From 6bd66237524ad46a3900f492913000e38c1f2fa4 Mon Sep 17 00:00:00 2001
From: BenLangmead <langmea@cs.jhu.edu>
Date: Tue, 13 Jun 2017 08:57:52 -0400
Subject: [PATCH] fix for gzip closing issue

---
 pat.h | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/pat.h b/pat.h
index 44b3992..9001468 100644
--- a/pat.h
+++ b/pat.h
@@ -590,13 +590,21 @@ class CFilePatternSource : public TrimmingPatternSource {
 
 	virtual ~CFilePatternSource() {
 		if(is_open_) {
-			assert(fp_ != NULL);
-			fclose(fp_);
-			fp_ = NULL;
-			if(qfp_ != NULL) {
+			if (compressed_) {
+				gzclose(zfp_);
+				zfp_ = NULL;
+			}
+			else if (fp_ != stdin) {
+				fclose(fp_);
+				fp_ = NULL;
+			}
+			if(qfp_ != NULL && qfp_ != stdin) {
 				fclose(qfp_);
 				qfp_ = NULL;
 			}
+			assert(zfp_ == NULL);
+			assert(fp_ == NULL || fp_ == stdin);
+			assert(qfp_ == NULL || qfp_ == stdin);
 		}
 	}