Does the "odgi sort " truncate the path?

[hui-liu]

Hi,

Do you know why the path of h1 (it is the reference sequence) in the sorted graph is truncated?

(1) the original graph was visualized using odgi viz.

odgi viz -i h1.full.og \
-o Chr10.png \
-M odgi_paths \
-t 24

(2) the sorted graph was visualized using odgi viz and path of h1 is truncated.

odgi sort \
-i h1.full.og \
-o h1.full.sort.og \
-t 24

odgi viz -i h1.full.sort.og \
-o h1.sorted.png \
-M odgi_paths \
-t 24

[subwaystation]

Hi @hui-liu,

odgi sort does not truncate any path. I suspect you see an artifact of odgi viz's 1D binning. Each pixel corresponds to several nucleotides, for example 100. If at least 50 of such nucleotides are traversed by a path, the pixel is colored for this path. If you are still in doubt if the sorting truncated your path, you can always use odgi paths -l -L to validate the length of the path in questions.