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feat: return mutation as object that does not need to be reparsed
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@Taepper
Taepper committed Mar 23, 2024
1 parent 208e8b2 commit 8df6f1d
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Showing 9 changed files with 394 additions and 133 deletions.
104 changes: 78 additions & 26 deletions endToEndTests/test/queries/aaMutDistribution.json
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Original file line number Diff line number Diff line change
Expand Up @@ -13,157 +13,209 @@
"expectedQueryResult": [
{
"count": 37,
"mutation": "T19R",
"mutationFrom": "T",
"mutationTo": "R",
"position": 19,
"proportion": 0.38144329896907214,
"sequenceName": "S"
},
{
"count": 37,
"mutation": "G142D",
"mutationFrom": "G",
"mutationTo": "D",
"position": 142,
"proportion": 0.4065934065934066,
"sequenceName": "S"
},
{
"count": 35,
"mutation": "E156-",
"mutationFrom": "E",
"mutationTo": "-",
"position": 156,
"proportion": 0.3723404255319149,
"sequenceName": "S"
},
{
"count": 35,
"mutation": "F157-",
"mutationFrom": "F",
"mutationTo": "-",
"position": 157,
"proportion": 0.3723404255319149,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "R158G",
"mutationFrom": "R",
"mutationTo": "G",
"position": 158,
"proportion": 0.3617021276595745,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "G339D",
"mutationFrom": "G",
"mutationTo": "D",
"position": 339,
"proportion": 0.3434343434343434,
"sequenceName": "S"
},
{
"count": 33,
"mutation": "S373P",
"mutationFrom": "S",
"mutationTo": "P",
"position": 373,
"proportion": 0.336734693877551,
"sequenceName": "S"
},
{
"count": 33,
"mutation": "S375F",
"mutationFrom": "S",
"mutationTo": "F",
"position": 375,
"proportion": 0.3333333333333333,
"sequenceName": "S"
},
{
"count": 38,
"mutation": "L452R",
"mutationFrom": "L",
"mutationTo": "R",
"position": 452,
"proportion": 0.4318181818181818,
"sequenceName": "S"
},
{
"count": 32,
"mutation": "S477N",
"mutationFrom": "S",
"mutationTo": "N",
"position": 477,
"proportion": 0.34408602150537637,
"sequenceName": "S"
},
{
"count": 69,
"mutation": "T478K",
"mutationFrom": "T",
"mutationTo": "K",
"position": 478,
"proportion": 0.7340425531914894,
"sequenceName": "S"
},
{
"count": 31,
"mutation": "E484A",
"mutationFrom": "E",
"mutationTo": "A",
"position": 484,
"proportion": 0.3333333333333333,
"sequenceName": "S"
},
{
"count": 31,
"mutation": "Q493R",
"mutationFrom": "Q",
"mutationTo": "R",
"position": 493,
"proportion": 0.3333333333333333,
"sequenceName": "S"
},
{
"count": 30,
"mutation": "Q498R",
"mutationFrom": "Q",
"mutationTo": "R",
"position": 498,
"proportion": 0.3225806451612903,
"sequenceName": "S"
},
{
"count": 41,
"mutation": "N501Y",
"mutationFrom": "N",
"mutationTo": "Y",
"position": 501,
"proportion": 0.44086021505376344,
"sequenceName": "S"
},
{
"count": 30,
"mutation": "Y505H",
"mutationFrom": "Y",
"mutationTo": "H",
"position": 505,
"proportion": 0.3225806451612903,
"sequenceName": "S"
},
{
"count": 98,
"mutation": "D614G",
"mutationFrom": "D",
"mutationTo": "G",
"position": 614,
"proportion": 0.98989898989899,
"sequenceName": "S"
},
{
"count": 37,
"mutation": "H655Y",
"mutationFrom": "H",
"mutationTo": "Y",
"position": 655,
"proportion": 0.37373737373737376,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "N679K",
"mutationFrom": "N",
"mutationTo": "K",
"position": 679,
"proportion": 0.34,
"sequenceName": "S"
},
{
"count": 42,
"mutation": "P681H",
"mutationFrom": "P",
"mutationTo": "H",
"position": 681,
"proportion": 0.42,
"sequenceName": "S"
},
{
"count": 38,
"mutation": "P681R",
"mutationFrom": "P",
"mutationTo": "R",
"position": 681,
"proportion": 0.38,
"sequenceName": "S"
