/**
   \mainpage Allpaths documentation

   This page contains Allpaths documentation.  It contains a small selection of Allpaths information that was documented in detail in Doxygen format.
   Links to complete documentation for everything in the Arachne/ CVS repository are included.

   Here are the various groups of related code:

   Stages of processing for genome assembly:

   \li \ref grp_kmerGathering
   \li \ref grp_edits

   Other groups of related code:

   <ul>
     <li>\ref grp_gc</li>
     <li>\ref grp_eval
       <ul>
         <li>\ref grp_refalign</li>
       </ul>
   </ul>

   General topics:
     \li \ref page_terms
     \li \ref page_files
*/


/**
   \defgroup grp_kmerGathering Extraction of kmers that occur in the reads

   Extraction of all kmers that occur in the reads.  This is parameterized by kmer length and shape.
*/

/**
   \defgroup grp_edits Error correction

   Fixing errors in reads.  This is also referred to as 'editing' or 'doing edits'.

   Several error correction methods are used:

   \li if there is a simultaneous change of a few
      bases that makes the kmers in the read much more likely, do the mutation (ProvisionalEdits.cc, MakeProvisionalChanges.cc)
   \li in all reads with a kmer, look at the position immediately after the kmer, and if there is strong consensus for
      one base then edit all reads to have that base there ( SolexaToAllpaths.cc )
   \li a generalization of the above, anchor (align) on a kmer all reads in which that kmer occurs, then see if there
     is strong consensus in the non-kmer columns, and if there is, edit the non-conensus positions in the reads to
     match the consensus ( AnchorConsensusEdits.cc )  
*/


/**
  \defgroup grp_gc Dealing with GC bias

  Dealing with GC bias.  How much coverage a genomic region with a given copy number gets depends on its GC content.  So, for example, if a kmer has
  an abnormally low frequency, maybe that's because the kmer is erroneous, but maybe that's because it falls in a region which is read abnormally rarely
  due to its GC bias or other content bias.
*/

/**
   \defgroup grp_refalign Alignment of reads to reference

   Alignment of reads from a known genome back to that reference genome.  Alignments of reads to reference are also referred to as "hits".

   \ingroup grp_eval
*/

/**
   \defgroup grp_eval Evaluating the quality of various steps
  
   Code that can be used to evaluate the quality of the various steps:
   assembly, error correction, read localization.
*/


/**
   \page page_terms Terms and concepts

   \section sec_basic_terms Basic terms

   \subsection term_kmer kmer

   A group of k letters from a read.

   \subsection term_path path, or kmer path

   A sequence of kmers where each next one is obtatined from a previous one by taking
   all letters of the previous one but the first, and adding a new letter:
   an example for k=3 would be ABCD, BCDE, EFGH, ...

   \subsection term_unipath

   A \ref term_path that does not branch.
*/


/**
   \page page_files Data file names and extensions

   Names and extensions of data files used in this system.

   \subsection ext_fastb

   .fastb files contain a list of basevectors; they're the binary equivalent of
   .fasta files.  See Basevector.h .
   
   \subsection ext_lookup

   .lookup files, produced by the program MakeLookupTable.cc, contain an index of all
   k-mers in a genome.

 */