Update README.md

Add files via upload

added -s and -m to specify the number of threads and the memory.

Add files via upload

Added the -q option to specify the code to extract uniquely mapped reads. By default -q is set to 255 for BAM generated with BAM. <br>
Adjusted criteria to count intronic reads.<br>
Fixed minor bugs/typos.

Delete independent_intron_annotation directory

independent intron file are removed to another repo to reduce package size.