I am wondering if there is a slick way access all the possible alignments for a read present in sam or bam file given the read header. Since the existing codebase is in perl I would prefer something which can be done in/via perl.
By default BAM's are indexed by location so the inbuilt samtools indexing wont work I guess.
I should also say the input bam file will have in the order of 500 million total alignments and many reads are expected to be aligned to more than one place in the genome. Given the size of the data loading it all in one big hash is not turning out to be memory friendly.