},
{
"count": 31,
"mutation": "N764K",
"mutationFrom": "N",
"mutationTo": "K",
"position": 764,
"proportion": 0.3263157894736842,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "D796Y",
"mutationFrom": "D",
"mutationTo": "Y",
"position": 796,
"proportion": 0.3434343434343434,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "D950N",
"mutationFrom": "D",
"mutationTo": "N",
"position": 950,
"proportion": 0.35051546391752575,
"sequenceName": "S"
},
{
"count": 33,
"mutation": "Q954H",
"mutationFrom": "Q",
"mutationTo": "H",
"position": 954,
"proportion": 0.336734693877551,
"sequenceName": "S"
},
{
"count": 34,
"mutation": "N969K",
"mutationFrom": "N",
"mutationTo": "K",
"position": 969,
"proportion": 0.3434343434343434,
"sequenceName": "S"
}
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48 changes: 36 additions & 12 deletions endToEndTests/test/queries/aaMutDistribution_all.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,73 +12,97 @@
"expectedQueryResult": [
{
"count": 46,
"mutation": "R203K",
"mutationFrom": "R",
"mutationTo": "K",
"position": 203,
"proportion": 0.46,
"sequenceName": "N"
},
{
"count": 46,
"mutation": "G204R",
"mutationFrom": "G",
"mutationTo": "R",
"position": 204,
"proportion": 0.46,
"sequenceName": "N"
},
{
"count": 64,
"mutation": "T3255I",
"mutationFrom": "T",
"mutationTo": "I",
"position": 3255,
"proportion": 0.6464646464646465,
"sequenceName": "ORF1a"
},
{
"count": 44,
"mutation": "S3675-",
"mutationFrom": "S",
"mutationTo": "-",
"position": 3675,
"proportion": 0.4489795918367347,
"sequenceName": "ORF1a"
},
{
"count": 44,
"mutation": "G3676-",
"mutationFrom": "G",
"mutationTo": "-",
"position": 3676,
"proportion": 0.4444444444444444,
"sequenceName": "ORF1a"
},
{
"count": 98,
"mutation": "P314L",
"mutationFrom": "P",
"mutationTo": "L",
"position": 314,
"proportion": 0.98,
"sequenceName": "ORF1b"
},
{
"count": 37,
"mutation": "G142D",
"mutationFrom": "G",
"mutationTo": "D",
"position": 142,
"proportion": 0.4065934065934066,
"sequenceName": "S"
},
{
"count": 38,
"mutation": "L452R",
"mutationFrom": "L",
"mutationTo": "R",
"position": 452,
"proportion": 0.4318181818181818,
"sequenceName": "S"
},
{
"count": 69,
"mutation": "T478K",
"mutationFrom": "T",
"mutationTo": "K",
"position": 478,
"proportion": 0.7340425531914894,
"sequenceName": "S"
},
{
"count": 41,
"mutation": "N501Y",
"mutationFrom": "N",
"mutationTo": "Y",
"position": 501,
"proportion": 0.44086021505376344,
"sequenceName": "S"
},
{
"count": 98,
"mutation": "D614G",
"mutationFrom": "D",
"mutationTo": "G",
"position": 614,
"proportion": 0.98989898989899,
"sequenceName": "S"
},
{
"count": 42,
"mutation": "P681H",
"mutationFrom": "P",
"mutationTo": "H",
"position": 681,
"proportion": 0.42,
"sequenceName": "S"
}
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14 changes: 10 additions & 4 deletions endToEndTests/test/queries/aaMutDistribution_min0.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"type": "AminoAcidMutations",
"sequenceName": "E",
"minProportion": 0.0,
"orderByFields": ["mutation"]
"orderByFields": ["mutationFrom", "position", "mutationTo"]
},
"filterExpression": {
"type": "True"
Expand All @@ -14,19 +14,25 @@
"expectedQueryResult": [
{
"count": 1,
"mutation": "F20L",
"mutationFrom": "F",
"mutationTo": "L",
"position": 20,
"proportion": 0.010101010101010102,
"sequenceName": "E"
},
{
"count": 1,
"mutation": "L18I",
"mutationFrom": "L",
"mutationTo": "I",
"position": 18,
"proportion": 0.010101010101010102,
"sequenceName": "E"
},
{
"count": 34,
"mutation": "T9I",
"mutationFrom": "T",
"mutationTo": "I",
"position": 9,
"proportion": 0.3469387755102041,
"sequenceName": "E"
}
Expand Down
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