open huge SAM files

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Razvan
Razvan on 7 Feb 2012
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

Accepted Answer

Lucio Cetto
Lucio Cetto on 6 Mar 2012
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.
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Razvan
Razvan on 6 Mar 2012
Thanks! I'm glad to hear that Matlab 2012a can handle these huge SAM files. BAM files seem easier to handle, though.

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