Bed marker ID is not identical in the alignment output

The process getFasta generates a new FASTA header which includes the start and stop of the extracted sequence. This complete header is required for the process adding the polymorphism inside the extracted sequence. While this extra info in the header is removed in further processes for other file types, it is not for the BED file. For example, Lcu.2RBY.Chr1_58402_A_G becomes Lcu.2RBY.Chr1_58402_A_G::Lcu.2RBY.Chr1:58301-58502

In the mean time, please remove it manually with: sed -re 's/::[^ ]+ / /' alignment.paf