29379430386
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Ran 15 Jul 2026 12:38AM UTC

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Committed 15 Jul 2026 12:34AM UTC coverage: 99.671%. Remained the same

Build # 29379430386

Build Type

Pull #2

github

Committed by

clintval

Commit Message

feat: hand the JVM a .jar-named handle so reflections-based tools work

Tools like GATK discover classes (e.g. -T walkers) via libraries such as
reflections, which only scan classpath entries whose filename ends in .jar.
A magicked file with a bare name (./gatk3) lands on the classpath via
java -jar $0, gets skipped, and the tool finds nothing
("Could not find walker").

When $0 lacks a .jar suffix, the preamble now exposes a .jar-named handle
in a temp dir (hardlink when possible, else a copy) and runs the JVM against
that; names already ending in .jar exec directly as before. An EXIT trap
removes the temp dir (verified to fire on normal exit and SIGINT/TERM/HUP);
only SIGKILL leaks it, which /tmp reaps anyway. Removing the hardlink never
touches the original jar.

Adds a unit test for the generated preamble and an integration test that
asserts an extensionless magicked file hands the JVM a .jar path.

Pull Request Pull Request #2: feat: hand the JVM a .jar-named handle so reflections-based tools work

Coverage Stats

303 of 304 relevant lines covered (99.67%)

8.54 hits per line

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ID	Job ID	Ran	Files	Coverage
1	29379430386.1	15 Jul 2026 12:38AM UTC	2	99.67	GitHub Action Run

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