AlignmentRecordConverter

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8. def convert(adamRecord: AlignmentRecord, header: SAMFileHeaderWritable, rgd: RecordGroupDictionary): SAMRecord

   Converts a single ADAM record into a SAM record.

   Converts a single ADAM record into a SAM record.

   adamRecord

   ADAM formatted alignment record 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.

9. def convertFragment(fragment: Fragment): Iterable[AlignmentRecord]

   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 AlignmentRecord per sequence in the Fragment.

10. def convertToFastq(adamRecord: AlignmentRecord, maybeAddSuffix: Boolean = false, outputOriginalBaseQualities: Boolean = false): String

    Converts a single record to FASTQ.

    Converts a single record to FASTQ. FASTQ format is:

    @readName
    sequence
    +<optional readname>
    ASCII quality scores

    If the base qualities are unknown (qual 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.

    outputOriginalBaseQualities

    If true and the original base quality field is set (SAM "OQ" tag), outputs the original qualities. Else, output the qual field. Defaults to false.

    returns

    Returns this read in string form.

11. def createSAMHeader(sd: SequenceDictionary, rgd: RecordGroupDictionary): 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 record groups.

    returns

    Converted SAM formatted record.

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