heaprinto

`heaprinto`

Displays the contents of the heap.

Synopsis :

The CarthaGene heaprinto command is invoked as either one of:

heaprinto Options
heaprinto NbMrk Blank Comp

heaprinto compares each map contained in the heap to the best current map. The position of each locus on the best map is printed at its new position on the current map. If the NbMrk argument is equal to 0, all the positions are printed. Otherwise, only the differences are printed. The NbMrk argument allows to visualize NbMrk consecutive differences or more with square brackets. If Blank argument is set to 1, the positions between the extremities of an interval are replaced by '-'. If Comp is set to 1, only the extremities of intervals are printed consecutively. At the end of each line, the contribution to the delta lod is printed for each data set "merged by order".

Arguments :

Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
NbMrk : The minimum number of markers needed to mention an area of change. The NbMrk argument must be a positive integer.
Blank : The flag to choose either to print blanks (1) or to print all the positions inside a interval (0). The Blank argument must be set to 0 or 1.
Comp : The flag to compress intervals (1) or not (0). The Blank argument must be set to 0 or 1.

Example :

CG> dsload Data/bc1.cg
{1 f2 backcross 17 208 /homes/thomas/carthagene/test/Data/bc1.cg}
CG> dsload Data/rh1.cg
{2 haploid RH 13 118 /homes/thomas/carthagene/test/Data/rh1.cg}
CG> dsmergor 1 2
{3 merged by order 21 326}
CG> sem

Map -1 : log10-likelihood =  -801.56
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS13 MS6 MS11 MS17 MS16 MS8 MS7 MS2 MS3 MS9 MS15 MS12 MS20 M...
   2 : MS4 MS5      MS6                MS8 MS7     MS3 MS9 MS15            ...

CG> flips 5 3.0 1
...
# To print all the positions.
CG> heaprinto 0 0 0
Loci Id  ..........
                  :                    1  1           1  1  1  1  2  2  1  ...
                  :  2  4  5  3  7  6  0  1  1  9  8  2  4  3  6  0  1  8  ...
Loci Pos ..........  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
Map Id : log10    :  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
     1 :  -693.62 :  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 1...
    12 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 18 15 16 1...
     3 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 18 1...
     4 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 14 16 17 1...
     5 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 16 17 14 1...
    13 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 1...
     7 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 14 18 16 1...
     8 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 14 16 18 1...
     9 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 16 14 18 1...
    10 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 16 14 17 1...
    11 :     0.00 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 18 16 1...
    14 :     0.19 =  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 18 20 19 1...
     6 :     0.77 =  1  0  2  3  4  5  6  7  8  9 10 11 12 13 14 15 18 16 1...
     2 :     0.77 =  1  0  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 1...
     0 :     0.77 =  1  0  2  3  4  5  6  7  8  9 10 11 12 13 14 18 15 16 1...

# To see consecutive differences of length greater than 3.
CG> heaprinto 3 0 0
Loci Id  ..........
                  :                    1  1           1  1  1  1  2  2  1  ...
                  :  2  4  5  3  7  6  0  1  1  9  8  2  4  3  6  0  1  8  ...
Loci Pos ..........  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
Map Id : log10    :  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
     1 :  -693.62 :  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 1...
    12 :     0.00 =                                              18[15 16 1...
     3 :     0.00 =                                                    18 1...
     4 :     0.00 =                                           15 14        ...
     5 :     0.00 =                                          [15 16 17]14  ...
    13 :     0.00 =                                                       1...
     7 :     0.00 =                                           15 14 18 16 1...
     8 :     0.00 =                                           15 14    18 1...
     9 :     0.00 =                                           15 16 14 18 1...
    10 :     0.00 =                                           15 16 14     ...
    11 :     0.00 =                                                 18 16 1...
    14 :     0.19 =                                              18 20 19[1...
     6 :     0.77 =  1  0                                           18 16 1...
     2 :     0.77 =  1  0                                                  ...
     0 :     0.77 =  1  0                                        18[15 16 1...

# To see the ends of the consecutive differences only.
CG> heaprinto 3 1 0
Loci Id  ..........
                  :                    1  1           1  1  1  1  2  2  1  ...
                  :  2  4  5  3  7  6  0  1  1  9  8  2  4  3  6  0  1  8  ...
Loci Pos ..........  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
Map Id : log10    :  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
     1 :  -693.62 :  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 1...
    12 :     0.00 =                                              18[15 -- 1...
     3 :     0.00 =                                                    18 1...
     4 :     0.00 =                                           15 14        ...
     5 :     0.00 =                                          [15 -- 17]14  ...
    13 :     0.00 =                                                       1...
     7 :     0.00 =                                           15 14 18 16 1...
     8 :     0.00 =                                           15 14    18 1...
     9 :     0.00 =                                           15 16 14 18 1...
    10 :     0.00 =                                           15 16 14     ...
    11 :     0.00 =                                                 18 16 1...
    14 :     0.19 =                                              18 20 19[1...
     6 :     0.77 =  1  0                                           18 16 1...
     2 :     0.77 =  1  0                                                  ...
     0 :     0.77 =  1  0                                        18[15 -- 1...

# To make the line shorter.
CG> heaprinto 3 1 1
Loci Id  ..........
                  :                    1  1           1  1  1  1  2  2  1  ...
                  :  2  4  5  3  7  6  0  1  1  9  8  2  4  3  6  0  1  8  ...
Loci Pos ..........  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
Map Id : log10    :  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  ...
     1 :  -693.62 :  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 1...
    12 :     0.00 = 18[15 17]  (     0.00 +     0.00 )
     3 :     0.00 = 18 17  (     0.00 +     0.00 )
     4 :     0.00 = 15 14  (     0.00 +     0.00 )
     5 :     0.00 =[15 17] 14  (     0.00 +     0.00 )
    13 :     0.00 = 19 18  (     0.00 +     0.00 )
     7 :     0.00 = 15 14 18 16 17  (     0.00 +     0.00 )
     8 :     0.00 = 15 14 18 17  (     0.00 +     0.00 )
     9 :     0.00 = 15 16 14 18 17  (     0.00 +     0.00 )
    10 :     0.00 = 15 16 14  (     0.00 +     0.00 )
    11 :     0.00 = 18 16 17  (     0.00 +     0.00 )
    14 :     0.19 = 18 20 19[17 15] (     0.00 +     0.19 )
     6 :     0.77 =  1  0 18 16 17  (     1.38 +    -0.62 )
     2 :     0.77 =  1  0  (     1.38 +    -0.62 )
     0 :     0.77 =  1  0 18[15 17]  (     1.38 +    -0.62 )

`heaprinto`

Synopsis :

Description :

Arguments :

Example :

See also :