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WaveGenerator
Parameters may be changed through the input file. A sample is provided, which can be copied and customized. Ideally, you will want to place the file with the data being processes (or the results) such that settings can later be confirmed. Parameter file can be overridden via command line arguments -data_file, -output_path, and -noise_compensation.
In order to call broader peaks, the test for peak fit is: area_under_peak_and_over_wig <= (noise_compensation) * area_under_wig/sigma (function sigma_test in MapDecomposingThread) Increasing noise_compensation allows fine-tuning of the fit of peaks. Noise_compensation of 16 allows for larger sigmas (Good for ChIP-chip data). In this case, significant peaks (above noise) tend to have sigma >= 20. Chip-seq data does better with noise_compensation = 1.
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input_file(File Path)
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map_type(Integer) -
triangle_min(Integer) -
triangle_median(Integer) -
fragment_length(Integer) -
round_leading_edge(Boolean) -
max_pet_length(Integer)
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min_height(Integer)
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processor_threads(Integer)
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output_path(File Path) -
file_name(String) -
number_waves(Boolean) -
make_wig(Boolean)
- clean exit on Ctrl-C
- make parameters set from a text file - Done
- make gui to change text file
- make gui for looking at results
- add code for dumping results to DB. - In progress
- add code for retrieving from db
- add code for visualizing results.
- compress/gzip wig file at end.
- code for comparing sample/control data sets
- set maximum number of cores to # of available processors.