bedSort fails for 0 length features
Opened this issue · 1 comments
bedSort outputs the following for the SNPs dataset from UCSC
...
chr22 17586594 17586595 rs34484815 0 +
chr22 17586605 17586605 rs536619616 0 +
chr22 17586604 17586605 rs560126106 0 +
...
I guess the problem are 0 length features which do not make sense. But bedtools should still output sorted data.
The note from UCSC on the validity of 0 length SNPs:
We consider point
insertions into the genome to be zero length features. You can see the
SNP in question in the following Genome Browser view:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg19_chr22PointInsertionwhere the highlighted SNP indicates a G or GG insertion between bases
17586605 and 17586606 on chromosome 22. Because we internally store
our coordinates as zero-based half open coordinates, these point
insertions end up as zero length coordinates. For more information on
our coordinate system please see the following blog post:
http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/