Methylpy

Fix bugs and add code for error handling

* Fix chr prefix issue in allc-to-bigwig
* Change the default to False for --remove-clonal in processing pipeline
* Change cytosine position encoding to allow the processing long reads

Allows speeding up merge-allc using multiple processors
methylpy now uses multithread feature of samtools
Optimized the manipulation of allc index
Fixed bugs

methylpy indexes allc files for faster accessing.

merge-allc function is optimized and runs faster.