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quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
MIT License
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L.start <= R.start #113

Open christopher-schroeder opened 1 year ago

christopher-schroeder commented 1 year ago

Hey, I get the following error for one of my samples in one of my projects

strling version: 0.5.1
using first reads in fragment_length_distribution calculation as there were not enough
Read 67332 bounds from results/strling/merge/tremor-ataxia-bounds.txt
fatal.nim(49)            sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start`  [AssertionDefect]

I may help to fix this by providing any information you need!

hdashnow commented 1 year ago

This suggests that one of the rows in tremor-ataxia-bounds.txt is incorrect, with the left side of the locus being larger than the right. Happy to look through the file to find the offending locus if that would help. Or just do right column - left column and look for a negative to find the bad line. Was tremor-ataxia-bounds.txt generated with STRling?

christopher-schroeder commented 1 year ago

yes tremor-ataxia-bounds.txt was generated by STRling mergeas well as all predecessor .bin files by STRling extract. I performed the column substraction and there are no negatives, but a lot of 0, which is also invalid? I should have mentioned before: This is group calling and calling for the other files (except for my other issue) worked without any problems. Therefore I doubt that the reason behind this can be found in the bounds.txt. If you still want the file, I would be glad to share!

christopher-schroeder commented 6 months ago

the error happens again, now with additional information

using first reads in fragment_length_distribution calculation as there were not enough
Read 15892 bounds from results/strling/merge/all-bounds.reduced.txt
fatal.nim(49)            sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start` (Record(6:94011350144480--1188996768):HWI-D00629:81:C7G26ANXX:3:2312:21292:22170, Record(6:94011349769008--1189373011):K00103:48:H3F5GBBXX:3:2128:28189:38381, (tid: 18, left: 1172137, left_most: 1171370, right: 1172151, right_most: 1172904, center_mass: 1172151, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)) [AssertionDefect]