Open yuifu opened 4 years ago
Below is line 68.
@PG ID:hisat2 PN:hisat2 VN: CL:"/opt/conda/envs/nf-core-ramdaq-1.0dev/bin/hisat2-align-s --wrapper basic-0 --no-softclip -p 1 -x /home/username/annotations/mouse/hisat2_index_GRCm38_primary/hisat2_index_GRCm38.primary_assembly --summary-file SRR8452726_1.hisat2_summary.txt -U /tmp/28.unp"
XAM is able to parse the meta info when the empty VN
tag is removed.
using XAM
line68_modified = """
@PG ID:hisat2 PN:hisat2 CL:"/opt/conda/envs/nf-core-ramdaq-1.0dev/bin/hisat2-align-s --wrapper basic-0 --no-softclip -p 1 -x /home/username/annotations/mouse/hisat2_index_GRCm38_primary/hisat2_index_GRCm38.primary_assembly --summary-file SRR8452726_1.hisat2_summary.txt -U /tmp/28.unp"
"""
SAM.MetaInfo(chomp(line2)) #Note: chomping to remove trailing new line character.
I think the PG line generated by HISAT2 is erroneous. However, I also think that the inclusion of a tag without a value shouldn't prevent XAM from processing the rest of the file.
@yuifu, I've put together a workaround, which I hope is sufficient to keep things moving for you.
pkg> add XAM#workaround_23
I intend to implement a more robust solution that is, in general, able to recover from line parsing errors.
@CiaranOMara It works! Thanks a lot!! I also thank you for adding a solution to future release.
I have used XAM.jl to treat BAM files. Today I came across an error when opening a BAM file generated by HISAT2 version 2.2.0. No error occurred for a BAM file generated by HISAT2 version 2.1.0 (from the same FASTQ file)
Expected Behavior
No errors are expected.
Current Behavior
Possible Solution / Implementation
I have no idea but the release note of HISAT2 might help.
Steps to Reproduce (for bugs)
Context
Your Environment