jmjuanes / bedjs Goto Github PK

Hello,
I had a question about your fasta sequence retrieval method. In this function, you read bytes into a new buffer, parse the buffer, and then if the global options object for the fetching method contains {strand: true}, then you automatically take the complementary sequence instead of checking the strand specificity of the BED object first to see if it is forward or reverse... am i missing something?

It seems that if strand specificity is set to true, you would read the sequence from the chromosome in the orientation specified by the BED record. Thus, if the BED record has forward strand specified, and you took the reverse complement a la fasta.jsL136 then that would produce an incorrect sequence.

Thanks for your work!