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test_fasta.gff
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##genome-build WormBase WS75
# To be lifted to WS76
# Non-overlapping mismatches
IV Test Testing 12345 12355 . . . ID=mm-fully-after; no change
IV Test Testing 16422615 16422620 . . . ID=mm-before-constant; no change
IV Test Testing 16424501 16424503 . . . ID=mm-before-increases; shifted
# Feature > mismatch on both ends
IV Test Testing 16426790 16426836 . . . ID=mm-in-remsome
X Test Testing 15981150 15981160 . . . ID=mm-in-noneleft
IV Test Testing 16449590 16449598 . . . ID=mm-in-added
IV Test Testing 16440864 16440944 . . . ID=mm-in-addsome
# Mismatch > Feature on both ends - mark all as indeterminate
IV Test Testing 16440900 16440920 . . . ID=mm-around-adding
IV Test Testing 16436333 16436343 . . . ID=mm-around-someleft
IV Test Testing 16436332 16436334 . . . ID=mm-around-allgone
# Mismatch overlaps left end of feature ; mismatch starting length > 0
IV Test Testing 16426800 16426835 . . . ID=mm-lol-remsome
IV Test Testing 16424050 16424061 . . . ID=mm-lol-addsome
IV Test Testing 16422609 16422618 . . . ID=mm-lol-change
# Mismatch overlaps right end of feature ; mismatch starting length > 0
IV Test Testing 16436330 16436335 . . . ID=mm-rol-remove
IV Test Testing 16440860 16440869 . . . ID=mm-rol-add
IV Test Testing 16422605 16422609 . . . ID=mm-rol-change
##FASTA
>mm-fully-after feature : no change
aaaaaAAAAAa
>mm-before-constant : no change
cccccc
>mm-before-increases : no change
acg
>mm-around-adding : indeterminate
aaaaacccccGGGGGtttttU
>mm-around-allgone : indeterminate
CGA
>mm-around-someleft : indeterminate
ATU
ATU
ATU
C
>mm-in-remsome : 47 bases. should result in 45 bases of x: the 3 beginning ok, and the 2 end.
AGG
TTTTTttttt
cccccCCCCC
AAAAAaaaaa
gggggGGGGG
UUUU
>mm-in-noneleft : entirely a's
aaaaa
G
aaaaa
>mm-in-added : one base added between g's and t's
gggggg
ttt
>mm-in-addsome : 8 bases added near the end
G
aaaaaccccc
aaaaaccccc
aaaaaccccc
aaaaaccccc
aaaaaccccc
aaaaaccccc
aaaaaccccc
aaaaaccccc
>mm-lol-remsome
aaaaaa
cccccc
tttttt
gggggg
uuuuuu
ATATAT
>mm-lol-addsome
aaaaa
ttttt
gg
>mm-lol-change
agtga
agtga
>mm-rol-remove
agtagt
>mm-rol-add
atataGCGCG
>mm-rol-change
acGTu