Directories

Commands

The Commands directory contains source codes for all subcommands.

1. callpeak_cmd.py
2. bdgpeakcall_cmd.py
3. bdgbroadcall_cmd.py
4. bdgcmp_cmd.py
5. bdgdiff_cmd.py
6. bdgopt_cmd.py
7. cmbreps_cmd.py
8. diffpeak_cmd.py
9. filterdup_cmd.py
10. pileup_cmd.py
11. predictd_cmd.py
12. randsample_cmd.py
13. refinepeak_cmd.py
14. callvar_cmd.py

IO

The IO directory contains Python and Cython source codes for read and write data files.

1. BedGraphIO.pyx
2. OutputWriter.py
3. Parser.pyx
4. PeakIO.pyx

Signal

The Signal directory contains Python, Cython and C source codes for data transformation and calculation.

1. BedGraph.pyx
2. CallPeakUnit.pyx
3. FixWidthTrack.pyx
4. PairedEndTrack.pyx
5. Pileup.pyx
6. Prob.pyx
7. ScoreTrack.pyx
8. Signal.pyx
9. cPosValCalculation.c, cPosValCalculation.h, cPosValCalculation.pxd
10. PeakModel.pyx
11. PeakDetect.pyx

Utilities

The Utilities directory contains source codes to validate command line options and to provide constants (including version number and buffer size).

1. Constants.py
2. OptValidator.py