aligned_bam_to_cpg_scores v2.1.0 raises an error

[JBinkowski]

Dear all,

I am trying to use aligned_bam_to_cpg_scores v2.1.0 and the BAM file from https://downloads.pacbcloud.com/public/revio/2022Q4/HG002-rep1/analysis/ but with no results. As expected BAM file contains MM and ML auxillary tags as well as HP tag, however command:

pb-CpG-tools-v2.1.0-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores \
  --bam HG002.m84011_220902_175841_s1.GRCh38.bam \ 
  --output-prefix HG002.m84011_220902_175841_s1.GRCh38_met \ 
  --model pb-CpG-tools-v2.1.0-x86_64-unknown-linux-gnu/models/pileup_calling_model.v1.tflite \
  --threads 12

raises an error:

[2023-03-31][14:34:30][aligned_bam_to_cpg_scores][INFO] Starting aligned_bam_to_cpg_scores
[2023-03-31][14:34:30][aligned_bam_to_cpg_scores][INFO] cmdline: pb-CpG-tools-v2.1.0-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores --bam HG002.m84011_220902_175841_s1.GRCh38.bam --output-prefix HG002.m84011_220902_175841_s1.GRCh38_met --model pb-CpG-tools-v2.1.0-x86_64-unknown-linux-gnu/models/pileup_calling_model.v1.tflite --threads 12
[2023-03-31][14:34:30][aligned_bam_to_cpg_scores][INFO] Running on 12 threads
[2023-03-31][14:34:30][aligned_bam_to_cpg_scores][INFO] Processing alignment file 'HG002.m84011_220902_175841_s1.GRCh38.bam'
thread '<unnamed>' panicked at 'called `Option::unwrap()` on a `None` value', src/meth_read_processor.rs:1245:48
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
[1]    14929 IOT instruction (core dumped)  pb-CpG-tools-v2.1.0-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores   

[ctsa]

Thanks for reporting this @JBinkowski - I'll check if we can reproduce this and see what's going on here.

[ctsa]

I can reproduce this. We'll look into a resolution next week.

[ctsa]

Hi @JBinkowski, I just issued a new release which should fix this issue, can you confirm?

https://github.com/PacificBiosciences/pb-CpG-tools/releases/tag/v2.1.1

[JBinkowski]

@ctsa now it works, thank You for Your quick response.