get_column_iterator SEGV

[diekhans]

1. get https://hgwdev.gi.ucsc.edu/~markd/cactus/bugs/taffy-column_iterator.tar.gz
2. untar
3. python taffyplay.py
4. Segmentation fault

meg9.taf was built with:

  taffy view -i output/meg9.maf -o output/meg9.taf                                
  taffy index -i output/meg9.taf                                                  
 

[glennhickey]

Yeah, looks like there are still some issues regarding errors in the input. The script has two problems:

• incorrect input file name: meg9.tafy instead of meg9.taf
• invalid coordinate range:1010643617 + 100. (the range in the file from taffy stats -b is hg38.chr14 101064367 101072358

The first one is triggering the segfault. I guess it's related to a bug in AlignmentReader() where when the taf_index parameter is not set, it's somehow opening the index of test_taf_file[:-1] + '.tai' (which exists) but failing after.

Your work-around is to follw the examples, where the index is passed in via

taf_index = TafIndex(test_taf_file + ".tai", is_maf=False)
with AlignmentReader(test_taf_file, taf_index=taf_index, ...

This way you can give it correct paths for both the taf and .tai file and get an exception for your invalid coordinate.

[diekhans]

Thanks. It was a quick yank and put experiment, but wanted to report the bug before I managed to aboid it. Glenn Hickey ***@***.***> writes:

…

Yeah, looks like there are still some issues regarding errors in the input. The script has two problems: * incorrect input file name: `meg9.tafy` instead of `meg9.taf` * invalid coordinate range:`1010643617 + 100`. (the range in the file from `taffy stats -b` is `hg38.chr14 101064367 101072358` The first one is triggering the segfault. I guess it's related to a bug in `AlignmentReader()` where when the `taf_index` parameter is not set, it's somehow opening the index of `test_taf_file[:-1] + '.tai'` (which exists) but failing after. Your work-around is to follw the [examples](https://github.com/ComparativeGenomicsToolkit/taffy/blob/main/docs/py_usage.md), where the index is passed in via ``` taf_index = TafIndex(test_taf_file + ".tai", is_maf=False) with AlignmentReader(test_taf_file, taf_index=taf_index, ... ``` This way you can give it correct paths for both the `taf` and `.tai` file and get an exception for your invalid coordinate. -- Reply to this email directly or view it on GitHub: #66 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>