Force diff/vimdiff to adjust line comparison

Question

I'm comparing a couple files for differences using vimdiff. In this case, one file has 11 lines of comments describing the file whereas the other has no comment lines. I was surprised that vimdiff (rather, the underlying 'diff' ) did not accurately assign which lines to compare, so every line is different. In this case, line 12 from the first file should be compared to line 1 from the second.

Question: Is there a way to adjust which lines vimdiff (or the underlying diff) compares (e.g., shift down by 12), without modifying the files?

Really appreciate your help.

Here are initial lines from the files:

File 1 (includes comments)

# This table shows the intersection of dark by MAPQ regions by a gene annotation gff3, showing where dark by MAPQ regions fall within gene body
# chrom : Chromosome of dark by MAPQ region
# region_start : start position of dark by MAPQ region within gene-body element
# region_end : end position of dark by MAPQ region within gene-body element
# gene_body_id : ID of gene body element that contains this dark by MAPQ region
# region_type : genebody element type (e.g. exon, intron, UTR, etc.)
# biotype : GENCODE biotype of gene that contains this dark by MAPQ reigon
# gene_body_chrom : Chromosome of the genebody element
# gene_body_start : start position of the genebody element
# gene_body_end : end position of the genebody element
#chrom  start   end gene_body_id    region_type biotype gene_body_chrom gene_body_start gene_body_end
1   11869   12227   DDX11L1_1   exon    transcribed_unprocessed_pseudogene  1   11869   12227
1   12228   12611   DDX11L1_intron_1    intron  transcribed_unprocessed_pseudogene  1   12228   12611
1   12612   12721   DDX11L1_2   exon    transcribed_unprocessed_pseudogene  1   12612   12721
1   12722   12751   DDX11L1_intron_2    intron  transcribed_unprocessed_pseudogene  1   12722   12973
1   12861   12973   DDX11L1_intron_2    intron  transcribed_unprocessed_pseudogene  1   12722   12973
1   13191   13219   DDX11L1_intron_3    intron  transcribed_unprocessed_pseudogene  1   13053   13219

File 2 (does not include comments)

chr1    11869   12227   DDX11L1_1   exon    transcribed_unprocessed_pseudogene  chr1    11869   12227
chr1    12228   12611   DDX11L1_intron_1    intron  transcribed_unprocessed_pseudogene  chr1    12228   12611
chr1    12612   12721   DDX11L1_2   exon    transcribed_unprocessed_pseudogene  chr1    12612   12721
chr1    12722   12752   DDX11L1_intron_2    intron  transcribed_unprocessed_pseudogene  chr1    12722   12973
chr1    12861   12973   DDX11L1_intron_2    intron  transcribed_unprocessed_pseudogene  chr1    12722   12973
chr1    13191   13219   DDX11L1_intron_3    intron  transcribed_unprocessed_pseudogene  chr1    13053   13219

VimDiff result

Answer 1

I also have the same problem so I developed https://github.com/rickhowe/spotdiff.vim. You have to specify the line range but can partially compare any line between 2 files or even in a single file. You can also select visual area and text object to compare.