Sortings for chain file - mengzhou/mschain GitHub Wiki

The program is written in a way that deals with input and chain file line by line. So the order of both files are important.

For example, if the chain file is sorted numerically as chr1, chr2, chr3, ..., chr10, ..., and the input BED file is sorted by alphabetic order for the first column with specifying LC_ALL=C, i.e. chr1, chr10, chr11, ..., the program fails.