htsjdk.samtools.Cigar cigar)

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.Cigar cigar)

createUniqueArtificialRead

public static GATKRead createUniqueArtificialRead(htsjdk.samtools.Cigar cigar)

Makes a new read with a name that is unique (so that it will return false to equals(otherRead)

createArtificialRead

public static GATKRead createArtificialRead(htsjdk.samtools.Cigar cigar,
                                            java.lang.String name)

createArtificialRead

public static GATKRead createArtificialRead(java.lang.String cigarString)

createArtificialUnmappedRead

public static GATKRead createArtificialUnmappedRead(htsjdk.samtools.SAMFileHeader header,
                                                    byte[] bases,
                                                    byte[] qual)

createArtificialUnmappedReadWithAssignedPosition

public static GATKRead createArtificialUnmappedReadWithAssignedPosition(htsjdk.samtools.SAMFileHeader header,
                                                                        java.lang.String contig,
                                                                        int alignmentStart,
                                                                        byte[] bases,
                                                                        byte[] qual)

createUniqueArtificialRead

public static GATKRead createUniqueArtificialRead(java.lang.String cigarString)

Makes a new read with a name that is unique (so that it will return false to equals(otherRead)

createSamBackedRead

public static GATKRead createSamBackedRead(java.lang.String name,
                                           int start,
                                           int length)

Creates an artificial GATKRead backed by a SAMRecord. The read will consist of the specified number of Q30 'A' bases, and will be mapped to contig "1" at the specified start position.

Parameters:

name - name of the new read

start - start position of the new read

length - number of bases in the new read

Returns:

an artificial GATKRead backed by a SAMRecord.

createSamBackedRead

public static GATKRead createSamBackedRead(java.lang.String name,
                                           java.lang.String contig,
                                           int start,
                                           int length)

Creates an artificial GATKRead backed by a SAMRecord. The read will consist of the specified number of Q30 'A' bases, and will be mapped to the specified contig at the specified start position.

Parameters:

name - name of the new read

contig - contig the new read is mapped to

start - start position of the new read

length - number of bases in the new read

Returns:

an artificial GATKRead backed by a SAMRecord.

createHeaderlessSamBackedRead

public static GATKRead createHeaderlessSamBackedRead(java.lang.String name,
                                                     java.lang.String contig,
                                                     int start,
                                                     int length)

Creates an artificial GATKRead backed by a SAMRecord with no header. The read will consist of the specified number of Q30 'A' bases, and will be mapped to the specified contig at the specified start position.

Parameters:

name - name of the new read

contig - contig the new read is mapped to

start - start position of the new read

length - number of bases in the new read

Returns:

an artificial GATKRead backed by a SAMRecord.

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  java.lang.String name,
                                                                  int refIndex,
                                                                  int alignmentStart,
                                                                  int length)

Create an artificial SAMRecord based on the parameters. The cigar string will be *M, where * is the length of the read

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

length - the length of the read

Returns:

the artificial SAMRecord

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  java.lang.String name,
                                                                  int refIndex,
                                                                  int alignmentStart,
                                                                  byte[] bases,
                                                                  byte[] qual)

Create an artificial SAMRecord based on the parameters. The cigar string will be *M, where * is the length of the read

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

Returns:

the artificial SAMRecord

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  java.lang.String name,
                                                                  int refIndex,
                                                                  int alignmentStart,
                                                                  byte[] bases,
                                                                  byte[] qual,
                                                                  java.lang.String cigar)

Create an artificial SAMRecord based on the parameters

Parameters:

header - the SAM header to associate the read with

name - the name of the read

refIndex - the reference index, i.e. what chromosome to associate it with

alignmentStart - where to start the alignment

bases - the sequence of the read

qual - the qualities of the read

cigar - the cigar string of the read

Returns:

the artificial SAMRecord

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  byte[] bases,
                                                                  byte[] qual,
                                                                  java.lang.String cigar)

Create an artificial SAMRecord with the following default parameters : header: numberOfChromosomes = 1 startingChromosome = 1 chromosomeSize = 1000000 read: name = "default_read" refIndex = 0 alignmentStart = 10000

Parameters:

header - SAM header for the read

bases - the sequence of the read

qual - the qualities of the read

cigar - the cigar string of the read

Returns:

the artificial SAMRecord

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(byte[] bases,
                                                                  byte[] qual,
                                                                  java.lang.String cigar)

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  htsjdk.samtools.Cigar cigar,
                                                                  java.lang.String name)

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.SAMFileHeader header,
                                                                  htsjdk.samtools.Cigar cigar)

createArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createArtificialSAMRecord(htsjdk.samtools.Cigar cigar)

createUniqueArtificialSAMRecord

public static htsjdk.samtools.SAMRecord createUniqueArtificialSAMRecord(htsjdk.samtools.Cigar cigar)

