reorganized repository to allow for tags and branches and created a makefile
Move source files to src directory
Updated makefile to add checks
Resolve absolute path for the samtools
Changed order of compile flags to fix linking error
Added documentation on compilation and moved SAMTOOLS definition to top-level makefile
 * Makefile now includes use of CXXFLAGS
Get the split-up versions in. Note: pindel.cpp is now a trimmed version.
letters of all file names from capital to normal
 * Framework for a trivial test on real data
 * Fix capitalization
 * Remove the actual test while the data is not in there yet
 * Added test data
 * Rewrote comparison with test results to accept running in a SVN directory
 * Added actually running the test
Made the .cpp files into independent units
 * Remove unneeded includes from reader.cpp
 * Remove unneeded includes from reporter.cpp
Made pattern rule to create cppcheck files
 * Cleanup includes in searcher.cpp
 * Cleanup includes in pindel.cpp
Updated code style with GNU indent -ts2
Added -I$(SAMTOOLS) to the cppcheck rule