shaomingfu / pinpoint Goto Github PK

#========
Abstract
#========

Process premature boundary prediction for DeepBound



#===========
Fast install
#===========

./install_pinpoint.sh



#=============
Detail install
#=============

 Execute the following commands to generate Makefile and compile:\\

	aclocal
	autoconf
	autoheader
	automake -a
	./configure
	make

 The executable file pinpoint will be present at src/.



#================
Usage and example
#================

Usage:

 The usage of pinpoint is: ./pinpoint: <sample-file> <prediction-file> <output-file> [-p probability-threshold] [-w window-size]
 The parameter <sample-file> specifies the sample file used for prediction (see gsamples program).
 The parameter <prediction-file> specifies the probability file generated by the DeepBound.
 The parameter <output-file> specifies the predicted boundaries: 0 for end-boundary, 1 for non-boundary, and 2 for start-boundary.
 The parameter [probability-threshold] is optional (default value is 0.60), which specifies the minimum average probability over a window that will be considerred as a true boundary.
 The parameter [window-size] is optional (default value is 10), which gives the window size.

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One-line Example:

src/pinpoint example/test.ReadCount example/test.premature test.boundary