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Node coverage stats deletions #336

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merged 2 commits into from
Sep 14, 2023
Merged

Node coverage stats deletions #336

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9821b8a
Added check to node coverage function to account for deletions in tot…
shreyasun Sep 13, 2023
343679b
added new tests for coverage function to validate deletions
shreyasun Sep 14, 2023
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27 changes: 27 additions & 0 deletions src/util/tubemap.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3241,6 +3241,15 @@ export function coverage(node, allReads) {
let readPathIndex = readVisit[1];
let currRead = allReads[readNum];
let numNodes = currRead.sequenceNew.length;
// identify deletion: if there's a deletion, then those bases must be deleted from total base count
for (let i = 0; i < currRead.sequenceNew.length; i += 1) {
currRead.sequenceNew[i].mismatches.forEach((mm) => {
if (mm.type === "deletion") {
console.log ("this read has a deletion", currRead)
countBases -= mm.length;
}
})
};
// if current node is the last node on the read path, add the finalNodeCoverLength number of bases
if (numNodes === readPathIndex + 1) {
countBases += currRead.finalNodeCoverLength;
Expand All @@ -3255,12 +3264,30 @@ export function coverage(node, allReads) {
// indicating read's starting and ending points within the node.
let readNum = readVisit;
let currRead = allReads[readNum];
// identify deletion: if there's a deletion, then those bases must be deleted from total base count
for (let i = 0; i < currRead.sequenceNew.length; i += 1) {
currRead.sequenceNew[i].mismatches.forEach((mm) => {
if (mm.type === "deletion") {
console.log ("this read has a deletion", currRead)
countBases -= mm.length;
}
})
};
countBases += currRead.finalNodeCoverLength - currRead.firstNodeOffset;
}
// outgoing reads
for (let readVisit of node.outgoingReads) {
let readNum = readVisit[0];
let currRead = allReads[readNum];
// identify deletion: if there's a deletion, then those bases must be deleted from total base count
for (let i = 0; i < currRead.sequenceNew.length; i += 1) {
currRead.sequenceNew[i].mismatches.forEach((mm) => {
if (mm.type === "deletion") {
console.log ("this read has a deletion", currRead)
countBases -= mm.length;
}
})
};
// coverage of outgoing read would be the the distance between the end of the node and the
// starting point of the read within the node
countBases += node.sequenceLength - currRead.firstNodeOffset;
Expand Down
237 changes: 237 additions & 0 deletions src/util/tubemap.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -607,4 +607,241 @@ describe('coverage', () => {
expect(checkNodeExample(node, reads)).toBe(undefined);
expect(coverage(node, reads)).toBe(6.57);
})
// TEST #5
it('it can handle nodes with deletions in 1 read', async () => {
const node = {
nodename: '3',
sequenceLength: 6,
incomingReads: [],
internalReads: [0, 1],
outgoingReads: [[2, 0], [3, 0]]
}
const reads = [
{
"id": 1,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 2
}
]
}
],
"firstNodeOffset": 0,
"finalNodeCoverLength": 3,
},
{
"id": 2,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "insertion",
"pos": 0,
"seq": "TCAAGAACAGTCATTCATG"
}
]
}
],
"firstNodeOffset": 1,
"finalNodeCoverLength": 5,
},
{
"id": 3,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": []
},
{
"nodeName": "11",
"mismatches": []
},
{
"nodeName": "13",
"mismatches": []
}
],
"firstNodeOffset": 2,
"finalNodeCoverLength": 6,
},
{
"id": 4,
"sourceTrackID": "1",
"sequence": [
"1",
"12",
"13"
],
"sequenceNew": [
{
"nodeName": "1",
"mismatches": []
},
{
"nodeName": "12",
"mismatches": []
},
{
"nodeName": "13",
"mismatches": []
}
],
"firstNodeOffset": 4,
"finalNodeCoverLength": 6,
}
];
//expect(checkNodeExample(node, reads)).toBe(undefined);
//console.log("coverage(node, reads) for test 5:", coverage(node, reads))
expect(coverage(node, reads)).toBe(1.83);
})
// TEST #6
it('it can handle larger node with deletions in all reads', async () => {
const node = {
nodename: '3',
sequenceLength: 24,
incomingReads: [[0, 1]],
internalReads: [1, 2],
outgoingReads: [[3, 0], [4, 0]]
}
const reads = [
{
"id": 1,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
}
],
"firstNodeOffset": 1,
"finalNodeCoverLength": 10,
},
{
"id": 2,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
}
],
"firstNodeOffset": 4,
"finalNodeCoverLength": 15,
},
{
"id": 3,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
},
{
"nodeName": "11",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 2
}
]
},
{
"nodeName": "13",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
}
],
"firstNodeOffset": 2,
"finalNodeCoverLength": 8,
},
{
"id": 4,
"sourceTrackID": "1",
"sequence": [
"1",
"12",
"13"
],
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
},
{
"nodeName": "12",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
},
{
"nodeName": "13",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 1
}
]
}
],
"firstNodeOffset": 9,
"finalNodeCoverLength": 12,
},
{
"id": 5,
"sequenceNew": [
{
"nodeName": "1",
"mismatches": [
{
"type": "deletion",
"pos": 0,
"length": 2
}
]
}
],
"firstNodeOffset": 2,
"finalNodeCoverLength": 14,
},
];
expect(coverage(node, reads)).toBe(2.79);
})
})
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