Organization of files.

Removed symbolic links (given that there is a script that creates them).

Removed binaries.
pairhmm.c: Modified to use openmp (time improved from 6min to 1min50sec in viete, for the testcase medium)
pairhmm.cu: Modified to use more than 32 threads (time improved from 1min29sec to 47s in viete for the testcase medium)
Added the forgotten benchmark of previous commit

Beautifying a bit the code pairhmm.cu

removed the need of having the script create_symlinks.sh (now the symlink is created when making the binary)

Added in pairhmm.cu a bit more of parallelism: m, x, y are computed by different threads (this fact has shown to improve the performance)
Modified makefile to work both in dijkstra AND viete; modified the compilation line of pairhmm-cuda

Modified common.c to mask all readQuality, insertionPenalty, deletionPenalty and gapContinuationPenalty values with 127.

pairhmm.cu:
	* modified to avoid use of two dimensional arrays
	* ph2pr only uses 128 doubles
	* removed hard-coded values for the number of threads
	* pre-computing of transitions values can be turned on/off with a macro
	* changed function name from go2 to go
	* overall cleaning of the source code
A major change has been implemented in this commit: now the computation
is being done not in the complete HAPLOTYPE_LEN x READ_SEQUENCE_LEN
matrices, but in smaller ROWS x DIAGS matrices.

WARNING: A numerical problem has been detected just before this commit,
so this code is not fully OK; but this is the first "acceptable" version
of this approach and, even having this numerical problem, is probably
going to be useful in the future to have a commit with this version.
This is the first correct version of the tiled-parallel computation.

Among the solved problems, are:

* rotation of the bytes in the load_hap_data function was being done in a buggy way... An order in the warps execution was being implicitly assumed
* concurrency problem in the way in which thread blocks picks the auxiliar lines of global memory
* there were some synchronization points in parts of the code not reachable by all threads

This version have been carefoully tested and it has produced correct answers. Some changes are already planned, in order to improve performance.
Removed some unnecesary __syncthreads()
Modified the number of pairs solved in each call to the GPU
* benchmark system rebuilt
* numerical bugs solved
* program tested on three diferents gpu's, with many diferent block sizes and with the three testcases (small, medium and large)
The measurements have been put inside a database, allowing to make SQL queries easily.