bedtools getfasta -split with single exon

[amirkarger]

I just downloaded the latest bedtools. When I run bedtools getfasta -split with two exons, it works. When I run with one exon, it doesn't.

cat a.bed12
chr1    0       20      ENST00000466557.1       0       +       0       20      0       1       2       3

cat a.fa
>chr1
aaaaannnnnnnnnnttttt

./bedtools.static.binary getfasta -fi a.fa -bed a.bed12 -split
>chr1:0-20
aaaaannnnnnnnnnttttt

But:

cat a.bed12
chr1    0       20      ENST00000466557.1       0       +       0       20      0       2       2,3     3,17

./bedtools.static.binary getfasta -fi a.fa -bed a.bed12 -split
>chr1:0-20
aattt

Are you not allowed to run getfasta with single exons? What am I not seeing in this super-simple example?

[arq5x]

Thanks for reporting this - a long undetected bug. I will fix and send a patch in the morning

[amirkarger]

Thanks for the quick response. Good to know I'm not halluciniating.

[arq5x]

Now fixed in master

[amirkarger]

Works on a tiny file. Will check with a bigger file shortly. Thanks for the quick fix!

[amirkarger]

... and worked a big file with real proteins too. Thanks.