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

[alyssa-ab]

Hi, just wanted to check a few things with you about the error.

1. Did you initially run your data through the pipeline and find that there were no results, or did you plug a bam directly into this process?
2. Was there any message about why the alignments were removed in the txt file?

As for the filtering, you can check the chimeric_contig_evidence_analyzer.py script in the bin, but the main points are:

FILTER step 1-3
        # 1: MapQuality score > value
        # 2: Entropy > Value
        # 3: Mismatches
FILTER step 4: check if soft or hard clipped, if so, check how many, if greater than specified amount, will filter out