From b2a12e167b813a9f61efec3ce17c779437164e28 Mon Sep 17 00:00:00 2001
From: Robert Aboukhalil <robert.aboukhalil@gmail.com>
Date: Tue, 17 Aug 2021 20:28:54 -0700
Subject: [PATCH] Flush stdout/stderr to fix issues with bcftools query not
 returning any output

---
 src/worker.js | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/worker.js b/src/worker.js
index 407ced5..059d3e6 100644
--- a/src/worker.js
+++ b/src/worker.js
@@ -248,6 +248,13 @@ const aioli = {
 		// Run command. Stdout/Stderr will be saved to "tool.stdout"/"tool.stderr" (see "print" and "printErr" above)
 		tool.module.callMain(args);
 
+		// Flush stdout/stderr to make sure we got everything. Otherwise, if use a command like 
+		// `bcftools query -f "%ALT" variants.bcf`, it won't output anything until the next
+		// invocation of that command!
+		try {
+			tool.module.FS.close( tool.module.FS.streams[1] );
+			tool.module.FS.close( tool.module.FS.streams[2] );
+		} catch (error) {}
 		// Re-open stdout/stderr (fix error "error closing standard output: -1")
 		tool.module.FS.streams[1] = tool.module.FS.open("/dev/stdout", "w");
 		tool.module.FS.streams[2] = tool.module.FS.open("/dev/stderr", "w");