Treesim Limited Instructions

Prerequisites

Linux environment with a C++ toolchain.
Access to the source bundle and test files.

Setup

Assuming you’re in a work directory of your choice:

tar -xf treesim.tar
tar -xf testFiles.tar
make

If successful, an executable named treesim will appear in the directory.

Prepare test data

Create an output directory (or use your own and pass -outputDir):

mkdir test_output/

Unzip the test data:

gunzip testFiles/*

Run example

Command-line arguments are passed as -flag value. Example (broken across lines and then as one line):

./treesim                                 \
  -haplotypes testFiles/testHaps1.txt     \
  -legend testFiles/testLegend1.txt       \
  -genMap testFiles/testMap1.txt          \
  -lower 14005000                         \
  -upper 14005200                         \
  -buffer 50

Single-line version (Linux, broken with backslashes for readability):

./treesim \
  -haplotypes testFiles/testHaps1.txt \
  -legend testFiles/testLegend1.txt \
  -genMap testFiles/testMap1.txt \
  -lower 14005000 \
  -upper 14005200 \
  -buffer 50

Outputs are written to your chosen output directory. Parameters are described in parameters.cpp and argumentsOfProgram.cpp.