splitChromosome without header?

[jtmorgan0]

Is it possible to have splitChromosome output without headers? I have an analysis where 500,000+ "chromosomes" are split, so adding that many lines as a header to every file is not efficient. I have an okay workaround of trimming .sam files after they are split, but it doesn't keep up with splitChromosome's speed and obviously writing and immediately deleting 250B lines isn't ideal.

I've done enough digging to know that many utilities expect headers to function, so I haven't found an easy solution on my own. Thanks for any insight!