#244 parseInt(~) puts max parameter setting lower than default

bowtie (178)

If I DON'T specify a -m value, Bowtie defaults it to 0xFFFFFFFF, which is 4294967295.
If I DO specify a -m value, Bowtie parses it into an Integer between 1 and INT_MAX, or 2147483647.

So no matter what value I give, if I specify -m, it will always be lower than what Bowtie can do without me.

Was UINT_MAX perhaps intended for parseInt(), instead?


  • Val

    Val - 2014-02-12

    If there are more hits than 0xFFFFFFFF then chances are the hit came from an intergenic region, and since the number of hits found are so high I would dare to say it is either just junk DNA or a very short repeat. Displaying more alignments in that case does not help much and it hurts the overall bowtie performance for the rest of the reads where the results have a better chance to be significant.

    I am not sure in what case one would want to use very high values for -m option, like more than 4 billions.


  • Val

    Val - 2014-02-12
    • status: open --> closed
    • assigned_to: Val
    • Group: --> v0.9.0

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