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.
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.
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.
Reference sequence dictionary to use for conversion.
Dictionary containing record groups.
Converted SAM formatted record.