AlignmentConverter

Instance Constructors

new AlignmentConverter()

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def convert(adamRecord: Alignment, header: SAMFileHeader, rgd: ReadGroupDictionary): SAMRecord

Converts a single ADAM record into a SAM record.
Converts a single ADAM record into a SAM record.
adamRecord
ADAM formatted alignment to convert.
header
SAM file header to attach to the record.
rgd
Dictionary describing the read groups that are in the RDD that this read is from.
returns
Returns the record converted to htsjdk format. Can be used for output to SAM/BAM.
def convertFragment(fragment: Fragment): Iterable[Alignment]

Converts a fragment to a set of reads.
Converts a fragment to a set of reads.
fragment
Fragment to convert.
returns
The collection of alignments described by the fragment. If the fragment doesn't contain any alignments, this method will return one unaligned Alignment per sequence in the Fragment.
def convertSecondReadToTab5(adamRecord: Alignment, writeOriginalQualityScores: Boolean = false): String

Converts a single record representing the second read of a pair to Bowtie tab5 format.
Converts a single record representing the second read of a pair to Bowtie tab5 format.
In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. A paired-end read line is [name]\t[seq1]\t[qualityScores1]\t[seq2]\t[qualityScores2]\n.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
adamRecord
Read to convert to FASTQ.
writeOriginalQualityScores
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
returns
Returns this read in string form.
def convertToFastq(adamRecord: Alignment, maybeAddSuffix: Boolean = false, writeOriginalQualityScores: Boolean = false): String

Converts a single record to FASTQ format.
Converts a single record to FASTQ format.
FASTQ format is:
```
@readName
sequence
+<optional readname>
ASCII quality scores
```
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
adamRecord
Read to convert to FASTQ.
maybeAddSuffix
If true, check if a "/%d" suffix is attached to the read. If there is no suffix, a slash and the number of the read in the sequenced fragment is appended to the readname. Default is false.
writeOriginalQualityScores
If true and the original base quality score field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
returns
Returns this read in string form.
def convertToTab5(adamRecord: Alignment, writeOriginalQualityScores: Boolean = false): String

Converts a single record to Bowtie tab5 format.
Converts a single record to Bowtie tab5 format.
In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. A paired-end read line is [name]\t[seq1]\t[qualityScores1]\t[seq2]\t[qualityScores2]\n.
The index suffix will be trimmed from the read name if present.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
adamRecord
Read to convert to FASTQ.
writeOriginalQualityScores
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
returns
Returns this read in string form.
def convertToTab6(adamRecord: Alignment, maybeAddSuffix: Boolean = false, writeOriginalQualityScores: Boolean = false): String

Converts a single record to Bowtie tab6 format.
Converts a single record to Bowtie tab6 format.
In Bowtie tab6 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. For paired-end alignments, the second end can have a different name from the first: [name1]\t[seq1]\t[qualityScores1]\t[name2]\t[seq2]\t[qualityScores2]\n.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
adamRecord
Read to convert to FASTQ.
maybeAddSuffix
If true, check if a "/%d" suffix is attached to the read. If there is no suffix, a slash and the number of the read in the sequenced fragment is appended to the readname. Default is false.
writeOriginalQualityScores
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
returns
Returns this read in string form.
def createSAMHeader(sd: SequenceDictionary, rgd: ReadGroupDictionary): SAMFileHeader

Creates a SAM formatted header.
Creates a SAM formatted header. This can be used with SAM or BAM files.
sd
Reference sequence dictionary to use for conversion.
rgd
Dictionary containing read groups.
returns
Converted SAM formatted record.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Doc: package converters

class AlignmentConverter extends Serializable

Instance Constructors

new AlignmentConverter()

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def convert(adamRecord: Alignment, header: SAMFileHeader, rgd: ReadGroupDictionary): SAMRecord

def convertFragment(fragment: Fragment): Iterable[Alignment]

def convertSecondReadToTab5(adamRecord: Alignment, writeOriginalQualityScores: Boolean = false): String

def convertToFastq(adamRecord: Alignment, maybeAddSuffix: Boolean = false, writeOriginalQualityScores: Boolean = false): String

def convertToTab5(adamRecord: Alignment, writeOriginalQualityScores: Boolean = false): String

def convertToTab6(adamRecord: Alignment, maybeAddSuffix: Boolean = false, writeOriginalQualityScores: Boolean = false): String

def createSAMHeader(sd: SequenceDictionary, rgd: ReadGroupDictionary): SAMFileHeader

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped