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