Why input folder storing new directory instead of folder storing assemblies

[yangyxt]

Dear Firtina,

Thanks for making this tool. But I had a few confusion about the input args of run_pipeline.sh.

First of all, why input OLDREF and NEWREF as folder storing assemblies instead of the path of the assemblies?

I tend to generate my own chain file. And to use that chain file to convert alignment against a custom assembly to alignment against hg19. According to your code in run_pipeline.sh, the new assembly is ${NEWREF}/${chr}.${SEQ_FILE_EXT} where ${chr} is the basename of my chain file.

I dunno why the new assembly's file name must be the same with my chain file's base name. Am I missing something here?