Is there any way for the user to change the 500,000 bp limit (besides doing changes in the source code)?
Also what is the minimum overhang of a read which subjuncs is able to handle (for example, is it able to map/split a read of 100 bp as: 80bp+20bp, or 83bp+17bp, or 85bp+15bp, or 90bp+10bp, or 95bp+5bp)? There must be a limit for overhang and as far as I know no aligner would split a read of 100bp as 95bp+5bp (here most of the aligners would just soft clip the last 5bp and this is ok)!
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