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[hail][bugfix]: fix out of bounds read in LoadVCF #7182

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merged 1 commit into from Oct 3, 2019

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@chrisvittal
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@chrisvittal chrisvittal commented Oct 3, 2019

When reading flag fields, we attempt to check if line(pos) == '='.
When a flag occurs at end of line, pos will be equal to line.length,
and thus caused an out of bounds read on the string.

Added the bounds check to prevent this.

When reading flag fields, we attempt to check if `line(pos) == '='`.
When a flag occurs at end of line, pos will be equal to line.length,
and thus caused an out of bounds read on the string.

Added the bounds check to prevent this.
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@chrisvittal chrisvittal commented Oct 3, 2019

ref: https://hail.zulipchat.com/#narrow/stream/123010-Hail-0.2E2.20support/topic/Error.20importing.20dbsnp.20VCF/near/177209550

I have confirmed that the test I added fails with the same error laurent saw in the linked conversation, and passes with the change.

@@ -914,7 +914,7 @@ final class VCFLine(val line: String, arrayElementsRequired: Boolean) {
if (infoType.hasField(key)) {
rvb.setFieldIndex(infoType.fieldIdx(key))
if (infoFlagFieldNames.contains(key)) {
if (line(pos) == '=') {
if (pos != line.length && line(pos) == '=') {
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@tpoterba tpoterba Oct 3, 2019

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should be !(endField(pos) I think?

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@chrisvittal chrisvittal Oct 3, 2019

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endField and pos != line.length are about as clear in my mind, and the second won't check needlessly for the presence of a tab.

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@tpoterba tpoterba Oct 3, 2019

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OK, fair.

@chrisvittal chrisvittal dismissed tpoterba’s stale review Oct 3, 2019

Pushing back. Think the change is fine as is.

@danking danking merged commit dcf1180 into hail-is:master Oct 3, 2019
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3 participants