argentum

To get started:

0. git clone https://github.com/nvalimak/argentum.git

1. Compile the software by issuing the command make.

2. Issue the test by ./main --input test.input --plaintext --verbose --debug --dot test

You will need the /Graphwiz DOT/ software package to compile the *.dot files with:

3. make dot

Modify the Makefile to turn on compiler optimizations, if needed.

Input file format

VCF files can be processed as, for example:

./main --vcf --input <(gunzip -c input.vcf.gz) --verbose

SCRM files (without the SCRM tree) can be processed as, for example:

./main --scrm --input input.scrm --verbose

Time estimation

Use --enumerate for ./main to extract an ARG as a single graph with node ranges. ./enumerate-example reads the standard output in the enumerate format. Please see guide_time_estimate.pdf for instructions.

TODO

• Optimize the tree representation
• Make the compiler optimizations on by default