org.bdgenomics.adam.converters

AlignmentRecordConverter

class AlignmentRecordConverter extends Serializable

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  1. new AlignmentRecordConverter()

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  8. def convert(adamRecord: AlignmentRecord, header: SAMFileHeaderWritable): 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 use.

    returns

    Returns the record converted to SAMtools format. Can be used for output to SAM/BAM.

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

    Converts a single record to FASTQ.

    Converts a single record to FASTQ. FASTQ format is:

    adamRecord

    Read to convert to FASTQ.

    returns

    Returns this read in string form.

  10. 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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