2bit sequence retrieval broken for all Ns
morrifeldman opened this issue · comments
If I try and retrieve a sequence that is all Ns by doing something like
puts hg19ref.find_by_interval("chr1:10-100")
or
puts hg19ref.subseq("chr1:10-100")
I get the following error:
ArgumentError: negative argument
from /Users/morriwork/.rvm/gems/ruby-1.9.3-p125@methAnalysis/gems/bio-ucsc-api-0.5.1/lib/bio-ucsc/file/twobit.rb:125:in *' from /Users/morriwork/.rvm/gems/ruby-1.9.3-p125@methAnalysis/gems/bio-ucsc-api-0.5.1/lib/bio-ucsc/file/twobit.rb:125:in
block in find_by_interval'
from /Users/morriwork/.rvm/gems/ruby-1.9.3-p125@methAnalysis/gems/bio-ucsc-api-0.5.1/lib/bio-ucsc/file/twobit.rb:117:in map' from /Users/morriwork/.rvm/gems/ruby-1.9.3-p125@methAnalysis/gems/bio-ucsc-api-0.5.1/lib/bio-ucsc/file/twobit.rb:117:in
find_by_interval'
from (irb):9
from /Users/morriwork/.rvm/rubies/ruby-1.9.3-p125/bin/irb:16:in `
I am using ruby 1.9.3-p125 and I installed bioruby-ucsc-api from the gem.
I have reproduced the trouble you reported. Thank you and please wait for a while.
Thank you for your patience. The bug is fiexed and new Ruby UCSC API version 0.5.2 has been released.