Output gff only changes start-coordinates with insertions

[KHajji]

It seems only the feature start position is changed for subsequent features in the gff. Example is for R1070_B01_4802200553, an omicron sample.

Original gff

##sequence-region MN908947.3 1 29903 ##species Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome MN908947.3 Genbank gene 266 13468 . + . ID=gene-orf1a;Name=orf1a;gbkey=Gene;gene=orf1a;gene_biotype=protein_coding;gene_name=orf1a MN908947.3 Genbank gene 13468 21555 . + . ID=gene-orf1b;Name=orf1b;gbkey=Gene;gene=orf1b;gene_biotype=protein_coding;gene_name=orf1b MN908947.3 Genbank gene 21563 25384 . + . ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;gene_name=S MN908947.3 Genbank gene 25393 26220 . + . ID=gene-ORF3a;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;gene_name=ORF3a MN908947.3 Genbank gene 26245 26472 . + . ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;gene_name=E MN908947.3 Genbank gene 26523 27191 . + . ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;gene_name=M MN908947.3 Genbank gene 27202 27387 . + . ID=gene-ORF6;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;gene_name=ORF6 MN908947.3 Genbank gene 27394 27759 . + . ID=gene-ORF7a;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;gene_name=ORF7a MN908947.3 Genbank gene 27756 27887 . + . ID=gene-ORF7b;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;gene_name=ORF7b MN908947.3 Genbank gene 27894 28259 . + . ID=gene-ORF8;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;gene_name=ORF8 MN908947.3 Genbank gene 28274 29533 . + . ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;gene_name=N MN908947.3 Genbank gene 29558 29674 . + . ID=gene-ORF10;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;gene_name=ORF10

Updated gff

##sequence-region MN908947.3 1 29903 ##species Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome MN908947.3 Genbank gene 266 13468 . + . ID=gene-orf1a;Name=orf1a;gbkey=Gene;gene=orf1a;gene_biotype=protein_coding;gene_name=orf1a MN908947.3 Genbank gene 13468 21555 . + . ID=gene-orf1b;Name=orf1b;gbkey=Gene;gene=orf1b;gene_biotype=protein_coding;gene_name=orf1b MN908947.3 Genbank gene 21563 25384 . + . ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;gene_name=S MN908947.3 Genbank gene 25402 26220 . + . ID=gene-ORF3a;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;gene_name=ORF3a MN908947.3 Genbank gene 26254 26472 . + . ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;gene_name=E MN908947.3 Genbank gene 26532 27191 . + . ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;gene_name=M MN908947.3 Genbank gene 27211 27387 . + . ID=gene-ORF6;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;gene_name=ORF6 MN908947.3 Genbank gene 27403 27759 . + . ID=gene-ORF7a;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;gene_name=ORF7a MN908947.3 Genbank gene 27765 27887 . + . ID=gene-ORF7b;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;gene_name=ORF7b MN908947.3 Genbank gene 27903 28259 . + . ID=gene-ORF8;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;gene_name=ORF8 MN908947.3 Genbank gene 28283 29533 . + . ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;gene_name=N MN908947.3 Genbank gene 29567 29674 . + . ID=gene-ORF10;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;gene_name=ORF10

[KHajji]

Fixed in 54967c6