Run error #9
Description
Hi
When I try to run the code directly sourced from github I run into this problem, Could you please let me know how to resolve this
Processing tumor bam file:
ffpe.bam
Minimum mapping quality is set to 0
Expect library: NEBNext-FFPE-DNA-Library-Prep-Kit in BAM
Traceback (most recent call last):
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 24, in to_numeric
return int(s)
ValueError: invalid literal for int() with base 10: 'A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/sahay/FFPolish/src/cli.py", line 55, in <module>
args.cores, args.seed, args.loglevel)
File "/home/sahay/FFPolish/src/filter.py", line 94, in filter
prep_data = dp.PrepareData(prefix, bam, bed_file_path, ref, outdir)
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 428, in __init__
self._run_bam_readcount(skip_readcount)
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 463, in _run_bam_readcount
tumor_rc = ReadCount(tumor_readcount_file_path)
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 51, in __init__
self.read_count_dict = self._parse(file_path)
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 77, in _parse
b = list(map(to_numeric, count[i + 1: i + 15]))
File "/home/sahay/FFPolish/src/deepsvr_utils.py", line 26, in to_numeric
return float(s)
ValueError: could not convert string to float: 'A'