Skip to content

Update validator.js to not allow length 0 & indels #10

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ShreyaKakhandiki wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update validator.js to not allow length 0 & indels #10

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions js/validator.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,16 @@ function traverseTree(node, expectedParentLen, {
errors.push(`Length mismatch at node ${label}: expected parent length ${expectedParentLen}, got ${parentLen}`);
}

// Rule: Zero-length branches cannot contain indels or mismatches
if (node.distance === 0) {
console.log("DISTANCE HERE IS ZERO")
const ops = expandCigar(node.cigar);
const hasIndel = ops.some(([_, op]) => op === "I" || op === "D" || op === "X");
if (hasIndel) {
errors.push(`Node at ${path} has zero-length branch but contains indels in CIGAR: '${node.cigar}'`);
}
}

const isLeaf = !node.child || node.child.length === 0;

// Rule: distance required on all but root
Expand Down