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 use.
Returns the record converted to SAMtools 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
Read to convert to FASTQ.
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.