TASK-7524 - Add new Variant output format: JSON_SPARSE

[j-coll]

No description provided.

[imedina]

Task linked: TASK-7524 Add new Variant output format: JSON_SPARSE

[Copilot]

Pull Request Overview

This PR tackles TASK-7524 by adding a new test for the Command class, deprecating SingleProcess, and refactoring the Command class to use asynchronous stream reading via Futures.

• Added CommandTest.java to validate execution and output handling of Command
• Marked SingleProcess as deprecated
• Updated Command.java to use an ExecutorService for stream reading and added a getStdin() method

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
commons-lib/src/test/java/org/opencb/commons/exec/CommandTest.java	Added tests to verify command execution and output correctness
commons-lib/src/main/java/org/opencb/commons/exec/SingleProcess.java	Deprecated the SingleProcess class
commons-lib/src/main/java/org/opencb/commons/exec/RunnableProcess.java	Initialized status to WAITING for improved state management
commons-lib/src/main/java/org/opencb/commons/exec/NamedThreadFactory.java	No functional changes
commons-lib/src/main/java/org/opencb/commons/exec/Command.java	Refactored to use asynchronous stream reading with Futures and added a new getStdin() accessor

Comments suppressed due to low confidence (1)

commons-lib/src/main/java/org/opencb/commons/exec/Command.java:208

• The log formatting appears incorrect; consider updating it to: logger.trace(outputName + " - last bytesRead = {}", bytesRead);

logger.trace(outputName + " - last bytesRead = {})", bytesRead);