FM-index representation of a de Bruijn graph
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.gitignore
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Makefile
README.md
alphabet.cpp
alphabet.h
bwtdisk_prepare.cpp
bwtdisk_reader.cpp
bwtdisk_reader.h
dbg_query.cpp
dbg_query.h
fm_index.cpp
fm_index.h
fm_index_builder.cpp
fm_index_builder.h
fm_markers.h
huffman_tree_codec.h
main.cpp
packed_table_decoder.h
run_bwtdisk.sh
sga_bwt_reader.cpp
sga_bwt_reader.h
sga_rlunit.h
stream_encoding.h
utility.cpp
utility.h

README.md

dbgfm

An FM-index representation of a de Bruijn graph.

The code in this repository is a stand-alone version of the FM-index from SGA (github/jts/sga). It is licensed under GPLv3.

Compiling

The code has no dependencies and should build by just running:

make

Testing

To test the code is functioning correctly, you can run:

make test

This will download human chromosome 20, index it with SGA then perform test queries using dbgfm. You will need to modify the Makefile to point to your version of SGA. This requires bwtdisk is installed.

API

A simple API for querying the structure of the de Bruijn graph is provided. See dbg_query.h and the test driver.