nf-core / nf-core/viralintegration
chimeric_contig_evidence_analyzer.py removed all reads
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- Dominant language
- Python
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- 19
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Description
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
Contributor guide
First steps
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Research direction
Start by reproducing the issue with chimeric_contig_evidence_analyzer.py and the command shown, then inspect how its filtering relates the input BAM to HN63/HN63_nf-core_T1.vif.removed.txt. Compare the removed-read count with samtools view output and determine why HN63/HN63_nf-core_T1.vif.evidence.bam is empty; done means the cause is documented and the analyzer no longer removes every read for this input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100