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I am using .bam files created by pbmm2. This minimap2 wrapper uses the --eqx minimap2 option by default. When I try to convert the .bam file to .gff, I get the following error message:
------------------------------------------------------------------------------ | Another GFF Analysis Toolkit (AGAT) - Version: v1.4.1 | | https://github.com/NBISweden/AGAT | | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | ------------------------------------------------------------------------------ => Using standard /home/eggrandio/miniconda3/envs/agat/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml config file Error, cannot parse cigar code [X] at /home/eggrandio/miniconda3/envs/agat/bin/agat_convert_minimap2_bam2gff.pl line 264, <FILE> line 18.
Are there plants to support cigar string [X] ?
The text was updated successfully, but these errors were encountered:
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I am using .bam files created by pbmm2. This minimap2 wrapper uses the --eqx minimap2 option by default.
When I try to convert the .bam file to .gff, I get the following error message:
Are there plants to support cigar string [X] ?
The text was updated successfully, but these errors were encountered: