search

berybox / KEC

Unique sequence search by K-mer exclusion
8 stars 1 forks source link

Error: slice out of bounds #1

Open beatrizvm opened 2 weeks ago

beatrizvm commented 2 weeks ago

Hi,

I was trying to run KEC version 1.1 on an example database. However, the kec exclude command seems to run into an error whenever there is more than one target sequence.

Attached is the small example that failed to run. data.zip

Here is a summary of the error:

./kec-linux-x64 e -t targets/ -n neighbors/ -o kecE.fasta
Reading NONTARGET file: "n1.fasta" took 1.75674ms
Reading TARGET file: "t2.fasta" took 1.309807ms
Reading TARGET file: "t1.fasta" took 1.240869ms
panic: runtime error: slice bounds out of range [4519:0]

goroutine 1 [running]:
github.com/berybox/KEC/pkg/maps/mmapbasic.(*MaskMap).Unmask(0xc00010cb10?, {0xc0002f79a7, 0xc}, {{0xc000015589?, 0xc00010cb10?}, 0xc000341b00?})
        c:/Users/pavel/Documents/Go-Projects/KEC/pkg/maps/mmapbasic/maskmap.go:35 +0xd4
github.com/berybox/KEC/pkg/keccore/kecoriginal.(*Excluder).Run.func2({0xc0002f79a7?, 0x1e0000c00021f688?}, {{0xc000015589?, 0x40d0c5?}, 0x5f7508?})
    ....
berybox commented 2 weeks ago

I'll take a look at the problem and if I can, I'll release a fixed version. In the meantime, I recommend simply merging the "target" files into one (for example, by using: cat seq1.fasta seq2.fasta > seqall.fasta)

beatrizvm commented 2 weeks ago

Thank you for the answer.

I hadn't understood that if the inclusion step is performed before the exclusion then the input consists of a single target sequence. If that is the case, then KEC runs without any other issues.