calculations of tophat BlockSizes and BlockStarts

[frymor]

Hi,

I know it has been discussed here a few times, but no one really explain how it is done.

I have this example of a tophat junction.bed file:

chr2L      11489   11856   JUNC00000001    6       -       11489   11856   255,0,0 2       29,78   0,289
chr2L      12168   12323   JUNC00000002    1       -       12168   12323   255,0,0 2       53,38   0,117
chr2L      12864   13603   JUNC00000003    34      -       12864   13603   255,0,0 2       64,84   0,655
chr2L      13538   13764   JUNC00000004    37      -       13538   13764   255,0,0 2       87,82   0,144
chr2L      17136   18331   JUNC00000005    5       -       17136   18331   255,0,0 2       76,71   0,1124
chr2L      17136   21136   JUNC00000006    5       -       17136   21136   255,0,0 2       76,71   0,3929
chr2L      26888   27124   JUNC00000007    6       -       26888   27124   255,0,0 2       76,72   0,164
chr2L      28838   29069   JUNC00000008    11      -       28838   29069   255,0,0 2       88,88   0,143
chr2L      34259   34604   JUNC00000009    2       -       34259   34604   255,0,0 2       29,47   0,298

I understand what it means in general. What I would like to know is how it is calculated.

Here is what I understand:
the last three columns determine how many blocks each bed segment will have. the third column from the end is always 2, as there are two blocks.
the column before last gives the block sizes. this means how many base positions each block is taking in the browser (IGV, UCSC etc.). the last columns gives the length of the connection between the two blocks.
as an example of the calculations - row 1:
length of segment - 11856 - 11489 = 367 bases
block1: start position 0 (relative) and has the length of 29 positions.
block2: start at position 289-78 = 211 and has the length 78 positions.
this is how it looks like in the browser:


What I don't get is how these numbers are being calculated.
Why tophat says the first block is 29 bases long and the second one 78 bases. What are these numbers?

thanks for the help
Assa