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rogerjms / bedtools

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genomes/mouse.mm9.genome broken by commit 9432b296f0fdeae39518275dcbb24de446eb003a #87

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Hello,

In the commit 9432b296f0fdeae39518275dcbb24de446eb003a, an extra space was 
added after ‘chr10’ in ‘genomes/mouse.mm9.genome’

  https://github.com/arq5x/bedtools/commit/9432b296f0fdeae39518275dcbb24de446eb003a

As a result, slopBed produces invalid coordinates:

$ cat ex1.gff 
chr11   test    mRNA    50  100 .   -   .   ID=2;Name=test2
chr10   test    mRNA    50  100 .   -   .   ID=1;Name=test1

$ slopBed -g /usr/share/bedtools/genomes/mouse.mm9.genome -s -l 0 -r 0 -i 
ex1.gff
chr11   test    mRNA    50  100 .   -   .   ID=2;Name=test2
chr10   test    mRNA    50  -1  .   -   .   ID=1;Name=test1

These invalid coordinates are not rejected and introduce errors in subsequent 
calculations:

$ cat ex2.gff 
chr11   test    mRNA    1000    2000    .   -   .   ID=2;Name=test2
chr10   test    mRNA    1000    2000    .   -   .   ID=1;Name=test1

$ slopBed -g /usr/share/bedtools/genomes/mouse.mm9.genome -s -l 0 -r 0 -i 
ex1.gff | intersectBed -a ex2.gff -b -
chr10   test    mRNA    1000    2000    .   -   .   ID=1;Name=test1

Cheers,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan

Original issue reported on code.google.com by Charles....@gmail.com on 23 Sep 2011 at 11:45

GoogleCodeExporter commented 9 years ago 
Thank you.  This is corrected in the repo.

Original comment by aaronqui...@gmail.com on 23 Sep 2011 at 1:06