clemaitre
commented
3 years ago Thanks for the bug report. It has been fixed in commit 07ec1aaa4b2d7485cb2f2fdfd4f2792a56ec0ccc . Claire
Closed thomcuddihy closed 3 years ago
clemaitre
commented
3 years ago Thanks for the bug report. It has been fixed in commit 07ec1aaa4b2d7485cb2f2fdfd4f2792a56ec0ccc . Claire
Issue with release 1.1.4 testing on provided C_elegans data:
python3 ../../svjedi.py -v test.vcf -r genome.fasta -i simulated-reads.fastq.gz
Traceback (most recent call last): File "../../svjedi.py", line 193, in
main(sys.argv[1:])
File "../../svjedi.py", line 186, in main
genotype.genotype(paf_file, vcf_file, output_file, min_support, d_over, d_end, l_adj)
File "/gpfs1/scratch/30days/s4356552/SVJedi/genotype.py", line 135, in genotype
decision_vcf(dict_of_informative_aln, vcf_without_gt, outputfile, min_aln, l_adj)
File "/gpfs1/scratch/30days/s4356552/SVJedi/genotype.py", line 323, in decision_vcf
if svtype in ('DEL', 'INS', 'INV', 'BND') and in_sv in list(dictReadAtJunction.keys()) and abs(in_length) >= 50:
UnboundLocalError: local variable 'in_length' referenced before assignment