Report missing extracted toassembly files in wrapper.

liulab-dfci · Oct 14, 2019 · b296a27 · b296a27
1 parent cc53ae6
commit b296a27
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git 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
@@ -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