Makes a new read with a name that is unique (so that it will return false to equals(otherRead)

createPair

public static java.util.List<GATKRead> createPair(htsjdk.samtools.SAMFileHeader header,
                                                  java.lang.String name,
                                                  int readLen,
                                                  int leftStart,
                                                  int rightStart,
                                                  boolean leftIsFirst,
                                                  boolean leftIsNegative)

createPair

public static java.util.List<GATKRead> createPair(htsjdk.samtools.SAMFileHeader header,
                                                  java.lang.String name,
                                                  int readLen,
                                                  int refIndex,
                                                  int leftStart,
                                                  int rightStart,
                                                  boolean leftIsFirst,
                                                  boolean leftIsNegative)

createIdenticalArtificialReads

public static java.util.Collection<GATKRead> createIdenticalArtificialReads(int size,
                                                                            htsjdk.samtools.SAMFileHeader header,
                                                                            java.lang.String name,
                                                                            int refIndex,
                                                                            int alignmentStart,
                                                                            int length)

Create a collection of identical artificial reads based on the parameters. The cigar string for each read will be *M, where * is the length of the read. Useful for testing things like positional downsampling where you care only about the position and number of reads, and not the other attributes.

Parameters:

size - number of identical reads to create

header - the SAM header to associate each read with

name - name associated with each read

refIndex - the reference index, i.e. what chromosome to associate them with

alignmentStart - where to start each alignment

length - the length of each read

Returns:

a collection of stackSize reads all sharing the above properties

createRandomRead

public static GATKRead createRandomRead(htsjdk.samtools.SAMFileHeader header,
                                        int length)

createRandomRead

public static GATKRead createRandomRead(int length)

createRandomRead

public static GATKRead createRandomRead(htsjdk.samtools.SAMFileHeader header,
                                        int length,
                                        boolean allowNs)

createRandomRead

public static GATKRead createRandomRead(int length,
                                        boolean allowNs)

createRandomReadQuals

public static byte[] createRandomReadQuals(int length)

Create random read qualities

Parameters:

length - the length of the read

Returns:

an array with randomized base qualities between 0 and 50

createRandomReadBases

public static byte[] createRandomReadBases(int length,
                                           boolean allowNs)

Create random read qualities

Parameters:

length - the length of the read

allowNs - whether or not to allow N's in the read

Returns:

an array with randomized bases (A-N) with equal probability

mappedReadIterator

public static ArtificialReadQueryIterator mappedReadIterator(int startingChr,
                                                             int endingChr,
                                                             int readCount)

create an iterator containing the specified read piles

Parameters:

startingChr - the chromosome (reference ID) to start from

endingChr - the id to end with

readCount - the number of reads per chromosome

Returns:

iterator representing the specified amount of fake data

mappedAndUnmappedReadIterator

public static ArtificialReadQueryIterator mappedAndUnmappedReadIterator(int startingChr,
                                                                        int endingChr,
                                                                        int readCount,
                                                                        int unmappedReadCount)

create an iterator containing the specified read piles

Parameters:

startingChr - the chromosome (reference ID) to start from

endingChr - the id to end with

readCount - the number of reads per chromosome

unmappedReadCount - the count of unmapped reads to place at the end of the iterator, like in a sorted bam file

Returns:

iterator representing the specified amount of fake data

createArtificialSamHeader

public static htsjdk.samtools.SAMFileHeader createArtificialSamHeader(htsjdk.samtools.SAMSequenceDictionary dict)

Creates an artificial SAM header based on the sequence dictionary dict

Returns:

a new SAM header

createSplicedInsertionPileupElement

public static PileupElement createSplicedInsertionPileupElement(int offsetIntoRead,
                                                                htsjdk.variant.variantcontext.Allele insertionAllele,
                                                                int lengthOfRead)

Create a pileupElement with the given insertion added to the bases. Assumes the insertion is prepended with one "reference" base.

Parameters:

offsetIntoRead - the offset into the read where the insertion Allele should appear. As a reminder, the insertion allele should have a single ref base prepend. Must be 0 - (lengthOfRead-1)

insertionAllele - the allele as you would see in a VCF for the insertion. So, it is prepended with a ref base. Never null

lengthOfRead - the length of the artificial read. Does not include any length differences due to the spliced indel. Must be greater than zero.

Returns:

pileupElement with an artificial read containing the insertion.

createSplicedDeletionPileupElement

public static PileupElement createSplicedDeletionPileupElement(int offsetIntoRead,
                                                               htsjdk.variant.variantcontext.Allele referenceAllele,
                                                               int lengthOfRead)

See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing the specified deletion.

Parameters:

offsetIntoRead - See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int)

referenceAllele - the reference allele as you would see in a VCF for the deletion. In other words, it is the deletion prepended with a single ref base. Never null

lengthOfRead - See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int)

Returns:

pileupElement with an artificial read containing the deletion.

createNonIndelPileupElement

public static PileupElement createNonIndelPileupElement(int offsetIntoRead,
                                                        htsjdk.variant.variantcontext.Allele newAllele,
                                                        int lengthOfRead)

See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int), except that this method returns a pileup element containing base-by-base replacement. As a result, the length of the read will not change.

Parameters:

offsetIntoRead - See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int)

newAllele - The new bases that should be in the read at the specified position. If this allele causes the replacement to extend beyond the end of the read (i.e. offsetIntoRead + length(newAllele) is greater than length of read), the replacement will be truncated.

lengthOfRead - See createSplicedInsertionPileupElement(int, htsjdk.variant.variantcontext.Allele, int)

Returns:

pileupElement with an artificial read containing the new bases specified by te given allele.