org.bdgenomics.adam.converters
Converts a single ADAM record into a SAM record.
Converts a single ADAM record into a SAM record.
ADAM formatted alignment record to convert.
SAM file header to attach to the record.
Dictionary describing the read groups that are in the RDD that this read is from.
Returns the record converted to htsjdk format. Can be used for output to SAM/BAM.
Converts a fragment to a set of reads.
Converts a fragment to a set of reads.
Fragment to convert.
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.
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.
Read to convert to FASTQ.
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.
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 this read in string form.
Creates a SAM formatted header.
Creates a SAM formatted header. This can be used with SAM or BAM files.
Reference sequence dictionary to use for conversion.
Dictionary containing record groups.
Converted SAM formatted record.
This class contains methods to convert AlignmentRecords to other formats.