README

/** @mainpage C++ binding for SAM/BAM files

The Sequence Alignment/Map (SAM) file format and its binary companion BAM
are formats for storing nucleotide sequence alignments.  They are designed
for the large volumes of short- to middling-length reads produced by
next-generation sequencing technologies, and are described at
http://samtools.sourceforge.net/ and elsewhere.

@b Cansam is a C++ library providing classes representing the records found in
these files, facilities for reading and writing SAM and BAM files, and several
algorithms for manipulating these files, including sorting and merging.

The main things to know about are sam::alignment and sam::header.

@section utilities Utilities

Several basic command-line utilities are provided along with the library.
They are intended to be of use in their own right, as well as providing
non-trivial examples of programming with the library.

  - @ref samcat  for converting between SAM and BAM formats
  - @ref samhead for displaying headers
  - @ref samsort and @ref samgroupbyname for sorting and merging files
  - @ref samsplit for partitioning files

@section colophon Colophon

This documentation was generated from comments in the source code using
<a href="http://doxygen.org/">doxygen</a>.
*/


/// @namespace sam
/// @brief All of Cansam is encapsulated within this namespace
namespace sam {
} // end of namespace sam

/* Not sure if this is a good idea... */
/// @namespace std
/// @brief Standard C++ namespace
namespace std {
/** @class std::ios
    @brief The relevant parts of std::ios

blah */
class ios {
};
}


// Example programs
// ================

/** @example simplecat.cpp
Simplecat demonstrates reading and writing SAM files from/to ordinary streams.

It copies alignment records from the files specified to standard output.
Headers from the first file are also copied, but those from subsequent files
are thrown away; simply copying them would not result in a valid SAM file,
as they would appear after previously-emitted alignment records.

(Real programs ought to handle such situations more carefully.)
*/

// vim:set filetype=doxygen: