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The Flux Capacitor needs the SAM input file to be indexed. The index is needed to access every locus indipendently, without the need to sequentially read the whole file. For this reason only BAM files are supported.

The BAM file used as input for the Flux Capacitor should be sorted by genomic position and indexed the reference id and then the leftmost coordinate before indexing (see SAM format specification above). The index file has to be placed in the same folder as the BAM file.