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Negative end of path positions in vg giraffe mapping #4249
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1. What were you trying to do?
I am working on a GAF parser, and currently trying to calculate alignment lengths. Alignment block length (column 11) typically mentions 151, even when the actual alignment is shorter. To obtain the length, I subtract the end position on the path (GFA column 9) from the start position (column 8), which gives me the correct length in 99.9% of the mappings. However, in some cases, the end position is lower than the start position. Sometimes, the end position is negative. I have two examples where I suspect the end position is incorrect.
2. What did you want to happen?
I expected end positions to be higher, at least not be negative.
3. What actually happened?
Negative end position example.
Alignment starts at 0 and ends at -273. I can’t seem to find any information about the end being negative, also the path is only 79 bases long.
Example where coordinates don't seem to match.
Unsure if this second example is a bug, but I’m unable to explain to obtained coordinates.
Alignment starts at 1274 and ends 955., I thought maybe the read is mapped in reverse. But looking at the cigar, there is no large insertion that explains why the alignment length is 319 bases. A length close to 151 is to be expected.
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here:5. What data and command can the vg dev team use to make the problem happen?
6. What does running
vg version
say?Thanks for reading!
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