dsbp

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

Synopsis:

The dsbp command is invoked either:

• dsbp Options
• dsbp SetId1 SetId2

Description:

The dsbp command computes the number of breakpoints between a biological dataset (the order of the markers is the original order in the file) and a reference order. All the markers which do not appear in both datasets 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.
• SetId1: the numerical id of the order dataset (see dsinfo).
• SetId2: the numerical id of the biological dataset (see dsinfo).

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> dsbp 2 1
6
CG>

See also:

• mapbp (2.7.16)