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Fixed crashes in new dangling head merging code #7086

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merged 4 commits into from
Feb 19, 2021

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jamesemery
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It looks like the last rebase in the previous PR broke some things and tests were insufficient to catch them. I have added checks to the tests as to the actual contents of the paths as well as some more extreme tests.

Fixes #7085

@jamesemery jamesemery requested a review from ahaessly February 19, 2021 18:30
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Travis reported job failures from build 32866
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling openjdk8 32866.4 logs

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Travis reported job failures from build 32864
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling openjdk8 32864.4 logs

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Mutect2IntegrationTest only has whitespace changes. no need to include it.
verified that this fixes the array out of bounds exception and corrects the off by 1 errors we were seeing as well.

@jamesemery jamesemery merged commit 8f6c736 into master Feb 19, 2021
@jamesemery jamesemery deleted the je_patchDanglingHeadIndelCode branch February 19, 2021 19:15
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new dangling head recovery leads to array index out of bounds
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