chimeric_contig_evidence_analyzer.py removed all reads

[qinting]

Description of the bug

Hi, the chimeric_contig_evidence_analyzer.py removed all reads from my input bam files and returned an empty bam file. I wonder what this function is filtering and what would cause the empty output.

Thanks, Tingting

Command used and terminal output

$ chimeric_contig_evidence_analyzer.py \
    --patch_db_bam HN63/HN63_nf-core_T1.dedup.bam \
    --patch_db_gtf HN63/HN63_nf-core_T1.vif.extract.gtf \
    --output_prefix HN63/HN63_nf-core_T1.vif \
    --debug

$ wc -l HN63/HN63_nf-core_T1.vif.removed.txt
1069666 HN63/HN63_nf-core_T1.vif.removed.txt

$ samtools view HN63/HN63_nf-core_T1.dedup.bam | wc -l
1069666

$ samtools view HN63/HN63_nf-core_T1.vif.evidence.bam | wc
      0       0       0

Relevant files

No response

System information

No response