Arachne code package
The Arachne code package is the complete set of source code and ancillary files that comprises the Arachne program. Its root directory is equivalent to ARACHNE_DIR and is named Arachne by default. For information on downloading, installing, and compiling the Arachne code package, see Setup.
Some of Arachne's source code is contained in ARACHNE_DIR, but much of it is in subdirectories. If you are looking for a module's source code, be sure to search in all subdirectories of the package. Here are some particularly important subdirectories:
- bin: Contains all executable modules, once Arachne is compiled. Might be differently named; see ARACHNE_BIN_DIR.
- assemble: Contains Assemble and Assemblez.
- reporting: Contains many output modules.
- xerces_include: Contains the Xerces XML-parsing software.
- Transparent compilation. Any executable module can be compiled simply by typing make <module-name> in ARACHNE_DIR. The compilation will be in the appropriate machine architecture, and the compiled binary will be put in ARACHNE_BIN_DIR.
- Easy searching. The CvsGrep module allows you to search all of the source code.
- Automatic tracebacks: Whenever a module fails, you should see something like this:
At Fri Feb 01 05:53:56 2008, Assert index[u] >= 0 failed, in void ReadsToPathsMainPartX(longlong, int, const vec<std::pair<int, int> >&, const unsigned int&, const vecbasevector&, vecbasevector&, vecbitvector&, vecbitvector&, std::map<long int, long int, std::less<long int>, std::allocator<std::pair<const long int, long int> > >&, longlong, Bool, int, vecKmerPath&) [with POS = short int], line 422 of file ./paths/ReadsToPathsCoreX.cc. Dump of stack: [raw stack entries = 0x8889c6 0x889330 0x88a8e1 0x5516fc 0x445b00 0x446263 0x4463db 0x404d0c 0x2a95affaaa 0x40491a] 0. void ReadsToPathsMainPartX<short>( ... ), in ReadsToPathsCoreX.cc:422 1. ReadsToPathsCoreX( ... ), in ReadsToPathsCoreX.cc:247 2. ReadsToPathsCoreY( ... ), in ReadsToPathsCoreX.cc:448 3. ReadsToPathsCoreY( ... ), in ReadsToPathsCoreX.cc:515 4. main, in TestEvil.cc:32
- Extendability: It is easy to write your own modules.
The Arachne code package has grown prodigiously since it was first begun in 2000. Here is a chart of that growth:
|Executables||Source files||Lines of code||Bytes of code|