mapbp

Compute the number of breakpoints between one order data set and a map.

Synopsis:

The mapbp command is invoked either:

• mapbp Options
• mapbp SetId MapId

Description:

The mapbp command computes the number of breakpoints between a map and a reference order. All the markers which do not appear in the reference order are not taken into account when computing the exact number of breakpoints. The number of breakpoints is the number of adjacent markers in an order which are not adjacent in the reference order. Two adjacent markers from two different chromosomes in the reference genome always count for one (obligate) breakpoint.

Arguments:

• Options : -u to obtain the synopsis of the normal use, -h to print a one line description, -H to print a short help.
• SetId: the numerical id of the order dataset (see dsinfo).
• MapId: the numerical id of the map in the heap.

Returns:

number of breakpoints.

Example:

CG> dsload Data/rh1_true.cg
{1 haploid RH 110 93 /home/tschiex/Dev/carthagene/test/Data/rh1_true.cg}
CG> dsload Data/order1_ref.cg
{2 order 110 /home/tschiex/Dev/carthagene/test/Data/order1_ref.cg}
CG> dsmergor 1 2
{3 merged by order 110 93}
CG> sem
...
CG> mapbp 2 0
6
CG>

See also:

• dsbp (2.7.17)