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

[eggrandio]

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] ?

[Juke34]

It has been requested see #422 but I need a detailed example (few sam lines and the expected results)

[eggrandio]

There are "converters" of the tags:

From M to X or =:

or BBMaps reformat to convert both ways:

sam=                    Set to 'sam=1.3' to convert '=' and 'X' cigar symbols (from sam 1.4+ format) to 'M'.
                        Set to 'sam=1.4' to convert 'M' to '=' and 'X' (sam=1.4 requires MD tags to be present, or ref to be specified).