Arachne code package

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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:


  • 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/

Dump of stack:

[raw stack entries =           0x8889c6           0x889330           0x88a8e1
                               0x5516fc           0x445b00           0x446263
                               0x4463db           0x404d0c       0x2a95affaaa

0. void ReadsToPathsMainPartX<short>( ... ), in
1. ReadsToPathsCoreX( ... ), in
2. ReadsToPathsCoreY( ... ), in
3. ReadsToPathsCoreY( ... ), in
4. main, in

Historical statistics

The Arachne code package has grown prodigiously since it was first begun in 2000. Here is a chart of that growth:

Version Date Number of...
Executables Source files Lines of code Bytes of code
1.0 2002-02-13 96 772 180k 6.5M
2.0.1 2003-03-11 96 765 194k 7.1M
2.1.0 2007-10-22 779 2120 428k 15M
3.1 2008-01-03 1129 2644 576k 18M
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