Hello,
Just reporting a potential bug or improvement. I encountered an error while using wiggletools overlaps command. I have a bed file sorted with GNU sort -k1,1 -k2,2n command which puts uppercase contig names such as GL000220.1 after lowercase chromosome names. wiggletools seem to expect GL000220.1 to come before chr1,2 etc. As a workaround, I sorted my bed file with LC_COLLATE=C sort -k1,1 -k2,2n which worked. However, I think most sorted bed files use the default locale settings which would lead to an error.
Thank you!
Hello,
Just reporting a potential bug or improvement. I encountered an error while using
wiggletools overlapscommand. I have a bed file sorted with GNUsort -k1,1 -k2,2ncommand which puts uppercase contig names such as GL000220.1 after lowercase chromosome names. wiggletools seem to expect GL000220.1 to come before chr1,2 etc. As a workaround, I sorted my bed file withLC_COLLATE=C sort -k1,1 -k2,2nwhich worked. However, I think most sorted bed files use the default locale settings which would lead to an error.Thank you!