From 3457c494850bd1e5b08d039380d5673c5d95e24f Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@ghic.org>
Date: Wed, 12 Oct 2016 14:26:04 -0700
Subject: [PATCH 1/4] Remove unused strstream header

---
 src/bed2vector.cpp | 1 -
 src/maqread.cpp    | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/bed2vector.cpp b/src/bed2vector.cpp
index 63e9499..ea45033 100644
--- a/src/bed2vector.cpp
+++ b/src/bed2vector.cpp
@@ -5,7 +5,6 @@
 #include <iostream>
 #include <fstream>
 #include <sstream>
-#include <strstream>
 #include <algorithm>
 #include <string>
 #include <functional>
diff --git a/src/maqread.cpp b/src/maqread.cpp
index 896068f..862839b 100644
--- a/src/maqread.cpp
+++ b/src/maqread.cpp
@@ -4,7 +4,6 @@
 #include <iostream>
 #include <fstream>
 #include <sstream>
-#include <strstream>
 #include <algorithm>
 #include <string>
 #include <functional>

From 7bb9f6a408a13e6badb2df6cc3bae1b926d3b442 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@ghic.org>
Date: Wed, 12 Oct 2016 15:03:55 -0700
Subject: [PATCH 2/4] Rename hash_* to ordered_*

The template was renamed when it was standardized, and the
old names are deprecated by gcc 6.1
---
 src/bed2vector.cpp | 52 +++++++++++++++++++++++-----------------------
 src/maqread.cpp    |  4 ++--
 src/pc.h           | 15 ++-----------
 3 files changed, 30 insertions(+), 41 deletions(-)

diff --git a/src/bed2vector.cpp b/src/bed2vector.cpp
index ea45033..6ff86fe 100644
--- a/src/bed2vector.cpp
+++ b/src/bed2vector.cpp
@@ -114,7 +114,7 @@ SEXP read_bed_ends(SEXP filename) {
   vector< vector<int> > pos;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
 
   typedef boost::tokenizer<boost::char_separator<char> >  tokType;
@@ -159,7 +159,7 @@ SEXP read_bed_ends(SEXP filename) {
       }
 
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -250,7 +250,7 @@ SEXP read_meland_old(SEXP filename) {
   vector< vector<int> > poslen; // length
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -292,7 +292,7 @@ SEXP read_meland_old(SEXP filename) {
       int fpos=atoi(str_pos.c_str());
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -428,7 +428,7 @@ SEXP read_meland_old(SEXP filename) {
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -472,7 +472,7 @@ SEXP read_meland_old(SEXP filename) {
       int fpos=atoi(str_pos.c_str());
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -620,7 +620,7 @@ SEXP read_eland_mismatches(SEXP filename) {
   vector< vector<int> > mm2; // position of the second mismatch
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -688,7 +688,7 @@ SEXP read_eland_mismatches(SEXP filename) {
       }
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -813,7 +813,7 @@ SEXP read_eland_mismatches(SEXP filename) {
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -864,7 +864,7 @@ SEXP read_eland_mismatches(SEXP filename) {
       }
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -1000,7 +1000,7 @@ SEXP read_eland_mismatches(SEXP filename) {
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -1074,7 +1074,7 @@ SEXP read_eland_mismatches(SEXP filename) {
       }
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -1209,7 +1209,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -1362,7 +1362,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       }
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -1496,7 +1496,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -1571,7 +1571,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
 
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -1710,7 +1710,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -1788,7 +1788,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       int nm=atoi(str_ndel.c_str())+atoi(str_nins.c_str())+atoi(str_nsub.c_str());
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -1937,7 +1937,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -1980,7 +1980,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       }
 
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -2115,7 +2115,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<int> > posnm; // number of mismatches
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -2157,7 +2157,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       int nm=atoi(str_qual.c_str());
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -2266,7 +2266,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<int> > posnm; // number of mismatches
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -2325,7 +2325,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
@@ -2437,7 +2437,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
   vector< vector<int> > poslen; // length of the match
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -2526,7 +2526,7 @@ SEXP read_eland_multi(SEXP filename,SEXP read_tag_names_R,SEXP eland_tag_length_
       
