From 261c794c55f2f55e8e92458ddfcbac9635ed2c99 Mon Sep 17 00:00:00 2001
From: Will Trimble <trimble@anl.gov>
Date: Wed, 5 Apr 2017 15:12:07 -0500
Subject: [PATCH 1/2] Fixed bug in input parser--failed to allocate space for
 the null terminator

---
 clipper/fastq-lib.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/clipper/fastq-lib.cpp b/clipper/fastq-lib.cpp
index e4e4321..dfefd2d 100644
--- a/clipper/fastq-lib.cpp
+++ b/clipper/fastq-lib.cpp
@@ -361,7 +361,7 @@ int getstr (char ** lineptr, size_t *n, FILE * stream, char terminator, int offs
 	 NUL-terminate the line buffer.  */
 
       assert(*n - nchars_avail == read_pos - *lineptr);
-      if (nchars_avail < 1)
+      if (nchars_avail < 2)
 	{
 	  if (*n > 64)
 	    *n *= 2;

From b6455beb1c1e34a1fd1dab853fd0e618c8f10efd Mon Sep 17 00:00:00 2001
From: Will Trimble <trimble@anl.gov>
Date: Wed, 5 Apr 2017 15:13:35 -0500
Subject: [PATCH 2/2] Removed --rsyncable from gzip invokation for portablity

---
 clipper/ea-bcl2fastq.cpp | 2 +-
 clipper/fastq-lib.cpp    | 2 +-
 clipper/mirna-quant.cpp  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/clipper/ea-bcl2fastq.cpp b/clipper/ea-bcl2fastq.cpp
index ece28c0..5bc0a1e 100644
--- a/clipper/ea-bcl2fastq.cpp
+++ b/clipper/ea-bcl2fastq.cpp
@@ -290,7 +290,7 @@ int main (int argc, char **argv) {
             ++output_fnum;                        // output file number is sequential
             masks[i].rnum=output_fnum;            // save file number as "read number"
             if (usegz) {
-                outtmp = string_format("gzip -2 --rsyncable -c > %s.%d.fq.gz",out.c_str(),output_fnum); 
+                outtmp = string_format("gzip -2  -c > %s.%d.fq.gz",out.c_str(),output_fnum); 
                 fo=popenordie(outtmp.c_str(),"w");
             } else {
                 outtmp = string_format("%s.%d.fq",out.c_str(),output_fnum); 
diff --git a/clipper/fastq-lib.cpp b/clipper/fastq-lib.cpp
index dfefd2d..df092c6 100644
--- a/clipper/fastq-lib.cpp
+++ b/clipper/fastq-lib.cpp
@@ -160,7 +160,7 @@ FILE *gzopen(const char *f, const char *m, bool*isgz) {
         if (!strcmp(ext,".gz")) {
             char *tmp=(char *)malloc(strlen(f)+100);
             if (strchr(m,'w')) {
-                    strcpy(tmp, "gzip -3 --rsyncable > '");
+                    strcpy(tmp, "gzip -3  > '");
                     strcat(tmp, f);
                     strcat(tmp, "'");
             } else {
diff --git a/clipper/mirna-quant.cpp b/clipper/mirna-quant.cpp
index d609dbc..98eae13 100644
--- a/clipper/mirna-quant.cpp
+++ b/clipper/mirna-quant.cpp
@@ -681,7 +681,7 @@ FILE *gzopen(const char *f, const char *m, bool*isgz) {
         if (!strcmp(fext(f),".gz")) {
                 char *tmp=(char *)malloc(strlen(f)+100);
                 if (strchr(m,'w')) {
-                        strcpy(tmp, "gzip --rsyncable > '");
+                        strcpy(tmp, "gzip  > '");
                         strcat(tmp, f);
                         strcat(tmp, "'");
                 } else {