From b296a27057e4de0838658a826567b6f191544870 Mon Sep 17 00:00:00 2001
From: Li <mourisl@hotmail.com>
Date: Mon, 14 Oct 2019 18:14:13 -0400
Subject: [PATCH] Report missing extracted toassembly files in wrapper.

---
 BamExtractor.cpp | 3 +++
 run-trust4       | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/BamExtractor.cpp b/BamExtractor.cpp
index d768a74..c3b65a5 100644
--- a/BamExtractor.cpp
+++ b/BamExtractor.cpp
@@ -392,6 +392,9 @@ void FinishWork( std::vector<struct _unmappedCandidate> work,
 	pthread_mutex_destroy( info.lockOutput ) ;
 	pthread_mutex_destroy( info.lockFreeThreads ) ;
 	pthread_cond_destroy( info.condFreeThreads ) ;
+	delete info.lockOutput ;
+	delete info.lockFreeThreads ;
+	delete info.condFreeThreads ;
 	ReleaseCustomData( threadArgs, threadCnt ) ;
 	delete[] threadArgs ;
 }
diff --git a/run-trust4 b/run-trust4
index 0f08822..88b5b2d 100755
--- a/run-trust4
+++ b/run-trust4
@@ -178,11 +178,15 @@ if ( @bamFiles > 0 )
 		push @secondMateFiles, $prefix."_toassemble_2.fq" ;
 		$mainArgs .= " -1 ".$prefix."_toassemble_1.fq -2 ".$prefix."_toassemble_2.fq" ;
 	}
-	else
+	elsif ( -e $prefix."_toassemble.fq" )
 	{
 		push @singleFiles, "${prefix}_toassemble.fq" ;
 		$mainArgs .= " -u ${prefix}_toassemble.fq" ;
 	}
+	else
+	{
+		die "Could not find files like ${prefix}_toassemble*.fq\n" ;
+	}
 }
 
 # Run the assembly