From c91bdefa1a25015f0ec0726830e15d12fe1ca653 Mon Sep 17 00:00:00 2001
From: jenniferliddle <jennifer@jsquared.co.uk>
Date: Tue, 11 Jul 2017 14:40:39 +0100
Subject: [PATCH] Bug fix: remove memory leak from decode

---
 src/decode.c    |  4 +++-
 test/t_decode.c | 11 +++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/decode.c b/src/decode.c
index 44d81f2..1d2b780 100644
--- a/src/decode.c
+++ b/src/decode.c
@@ -739,9 +739,11 @@ int processTemplate(va_t *template, BAMit_t *bam_out, va_t *barcodeArray, opts_t
     for (int n=0; n < template->end; n++) {
         bam1_t *rec = template->entries[n];
         if (bc_tag) {
-            char *newtag = strdup(bc_tag);
+            char *newtag;
             if (opts->convert_low_quality) {
                 newtag = checkBarcodeQuality(bc_tag,rec,opts);
+            } else {
+                newtag = strdup(bc_tag);
             }
             if (strlen(bc_tag) > opts->tag_len) {
                 newtag[opts->tag_len] = 0;  // truncate seq to barcode length
diff --git a/test/t_decode.c b/test/t_decode.c
index c3ce58c..4b30c32 100644
--- a/test/t_decode.c
+++ b/test/t_decode.c
@@ -82,6 +82,12 @@ void setup_test_2(int* argc, char*** argv, char *outputfile)
     (*argv)[17] = strdup("RT");
 }
 
+void free_argv(int argc, char *argv[])
+{
+    for (int n=0; n < argc; free(argv[n++]));
+    free(argv);
+}
+
 void test_noCalls(char *s, int e)
 {
     int n;
@@ -163,6 +169,7 @@ int main(int argc, char**argv)
 
     setup_test_1(&argc_1, &argv_1, outputfile);
     main_decode(argc_1-1, argv_1+1);
+    free_argv(argc_1,argv_1);
 
     char *cmd = calloc(1,1024);
     sprintf(cmd,"diff -I ID:bambi %s %s", outputfile, MKNAME(DATA_DIR,"/out/6383_9_nosplit_nochange.sam"));
@@ -180,6 +187,7 @@ int main(int argc, char**argv)
     sprintf(outputfile,"%s/decode_2.sam",TMPDIR);
     setup_test_2(&argc_2, &argv_2, outputfile);
     main_decode(argc_2-1, argv_2+1);
+    free_argv(argc_2,argv_2);
 
     sprintf(cmd,"diff -I ID:bambi %s %s", outputfile, MKNAME(DATA_DIR,"/out/6383_8_nosplitN.sam"));
     result = system(cmd);
@@ -190,6 +198,9 @@ int main(int argc, char**argv)
         success++;
     }
 
+    free(outputfile);
+    free(cmd);
+
     printf("decode tests: %s\n", failure ? "FAILED" : "Passed");
     return failure ? EXIT_FAILURE : EXIT_SUCCESS;
 }