agat_convert_minimap2_bam2gff.pl handle Insertion and deletion

[tjwu]

Is your feature request related to a problem? Please describe. A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] I use magicblast to align NM_021983.5 cds to hg19 and hg38 chr6. The alignment works as expected. This is what I got.

@HD VN:1.0 GO:query @SQ SN:chr6 LN:170805979 @PG ID:magicblast PN:magicblast CL:magicblast -query NM_021983.5.fasta -db /magicblast/hg38_seq_db/hg38_chr6.db NM_021983.5 16 chr6 32552766 60 32S295M316D23M456N108M27590D285M2270N200M73I5337D160M * 0 0 TCCATGTTTGAGAAACATTTAATAATGCAATGTGTGGCACAAGGGGAGTACAGATGCACGGGAGGCAGGACAGTTTAGGTAAAGGGAAGCACAAAAGTTGAAGATGAGGCACTGCCATCAAAGCTGTGAGGCTTCAGGCCAAGAACAGGAGCTAAGGAAGCCACAAGGGAGGACATTTTCTGCAGAGTTGCTGAACCAGTAACAACCTGGTCCTGACAAAGCTCTTGTGGAAGAATAAGAGCCAAGTGGGAAAGCTTTTCATCTTGCAAAGCTGGGGCAGAAGGTTCTTCCTTGAATGTGGTCATCTGCACTTCAGCTCAAGAGTCCTGTTGGCTGAAGTCCAGAGTGTCCTTTCTGATTCCTGAAGTAGATGAACAGCCCTGTCCCAAGGAAGAGCAGGCCCAGCACAAAGCCCCCGACTCCACTCAGCATCTTGCTCTGTGCAGATTCAGACCGTGCACTCCATTGCACCGTGAGAGGGCTCATCATGCTTGGATGCTCCACTTGGCAGGTGTAAACCTCTCCACTCCGAGGAACTGTTTCCAGCATCACCAGGGTCTGGAAGGTCCAGTCTCCATTCTGGATCAGGCCTGTGGACACCACCCCAGCCTTCTCTTCCTGGCCGTTCCGGAACCACCTGACTTCAATGCTGCCTGGATAGAAACCATTCACAGAGCAGACCAGGAGGTTGTGGTGCTGCAGGGGCTGGGTCTTTGAAGGATACACAGTCACCTTAGGTTGGACTCGCCGCTGCACTGTGAAGCTCTCCACAACCCCGTAGTTGTATCTGCAGTAGGTGTCCACCTCGGCCCGCCTCCGCTCCAGGAGGTCCTTCTGGCTGTTCCAGTACTCAGCGTCAGGCCGCCCCAGCTCCGTCACCGCCTGGTACTCCCCCAGGTCACTGTTGTAGCGCGCGTACTCCTCTTGGTTATAGATGTATCTGATCAGGTTCCACACTCGCTCCGTCCCATTGAGGAAATGACACTCACACTTAGCCTGCTCCAAGAAACGTGGTTGGGTGTCCCCAGCCAAAGCCAGTGGGGAGCTCAGCACCGTCAATGTCACTGTCAGCGCTGCCATACAGGAGCCTCCAGGGAGCTTCAGACACACCATGCTGGAGAAGAGGACAAGACCAGTGGTCACAGCAGCAGGCAAGTCTCAATCAGGGAGAACTAT * NH:i:1 AS:i:702 NM:i:33377 XS:A:-

When using bam2gff. It's unable to convert the sam content into gff file format. It seems like when "I", "D", and "N" (insertion and deletion) exist. The conversion is unable to run.

Describe the solution you'd like Add the feature to handle insertion and deletion.

Thank you.