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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.
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;