cLoops v0.9

1. Pre-set parameters for our tested ChIA-PET, Hi-C and HiChIP data, with the parameter -m (--mode) to set, -m 0 accepts user settings; -m 1 for sharp peak like ChIA-PET data; -m 2 for broad peak like ChIA-PET data; -m 3 for deep sequenced Hi-C (~200 million cis PETs); -m 4 for HiChIP (~100 million cis PETs);
2. Multiple minPts options added;
3. Fixed bug of merging overlapped loops;
4. The generation of self-ligation and inter-ligation PETs distance distribution plot can be determine by user using -plot option;
5. Turn off deLoops for further development;
6. Roll back cDBSCAN for Yaqiang Cao's version, Zhaoxiong Chen's version is under further improvement;
7. fixed several small bugs
8. for old option like -j 1, now set -j is OK.