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Readme cosmetics.
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MrAlexSee committed May 30, 2018
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Expand Up @@ -13,15 +13,15 @@ Add Boost library to the path for compilation by setting `BOOST_DIR` in the make
Type `make` for optimized compile.
Comment out `OPTFLAGS` in the makefile in order to disable optimization.

Tested with gcc 64-bit 7.2.0 and Boost 1.67.0 (not time-critical, used only for parameter and data parsing and formatting) on Ubuntu 17.10 Linux version 4.13.0-36 64-bit.
Tested with gcc 64-bit 7.2.0 and Boost 1.67.0 (the latter is not time-critical, used only for parameter and data parsing and formatting) on Ubuntu 17.10 Linux version 4.13.0-36 64-bit.

## Usage

Basic usage: `./sopang [options] <input text file> <input pattern file>`

Input text file (positional parameter 1 or named parameter `-i` or `--in-text-file`) should contain the elastic-degenerate text in the format `{A,C,}GAAT{AT,A}ATT`.
Input pattern file (positional parameter 2 or named parameter `-I` or `--in-pattern-file`) should contain the list of patterns, each of the same length, separated with newline characters.
Attached as part of the this package is a script `run_all.sh`, which allows for processing multiple input text (chromosome) and pattern files.
Attached as part of this package is a script `run_all.sh`, which allows for processing multiple input text (chromosome) and pattern files.

#### Command-line parameter description

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