BamIO.jl is a simple reader for working with next generation sequencing alignment files in bam format. It is able to sequentially extract read information.
example
using BamIO
reader = BamReader("small.bam")
for i = 1:10
read = nextread(reader)
print(read_name(read), "\t")
print(flag(read), "\t")
#print(refid(read), "\t")
print(reference_name(reader, refid(read)), "\t")
print(position(read), "\t")
print(mq(read), "\t")
print(cigar(read), "\t")
print(next_refid(read), "\t")
print(next_position(read), "\t")
print(seq(read), "\t")
print(qualities(read), "\t")
println()
#print(BamIO.bin(read), "\t")
#print(l_read_name(read), "\t")
#print(n_cigar_op(read), "\t")
#print(l_seq(read), "\t")
end