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epic2 fails when reading a BEDPE file with a -1 value for a start or end position:
Traceback (most recent call last):
File "/share/pkg.7/epic2/0.0.52/install/epic2_env/bin/epic2", line 257, in <module>
_main(args)
File "/share/pkg.7/epic2/0.0.52/install/epic2_env/lib/python3.10/site-packages/epic2/main.py", line 35, in _main
effective_genome_length, chromsizes = egl_and_chromsizes(args)
File "epic2/src/genome_info.pyx", line 320, in epic2.src.genome_info.egl_and_chromsizes
File "epic2/src/genome_info.pyx", line 136, in epic2.src.genome_info.find_readlength
OverflowError: can't convert negative value to uint32_t
uint32_t types are used to read the start/end positions in genome_info.pyx and read_files.cpp, which of course won't correctly handle a negative value. The BEDPE format allows the -1 value to indicate unknown positions.
start1 - The zero-based starting position of the first end of the feature on chrom1.
The first base in a chromosome is numbered 0.
As with BED format, the start position in each BEDPE feature is therefore interpreted to be 1 greater than the start position listed in the feature. This column is required.
Use -1 for unknown.
Any suggestion on how to handle this?
The text was updated successfully, but these errors were encountered:
On Fri, Dec 16, 2022 at 8:18 PM Brian Gregor ***@***.***> wrote:
epic2 fails when reading a BEDPE file with a -1 value for a start or end
position:
Traceback (most recent call last):
File "/share/pkg.7/epic2/0.0.52/install/epic2_env/bin/epic2", line 257, in <module>
_main(args)
File "/share/pkg.7/epic2/0.0.52/install/epic2_env/lib/python3.10/site-packages/epic2/main.py", line 35, in _main
effective_genome_length, chromsizes = egl_and_chromsizes(args)
File "epic2/src/genome_info.pyx", line 320, in epic2.src.genome_info.egl_and_chromsizes
File "epic2/src/genome_info.pyx", line 136, in epic2.src.genome_info.find_readlength
OverflowError: can't convert negative value to uint32_t
uint32_t types are used to read the start/end positions in genome_info.pyx
and read_files.cpp, which of course won't correctly handle a negative
value. The BEDPE format
<https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format>
allows the -1 value to indicate unknown positions.
start1 - The zero-based starting position of the first end of the feature
on chrom1.
The first base in a chromosome is numbered 0.
As with BED format, the start position in each BEDPE feature is therefore
interpreted to be 1 greater than the start position listed in the feature.
This column is required.
Use -1 for unknown.
Any suggestion on how to handle this?
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epic2 fails when reading a BEDPE file with a -1 value for a start or end position:
uint32_t types are used to read the start/end positions in genome_info.pyx and read_files.cpp, which of course won't correctly handle a negative value. The BEDPE format allows the -1 value to indicate unknown positions.
Any suggestion on how to handle this?
The text was updated successfully, but these errors were encountered: