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Fix vcfwave.cpp #407

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Merged
merged 1 commit into from
Oct 31, 2024
Merged

Fix vcfwave.cpp #407

merged 1 commit into from
Oct 31, 2024

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AndreaGuarracino
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When decomposing this variant

SGDref#0#chrI	92298	>6309685>6309691	TTG	TGT,TTT,TTTGG	60	.	AC=2,1,1;AF=0.111111,0.0555556,0.0555556;AN=18;AT=>6309685>6309687>6309690>6309691,>6309685>6309686>6309689>6309691,>6309685>6309687>6309689>6309691,>6309685>6309687>6309688>6309690>6309691;NS=14;LV=0	GT	0	0|0	0	0|0	0	0|0	1	0|0	0	1	2	0	3	0

We were getting

SGDref#0#chrI	92299	>6309685>6309691_1	T	TTG	60	.	AC=2,1,1;AF=0.111111,0.0555556,0.0555556;AN=18;AT=>6309685>6309687>6309690>6309691,>6309685>6309686>6309689>6309691,>6309685>6309687>6309689>6309691,>6309685>6309687>6309688>6309690>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=2	GT	0	0|0	0	0|0	0	0|0	0	0|0	0	0	0	0	1	0
SGDref#0#chrI	92299	>6309685>6309691_2	TG	GT	60	.	AC=2;AF=0.111111;AN=18;AT=>6309685>6309687>6309690>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=2	GT	0	0|0	0	0|0	0	0|0	1	0|0	0	1	0	0	0	0
SGDref#0#chrI	92300	>6309685>6309691_3	G	T	60	.	AC=1;AF=0.055556;AN=18;AT=>6309685>6309686>6309689>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=1	GT	0	0|0	0	0|0	0	0|0	0	0|0	0	0	1	0	0	0

where the first variant has wrong AC, AF, and AT fields (3 values each instead of just 1).

The fix avoids that and now we get

SGDref#0#chrI  92299  >6309685>6309691_1  T   TTG  60  .  AC=1;AF=0.055556;AN=18;AT=>6309685>6309687>6309689>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=2;TYPE=ins  GT  0  0|0  0  0|0  0  0|0  0  0|0  0  0  0  0  1  0
SGDref#0#chrI  92299  >6309685>6309691_2  TG  GT   60  .  AC=2;AF=0.111111;AN=18;AT=>6309685>6309687>6309690>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=2;TYPE=mnp  GT  0  0|0  0  0|0  0  0|0  1  0|0  0  1  0  0  0  0
SGDref#0#chrI  92300  >6309685>6309691_3  G   T    60  .  AC=1;AF=0.055556;AN=18;AT=>6309685>6309686>6309689>6309691;NS=14;LV=0;ORIGIN=SGDref#0#chrI:92298;LEN=1;TYPE=snp  GT  0  0|0  0  0|0  0  0|0  0  0|0  0  0  1  0  0  0

@pjotrp pjotrp merged commit 6afe429 into vcflib:master Oct 31, 2024
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@AndreaGuarracino @pjotrp
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