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.

Name		Name	Last commit message	Last commit date
Latest commit History 14 Commits
COPYING		COPYING
Makefile		Makefile
README.md		README.md
alphabet.cpp		alphabet.cpp
alphabet.h		alphabet.h
bwtdisk_prepare.cpp		bwtdisk_prepare.cpp
bwtdisk_reader.cpp		bwtdisk_reader.cpp
bwtdisk_reader.h		bwtdisk_reader.h
dbg_query.cpp		dbg_query.cpp
dbg_query.h		dbg_query.h
fm_index.cpp		fm_index.cpp
fm_index.h		fm_index.h
fm_index_builder.cpp		fm_index_builder.cpp
fm_index_builder.h		fm_index_builder.h
fm_markers.h		fm_markers.h
huffman_tree_codec.h		huffman_tree_codec.h
main.cpp		main.cpp
packed_table_decoder.h		packed_table_decoder.h
run_bwtdisk.sh		run_bwtdisk.sh
sga_bwt_reader.cpp		sga_bwt_reader.cpp
sga_bwt_reader.h		sga_bwt_reader.h
sga_rlunit.h		sga_rlunit.h
stream_encoding.h		stream_encoding.h
utility.cpp		utility.cpp
utility.h		utility.h

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sjackman/dbgfm

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