(edited for real example):
wget -q https://public.gi.ucsc.edu/~hickey/debug/irwin/case2-tiny-h2m.raw.maf.gz
wget -q https://public.gi.ucsc.edu/~hickey/debug/irwin/genome.list
taffy view -i case2-tiny-h2m.raw.maf.gz | taffy norm -k | mafFilter -i hg38,Tarsius_lariang -m - > norm.maf
zcat case2-tiny-h2m.raw.maf.gz | mafRowOrderer -m - --order-file genome.list | taffy view | taffy norm -k | mafFilter -i hg38,Tarsius_lariang -m - > sort.norm.maf
Tarsius is is one row in the first maf
a
s hg38.chr1 11707 6 + 248956422 GGGGC-C
s Tarsius_lariang.k141_1886670 1879 6 - 2088 AGGGC-C
s hg38.chr1 182226 6 + 248956422 GGGGC-C
s hg38.chr12 9309644 6 + 133275309 GGGGC-C
s hg38.chr12 123853115 6 - 133275309 GGGGC-C
s hg38.chr12 31100331 6 + 133275309 GGGGC-C
s hg38.chr12 11838 6 + 133275309 GGGGC-C
s hg38.chr15 11930 6 - 101991189 GGGGC-C
s hg38.chr16 11388 6 + 90338345 GGGGC-C
s hg38.chr2 128591799 6 - 242193529 GGGGC-C
s hg38.chr9 11820 6 + 138394717 GGGGC-C
s hg38.chrX 12546 6 - 156040895 GGGGC-C
but two rows in the second maf
a
s hg38.chr1 11707 6 + 248956422 GGGG-C-C
s hg38.chr1 182226 6 + 248956422 GGGG-C-C
s hg38.chr12 9309644 6 + 133275309 GGGG-C-C
s hg38.chr12 123853115 6 - 133275309 GGGG-C-C
s hg38.chr12 31100331 6 + 133275309 GGGG-C-C
s hg38.chr12 11838 6 + 133275309 GGGG-C-C
s hg38.chr15 11930 6 - 101991189 GGGG-C-C
s hg38.chr16 11388 6 + 90338345 GGGG-C-C
s hg38.chr2 128591799 6 - 242193529 GGGG-C-C
s hg38.chr9 11820 6 + 138394717 GGGG-C-C
s hg38.chrX 12546 6 - 156040895 GGGG-C-C
s Tarsius_lariang.k141_1886670 1882 3 - 2088 ---G-C-C
s Tarsius_lariang.k141_1886670 1879 3 - 2088 AGG-----
(edited for real example):
Tarsius is is one row in the first maf
but two rows in the second maf