class AlignmentConverter extends Serializable with Logging
Conversions between Alignments and other formats.
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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.
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def
convert(samRecord: SAMRecord): Alignment
Converts a SAM record into an Avro Alignment.
Converts a SAM record into an Avro Alignment.
- samRecord
Record to convert.
- returns
Returns the original record converted into Avro.
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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.
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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.
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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.
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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.
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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.
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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.
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