thread '<unnamed>' panicked at 'called `Option::unwrap()` on a `None` value', src/bam_scanner.rs:234:41

PacificBiosciences / HiFiCNV

Copy number variant caller and depth visualization utility for PacBio HiFi reads

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thread '<unnamed>' panicked at 'called `Option::unwrap()` on a `None` value', src/bam_scanner.rs:234:41 #11

Closed linlin-coder closed 1 year ago

linlin-coder commented 1 year ago

tool version:0.1.6 command example:

hificnv-v0.1.6-x86_64-unknown-linux-gnu/hificnv \
 --bam sample1.sort.bam \
 --ref Homo_sapiens_assembly38.onlychr.fasta \
 --exclude hificnv-v0.1.5-x86_64-unknown-linux-gnu/data/excluded_regions/cnv.excluded_regions.common_50.hg38.bed.gz \
 --threads 20 \
 --output-prefix CallCNV_hificnv-v0.1.6

problem description: When I run a command, an error always occurs, thread '<unnamed>' panicked at 'called' Option:: unwrap() on a 'None' value ', src/bam_ scanner.rs:234:41`

linlin-coder commented 1 year ago

The software version v0.1.5 can run, but the results do not match my expectations. Please refer to the issue for details #12

holtjma commented 1 year ago

Couple notes from this:

It looks like we accidentally uploaded an incorrect version of the v0.1.6 binary, I've create a new release with the corrected binary here: https://github.com/PacificBiosciences/HiFiCNV/releases/tag/v0.1.6b.
This error should only occur if there is a mismatch between the BAM file chromosome and the reference genome chromosomes. If you use the new version of the binary, it should clarify which chromosomes are absent in the reference.

Sorry about the incorrect upload!

linlin-coder commented 1 year ago

Hello developer, thank you for your answer to this question and for fixing this anomaly. I have tested the new version of the software ,and the software can output chromosome information for differences between Fasta and Bam files. Thank you again for your help