v1.2.0-alpha

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.

PIPE-CLIP v1.1.2

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

v1.0.1

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

PIPE-CLIP v1.1.1

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

PIPE-CLIP v1.1.0

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;