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Hello,
I am running reconstruct using Nanopore long read data and getting the following error:
It works fine for most data, but I got the error with certain data.
Traceback (most recent call last):
File "~/CoRAL/src/CoRAL.py", line 145, in <module>
reconstruct_mode(args)
File "~/CoRAL/src/CoRAL.py", line 23, in reconstruct_mode
infer_breakpoint_graph.reconstruct(args)
File "~/CoRAL/src/infer_breakpoint_graph.py", line 1656, in reconstruct
b2bn.build_graph()
File "~/CoRAL/src/infer_breakpoint_graph.py", line 1037, in build_graph
self.lr_graph[amplicon_idx].add_discordant_edge(bp[0], bp[1], bp[2], bp[3], bp[4], bp[5], lr_count = len(bp[-1]), reads = bp[-1])
File "~/CoRAL/src/breakpoint_graph.py", line 199, in add_discordant_edge
raise Exception("Breakpoint node must be added first.")
Exception: Breakpoint node must be added first.
I noticed that in the build_graph function, there was a case where 2nd bp in self.new_bp_list was included in split_int and the 1st bp was not included, and this seemed to be the cause of the error.
It seems that the error can be avoided by changing the script as follows.
However, I am worried that this may affect the analysis results.
Is anyone else dealing with this kind of issue?
Here is edited code: src/infer_breakpoint_graph.py.
Hello,
I am running reconstruct using Nanopore long read data and getting the following error:
It works fine for most data, but I got the error with certain data.
Below is the script:
I noticed that in the
build_graph
function, there was a case where 2nd bp inself.new_bp_list
was included insplit_int
and the 1st bp was not included, and this seemed to be the cause of the error.It seems that the error can be avoided by changing the script as follows.
However, I am worried that this may affect the analysis results.
Is anyone else dealing with this kind of issue?
Here is edited code:
src/infer_breakpoint_graph.py.
Thanks
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