hello - i'm trying to set the -e flag in bwa aln and it doesn't appear to change. normally when i edit the flags and hit enter, the stdout shows the updated parameter settings.

i type:

./bwa aln -o 6

and it prints:

Options:

     -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
     -o INT    maximum number or fraction of gap opens [6]
     -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]

where the number in brackets after the -o option is what i've entered. when i do this for the -e flag, it doesn't change.

i type:

./bwa aln -e 5 and it prints:

Options:

     -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
     -o INT    maximum number or fraction of gap opens [1]
     -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]

any ideas what's going on here? has anyone been able to successfully change this parameter? it's entirely possible i'm misunderstanding how something works. any help would be great.

thank you!

SH1

asked 20 Aug '10, 15:13

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SH2
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accept rate: 0%

edited 20 Aug '10, 15:19


All the other parameters update the value in brackets to equal the parameter you enter, but that's not the case with the -e parameter. (see line 270 of bwtaln.c) It may be a bug or may have been intentional.

Looking at the rest of the code, though, it seems that it does change the value of -e, it just doesn't report it in the usage message. Just put in -e 5 and it should work just fine, even if the usage message reports it as -1.

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answered 20 Aug '10, 17:15

mrawlins's gravatar image

mrawlins
431119
accept rate: 16%

thanks! i wouldn't have even known where to start.

(23 Aug '10, 14:41) SH2
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Asked: 20 Aug '10, 15:13

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Last updated: 23 Aug '10, 14:41

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