Table 1.

Attributes and methods of the Bio::DB::Sam object

binary	denotes whether this is a binary file
compressed	denotes whether this file is compressed
fasta_path	path to the reference FASTA file
sam	path to the associated BAM file
chromosome_coverage	return Ruby Array of coverage over a region
fetch	fetch alignment in a region from a bam file, returning a Ruby Array object
fetch_reference	fetch regions of the reference file returning a String object of the relevant sequence
fetch_with_function	fetch all alignments in a region passing in a Ruby Proc object as a callback, returning an iterator
index_stats	get information about reference and number of mapped reads
merge	merge two or more bam files
mpileup	an iterator that returns Pileup objects representing the reads over a single position
sort	sort the BAM file