pattern and query sequence mismatched

[xiaoyunguo]

Hi,

Thanks for making this tool available. I kept running into this issues when testing the tool. If I include the number of DNA and RNA bulges in the input file just as the example, it will return an error complaining "Critical error! The length of target sequences should match with the length of pattern sequence."

The simple test input file is copy from the example:

/ref_genome_fa_folder
NNNNNNNNNNNNNNNNNNNNNRG 2 1
GGCCGACCTGTCGCTGACGCNNN 5

It seems to run fine without the inputs for bulges following the pattern sequence. I wonder what I did wrong here.

Thanks