createRepeatLandscape.pl changes for EDTA/TESorter classes

I changed the following in RepeatMasker/util/createRepeatLandscape.pl to make classes reported by EDTA and TESorter appear in the plot.

Around line 220 I added CACTA repeats as their own class:

              [ 'DNA/Transib',    '#FF9972' ],
              [ 'DNA/CACTA',      '#D45B2C' ],

I got the color by googling #FF9972 and then clicking around in that feature to get a similar looking color.

Then, around line 700, I added all these translations:

"LTR/Gypsy/Ogre" => "LTR/Gypsy",
"LTR/Gypsy/Athila" => "LTR/Gypsy",
"LTR/Gypsy/CRM" => "LTR/Gypsy",
"LTR/Copia/Ivana" => "LTR/Gypsy",
"LTR/Copia/Ikeros" => "LTR/Gypsy",
"LTR/Gypsy/Reina" => "LTR/Gypsy",
"LTR/Gypsy/Galadriel" => "LTR/Gypsy",
"LTR/Gypsy/Retand" => "LTR/Gypsy",
"LTR/Gypsy/Tekay" => "LTR/Gypsy",
"LTR/Copia/Tork" => "LTR/Copia",
"LTR/Copia/mixture" => "LTR/Copia",
"LTR/Copia/Ale" => "LTR/Copia",
"LTR/Copia/SIRE" => "LTR/Copia",
"LTR/Copia/TAR" => "LTR/Copia",
"LTR/unknown" => "LTR",
"MITE/DTM" => "DNA/DTM",
"TIR/hAT" => "DNA/hAT",
"MITE/DTT" => "DNA/TcMar",
"DNA/DTT" => "DNA/TcMar",
"MITE/DTH" => "DNA/Harbinger",
"DNA/DTH" => "DNA/Harbinger",
"DNA/DTC" => "DNA/CACTA",
"MITE/DTC" => "DNA/CACTA",
"DNA/DTA" => "DNA/hAT",
"MITE/DTA" => "DNA/hAT",
"TIR/PIF_Harbinger" => "DNA/Harbinger",
"TIR/MuDR_Mutator" => "DNA/MULE",
"pararetrovirus" => 'Other',
"LTR/mixture" => 'LTR',
'LTR/Copia/Angela' => 'LTR/Copia',
'LTR/Copia/Osser' => 'LTR/Copia',
'LTR/Gypsy/mixture' => 'LTR/Gypsy',
'TIR/EnSpm_CACTA' => "DNA/CMC",
'mixture' => 'Other'

making sure that only the very last line has no comma. That way the more complex TEs from TESorter are classified as their class or group, not themselves. That's already it!

philippbayer/changes.md