Pipeclip

Attempts to make use of control data
- If provided, the mutation rate in the control data will be used as background for looking for reliable mutations.
- You can use "-t" to specify control data.
- Not fully tested.

- Fixed clustering bug
- Fixed file name bug
- Reduced memory use

- Allow ZTNB to use default setting to do regression
- Revised typos

**Code re-structure and bug fixes.**
- Fixed bugs in finding mutations when there are multiple consecutive insertions;
- Added more options for startcoef for zero-truncated negative binomial regression to make sure program can converge;
- Modified the algorithm to count coverage for each mutation site, improved speed;
- Replace bar charts with log file;

- Bug fix in finding mutations
- Update R code with error control