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emmanuelparadis / New-code-for-VCF

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New Code Not loading VCF File #1

Closed mgiresi closed 7 years ago

mgiresi commented 9 years ago

Hi,

I think that peas was updated to include the new vcc info into the workflow, but I tried to load a vcf file into R and got the following error messages (after I force quit after an hour waiting for file to load); including both command and error:

read.vcf("2015_termiteRF.vcf", from = 1, to = 10000, which.loci = NULL, quiet = FALSE)

Warning messages: 1: In i + 0:5 : NAs produced by integer overflow 2: In i + 0:5 : NAs produced by integer overflow 3: In i + 0:5 : NAs produced by integer overflow 4: In i + 0:5 : NAs produced by integer overflow 5: In i + 0:5 : NAs produced by integer overflow 6: In i + 1L : NAs produced by integer overflow

Also, if I try using the command to get info from the vcc file, I get the following error:

RF_info <-VCFlociinfo("2015_termiteRF.vcf") Error: could not find function "VCFlociinfo"

emmanuelparadis commented 9 years ago

Hi,

It's difficult to help with the first command. Maybe your VCF file is not arranged following the standard.

For the 2nd command: the function has been renamed VCFloci(). Try with that, and you'll if you have something that makes sense.