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README.md

cassiopee-c

Cassiopee index and search library C implementation. It is a complete rewrite of the ruby Cassiopee gem. It scan an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions.

This program provides both a binary (Cassiopee) and a shared library.

Index is based on a suffix tree with compression. It is possible to save the indexed sequence for later use without the need to reindex the whole sequence (for large data sets).

See Cassiopee -h for all options.

Expected input sequence is a one-line sequence with no header. CassiopeeKnife (see later chapter) can be used to convert Fasta sequences in cassiopee input sequences.

Compilation dependencies

  • cppunit
  • Google log (glog)
  • tree.hh (included):
  • libboost-serialization-dev,libboost-iostreams-dev

Runtime dependencies

  • Google log (glog)

  • libboost-serialization, libboost-iostreams

Compilation

cmake -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_BUILD_TYPE=Debug .
make

Valgrind

valgrind --leak-check=full bin/Cassiopee  -s test/sequence.txt -p ggc

Static analysis

CXX=/usr/share/clang/scan-build/c++-analyzer cmake .

Tests

bin/test_cassiopee

or

cd test; ctest -V

Tree graph generation

API provides the graph method to generate a cassiopee.dot file. To generate the image from the file:

dot -Tpng cassiopee.dot > cassiopee.png

Documentation

doxygen bin/Doxyfile

BUGS

CassiopeeKnife

Convert an input Fasta sequence in a cassiopee input format (one line sequence with no header).

TODO

COPYRIGHT

See license file.

Code under src/tree from http://tree.phi-sci.com/, copyright kasper.peeters@phi-sci.com

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