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Program parameters:

 

Final Algorithm description: 

1. Determine the elimination order of the given problem.

2. If the Complexity Coefficient of the problem is higher than the defined threshold MIN_COMPLEXITY, go to 3. Else, perform the exact inference and go to 7.

3.   Clipping markers in order to reduce the Complexity Coefficient of the problem without influence on the final LOD score:

4.  Determine the elimination order of the current problem.

5.  If the Complexity Coefficient of the problem is higher than the defined threshold, go to 6. Else, continue on to computing the likelihood and go to 7.

6.  Clip the farthest marker and go to 4.

7.  End.

 

    Added functions:

 

FindFarthestLocus- The function finds the farthest marker from the iterated locus and returns it's index on the map and  it's distance   from the varied locus in CM.

clipMarker - The function clips given marker from the map by updating map to data structures and changes relevant recombination value between neighbors of clipped marker.

findDistanceRatio - The function computes the distance ratio of the given marker by finding the distance from it to varied locus divided by given maximum distance.                                                       

 

Modification performed to  the original code of SUPERLINK:

In the file LociData.c  in function readLocusFile was added condition to swich that reads program specific data:

case SUPER_LINKMAP_APPROX_PROG.

The code that performs in this case is identical to the code of case SUPER_LINKMAP_PROG ( original superLinkMap program).

 

Const Definitions

   

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