MATLAB: Open huge SAM files

.bam.samBioinformatics Toolbox

Hi! I try to import a SAM (Sequence Alignment/Map) file (or parts of it) into Matlab but because it has 10GB, I don't know any good way to do this… I guess I need to create a BioMap object but that is possible only for files < 4GB.
Any help is appreciated.
Best, Razvan

Best Answer

  • The 4GB limitation for BioIndexedFile (which is the back-end support to read SAM files into BioMap) has been removed in 12a. Before 12a you could also change your SAM file to BAM, a 10GB SAM file should result into a 2.5 GB BAM file, BioMap should be able to load it.