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Add support for [X] cigar string on agat_convert_minimap2_bam2gff.pl #520

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eggrandio opened this issue Jan 24, 2025 · 0 comments
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@eggrandio
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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] ?

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