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Cannot load a file containing segments without sequence #45

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paoloczi opened this issue Jun 2, 2022 · 2 comments
Closed

Cannot load a file containing segments without sequence #45

paoloczi opened this issue Jun 2, 2022 · 2 comments
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@paoloczi
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paoloczi commented Jun 2, 2022

If I try to load a gfa file containing no sequence, I get the following error message:

image

Here is the beginning of the file I am trying to load:

H       VN:Z:1.0
S       0       *
S       1       *
S       2       *
S       3       *

According to the GFA specification, the sequence can be omitted and specified as *. The specification also says that, if the sequence is missing, "its length may be specified using the LN tag", but this is not required. The LN field is clearly described as optional, and the original Bandage has no problem loading this file.

GFA files without sequence are very useful to inspect an assembly without having to load a large file. This is useful for applications where the sequence is not needed, and one is interested only in the structure of the assembly graph.

@asl asl added the duplicate This issue or pull request already exists label Jun 2, 2022
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asl commented Jun 2, 2022

Dup of #43

@asl asl closed this as not planned Won't fix, can't repro, duplicate, stale Jun 2, 2022
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asl commented Jun 2, 2022

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