The option -discardInOutputFiles=particleType[,...] in the command line is used to discard particles of one or more types in the output files, which is useful in reducing the size of the files if a particular particle type is not needed in the results. This option applies to all output files produced in a shower run.
The file produced by the -outOfBounds, and -undefinedRegion contain the full coordinates of particles going out of bounds, or going into a volume within bounds but not defined. Usually these particles aren't interesting. These files can be used for debugging purposes. For instance, one could check whether total energy is conserved.
Beam data coordinates are buffered in internal data pages of 500 rows in length before being written to the output file. Thus one may find interleaved data pages for electrons, positrons, and photons. When processing data one should realize that the output files are split into pages. For instance before histogramming, say the energy coordinate, the command sddscombine should be used on the output file to merge all data pages into one.