...
Based on that, I made a chromosome synonyms file: MySyns.txt
KlingonChr1 chr1 Chr1
KlingonChr2 chr2 Chr2
KlingonChr3 chr3 Chr3
KlingonChr4 chr4 Chr4
KlingonChr5 chr5 Chr5
...
And I made an example bed file by taking segments from the A_thaliana gene annotations and replacing the chromosome names: exBed.bed
KlingonChr5 550034 552647 AT5G02490.1 0 - 550295 552565 0 2 2009,296, 0,2317,
KlingonChr5 553744 556442 AT5G02500.1 0 - 554054 556334 0 2 2052,322, 0,2376,
KlingonChr5 553744 556442 AT5G02500.2 0 - 554054 556334 0 3 697,965,322, 0,1087,2376,
KlingonChr5 558284 559235 AT5G02502.1 0 - 558603 558711 0 2 427,94, 0,857,
KlingonChr5 560134 560860 AT5G02510.1 0 + 560134 560860 0 3 273,177,90, 0,356,636,
...