Get the prerequisites, compile, create documentation, test. Also see the Github Wiki.
Prerequisites are...
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Not too ancient G++; 4.0 and later work fine, 3.x might cause some difficulties. Also make, a shell, and so on.
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protobuf. Find it at http://code.google.com/p/protobuf
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popt. You might already have it, else ask your admin or grab it at http://rpm5.org/files/popt
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Doxygen, if you want the documentation. Can be found at http://doxygen.org
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zlib from zlib.net
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libbz2 from bzip2.org
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Elk from http://sam.zoy.org/elk/
If you have those, call './configure', 'make', then 'make doc' to create the documentation, then 'make install'.
To test, you need a genome, an index, and some input in FastA or FastQ format:
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Locate a genome in FASTA format (or any other format that has a converter; .2bit is fine, my own .dna isn't). Run fa2dna on it (--help tells you how); you can pipe the input if you want.
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On your new .dna file, run file-info. It should spit out the meta data for that genome. If not, you're hosed...
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Build an index for the .dna file using dnaindex (--help tells you how, the defaults are probably fine). Use only the basename of the genome, it will figure the extension out by itself.
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You can run file-info on that, too. It will tell you the word size you just set. If not, you're hosed again...
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Write a sensible anfo.cfg using the examples in example/ and config.proto as guideline.
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You can run index-test or anfo now. Index-test just does lookups in the index, and optionally (on simulated data) checks if a seed in the correct region was found.
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anfo can be run on any FASTA/FASTQ file now.
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anfo-tool can operate on the output files (but it's cumbersome to use)
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the Elk binding can do what anfo and anfo-tool do, is much more flexible, but undocumented.
Pretty much stabilized are...
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Genome handling and creation (files sequence.h, sequence.cc, index.h, index.cc, fa2dna.cc)
I store genomes with four bits per nucleotide, which sounded like a fscking brilliant idea, since it's only half as wasteful as the text form and still allows ambiguity codes. The headaches came with the implementation of the auxilliary DnaP class... Anyway, the nucleotides A,C,T,G map to bits 0,1,2,3. That order (you did notice T coming before G, didn't you?) also sounded like a fscking brilliant idea, but in realilty it doesn't matter and I keep mixing it up. Chromosomes are split into contigs at long stretches of Ns, contigs are separated by single gaps and the first and last ones terminate in a gap at either side. This means you can start anywhere and safely run forward or backward until you hit a gap.
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Index handling and creation (files index.h, index.cc, dnaindex.cc)
The index is quite simple: oligos are mapped to integer offsets, a first level array contains a pointer to a second array for each of the possible oligos, and the second level array contains one long list of positions where these oligos were found. Only the forward strand is indexed, but lookup is of course done for both strands. (This primitive thing seems such a waste when the much better FM-index family is just out of reach... to bad, for now.)
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Handling of reads (files sequence.h and sequence.cc)
Just a simple structure for sequences with quality scores and a FastA/FastQ/FourQ reader. There's no support for mate pairs, I haven't even decided what to do about them.
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File formats (genome, index, config file, output)
Genome and index files are documented somewhere in the code. Metadata, config, complex output, etc. is encapsulated in protobuf messages. That way I don't need to mess with parsers and pretty printers and the messages are extensible. The two .proto files are more or less finalized, but it's easy to change them without breaking stuff, which also means you should think before changing them.
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The aligner (align.h, align.cc)
Completely rewritten now, it is much faster than the previous version and practically finished. The general structure and the specific alignment mechanisms are somewhat separated from each other, making extensions like a special 454 aligner possible at least in principle.
Copyright
Anfo is (C) 2009 by Udo Stenzel udo_stenzel@eva.mpg.de
ANFO is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.