       
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
diff --git a/src/maqread.cpp b/src/maqread.cpp
index 862839b..5b3d6b9 100644
--- a/src/maqread.cpp
+++ b/src/maqread.cpp
@@ -54,7 +54,7 @@ extern "C" {
   vector< vector<string> > tagnames;
 
   // chromosome map
-  hash_map<string, int, hash<string>,equal_to<string> > cind_map;
+  unordered_map<string, int, hash<string>,equal_to<string> > cind_map;
   vector<string> cnames;
   
 
@@ -88,7 +88,7 @@ extern "C" {
     
 
       // determine the chromosome index
-      hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
+      unordered_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
       int cind=-1;
       if(li==cind_map.end()) {
 	// register new chromosome
diff --git a/src/pc.h b/src/pc.h
index 3611c97..b77cd4a 100644
--- a/src/pc.h
+++ b/src/pc.h
@@ -1,17 +1,6 @@
 #ifndef PC_H
 #define PC_H 1
 #include <functional>
-#include <ext/hash_map>
-
-namespace __gnu_cxx
-{
-        template<> struct hash< std::string >
-        {
-                size_t operator()( const std::string& x ) const
-                {
-                        return hash< const char* >()( x.c_str() );
-                }
-        };
-}
-
+#include <unordered_set>
+#include <unordered_map>
 #endif

From fec09937a79b142855f549ebd6da0f7175f8f0d8 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@ghic.org>
Date: Wed, 12 Oct 2016 15:05:10 -0700
Subject: [PATCH 3/4] Remove using namespace __gnu_cxx

since the maps and sets are now standard there's no need to use a gcc
specific namespace
---
 src/bed2vector.cpp | 1 -
 src/maqread.cpp    | 1 -
 src/peaks.cpp      | 1 -
 src/wdl.cpp        | 1 -
 4 files changed, 4 deletions(-)

diff --git a/src/bed2vector.cpp b/src/bed2vector.cpp
index 6ff86fe..f0e5f00 100644
--- a/src/bed2vector.cpp
+++ b/src/bed2vector.cpp
@@ -30,7 +30,6 @@ ssize_t getline_local(char **lineptr, size_t *n, FILE *stream);
 }
 
 using namespace std;
-using namespace __gnu_cxx; 
 
 
 class lessAbsoluteValue {
diff --git a/src/maqread.cpp b/src/maqread.cpp
index 5b3d6b9..999f07d 100644
--- a/src/maqread.cpp
+++ b/src/maqread.cpp
@@ -19,7 +19,6 @@ extern "C" {
 }
 
 using namespace std;
-using namespace __gnu_cxx; 
 
 
 class lessAbsoluteValue {
diff --git a/src/peaks.cpp b/src/peaks.cpp
index 37770d5..b55824f 100644
--- a/src/peaks.cpp
+++ b/src/peaks.cpp
@@ -14,7 +14,6 @@ extern "C" {
 }
 
 using namespace std;
-using namespace __gnu_cxx; 
 
 /**
  * Calculate all local peaks
diff --git a/src/wdl.cpp b/src/wdl.cpp
index 18a2258..fd4f1c1 100644
--- a/src/wdl.cpp
+++ b/src/wdl.cpp
@@ -14,7 +14,6 @@ extern "C" {
 }
 
 using namespace std;
-using namespace __gnu_cxx; 
 
 //#define DEBUG 1
 

From c2780c4ab193c385da20b2dc50d459c9b13f6ee0 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@ghic.org>
Date: Wed, 12 Oct 2016 15:09:08 -0700
Subject: [PATCH 4/4] add -std=c++11 so gcc 5 provides unordered_*

---
 src/Makevars.in | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/Makevars.in b/src/Makevars.in
index 61631ba..8f3085b 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -1,4 +1,3 @@
 PKG_LIBS=@LIBS@ -lz
-PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@  
-PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS	@HAVE_LIBBZ2@  @BOOST_CPPFLAGS@
-
+PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 @HAVE_LIBBZ2@
+PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 @HAVE_LIBBZ2@  @BOOST_CPPFLAGS@