From 7f530324f4d6e26a8a471791c5ff62b33dc8df44 Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Mon, 26 Feb 2018 23:31:04 +0000
Subject: [PATCH 1/7] running single end as a separated function

---
 src/Makefile.in |  3 ++
 src/main.cpp    | 82 ++++++++++++++++++++++++++++++++-----------------
 src/reads.cpp   |  5 +++
 src/reads.h     |  9 ++++++
 4 files changed, 70 insertions(+), 29 deletions(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index dd4910f..89e40ee 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -38,6 +38,9 @@ test: all
 	./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -trim_qual_right=25 -out_name Test_2 && \
     ./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -min_qual_mean 25 -ns_max_n 2 -out_name Test_3 && \
 	echo "*** ALL TEST PASSED***"
+	
+test_single: all
+	./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single
 
 install:
 	install -d $(DESTDIR)$(bindir)/bin
diff --git a/src/main.cpp b/src/main.cpp
index 476e68c..3500bd7 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -20,8 +20,13 @@
 #include "reads.h"
 using namespace std;
 
-int main (int argc, char **argv)
-{
+#ifndef PTHREAD
+#define PTHREAD
+#include <pthread.h>
+#endif
+
+
+
     char *forward_read_file = NULL;
     char *reverse_read_file = NULL;
     string out_ext="fastq";
@@ -36,7 +41,7 @@ int main (int argc, char **argv)
     int max_len=0;
     float max_gc=100;
     float min_gc=0;
-    opterr = 0;
+    int opterr = 0;
     int derep;
     float entropy_threshold=0.5 ;
     int lc_entropy=0;
@@ -55,6 +60,7 @@ int main (int argc, char **argv)
     int rm_header=0;
     int trim_tail_left=0;
     int trim_tail_right=0;
+    int threads=5;
 
     struct option longopts[] = {
         { "fastq"           , required_argument , NULL     ,  1 },
@@ -83,8 +89,16 @@ int main (int argc, char **argv)
         { "trim_tail_right" , required_argument , NULL     , 21 },
 {0,0,0,0}
     };    
+    
+struct arg_struct {
+    single_read * read;
+    bloom_filter * filter;
+};
 
+void do_single (arg_struct * arguments);
 
+int main (int argc, char **argv)
+{
 
     // Readin inout from the command line
     while ((c = getopt_long_only(argc, argv, "",longopts, NULL)) != -1)
@@ -225,7 +239,8 @@ int main (int argc, char **argv)
         bad_out_file_R1.open(out_name  + "_bad_out." + out_ext );
         good_out_file_R1.open(out_name  + "_good_out." + out_ext);
     }
-
+    
+    
     single_read read_f(inFile_f);
     single_read read_r(inFile_r);
     pair_read read_rf(inFile_f,inFile_r);
@@ -249,7 +264,10 @@ int main (int argc, char **argv)
         parameters.compute_optimal_parameters();
         filter  = new bloom_filter(parameters);
     }
-    
+    // declare structure for the thread
+    arg_struct ttt;
+    ttt.read= & read_f;
+    ttt.filter= filter;
     // main loop
     if (reverse_read_file) {
         ////////////////////////////////////////for pair end
@@ -280,30 +298,7 @@ int main (int argc, char **argv)
         } 
     /////////////////////////////////////////// for single end    
     } else {
-        while(read_f.read_read()) {
-            if (trim_tail_left) {read_f.trim_tail_left(trim_tail_left);}
-            if (trim_tail_right) {read_rf.trim_tail_right(trim_tail_right);}
-            if (trim_qual_right) {read_f.trim_qual_right("mean","lt",trim_qual_step,trim_qual_window,trim_qual_right_threshold);}
-            if (trim_qual_left) {read_f.trim_qual_left("mean","lt",trim_qual_step,trim_qual_window,trim_qual_left_threshold);}
-            if (ns_max_n > -1 ) {read_f.ns_max_n(ns_max_n);}
-            if (min_qual_mean)  {read_f.min_qual_mean(min_qual_mean);}
-            if (min_qual_score) { read_f.min_qual_score(min_qual_score);}
-            if (noiupac) {read_f.noiupac();}
-            if (min_len) {read_f.min_len(min_len);}
-            if (max_len) {read_f.max_len(max_len);}
-            if (max_gc < 100) {read_f.max_gc(max_gc);}
-            if (min_gc > 0) {read_f.min_gc(min_gc);}
-            if (derep) {
-                if(filter->contains(read_f.seq_seq)) { read_f.set_read_status(2);}
-                filter->insert(read_f.seq_seq);
-                
-            }
-        
-            if (lc_entropy) {read_f.entropy(entropy_threshold);}
-            if (lc_dust) {read_f.dust(dust_threshold);}
-            if (rm_header) {read_f.rm_header();}
-            read_f.print(out_format);
-        }
+        do_single(& ttt);
     }
     
     inFile_f.close();
@@ -315,4 +310,33 @@ int main (int argc, char **argv)
 }
 
 
+void do_single (arg_struct * arguments) {
+    struct arg_struct *args = arguments;
+    single_read * read=args->read;
+    bloom_filter* filter=args->filter;
+    while( read->read_read()) {
+        if (trim_tail_left) {read->trim_tail_left(trim_tail_left);}
+        if (trim_tail_right) {read->trim_tail_right(trim_tail_right);}
+        if (trim_qual_right) {read->trim_qual_right("mean","lt",trim_qual_step,trim_qual_window,trim_qual_right_threshold);}
+        if (trim_qual_left) {read->trim_qual_left("mean","lt",trim_qual_step,trim_qual_window,trim_qual_left_threshold);}
+        if (ns_max_n > -1 ) {read->ns_max_n(ns_max_n);}
+        if (min_qual_mean)  {read->min_qual_mean(min_qual_mean);}
+        if (min_qual_score) {read->min_qual_score(min_qual_score);}
+        if (noiupac) {read->noiupac();}
+        if (min_len) {read->min_len(min_len);}
+        if (max_len) {read->max_len(max_len);}
+        if (max_gc < 100) {read->max_gc(max_gc);}
+        if (min_gc > 0) {read->min_gc(min_gc);}
+        if (derep) {
+            if(filter->contains(read->seq_seq)) { read->set_read_status(2);}
+            filter->insert(read->seq_seq);
+            
+        }
+    
+        if (lc_entropy) {read->entropy(entropy_threshold);}
+        if (lc_dust) {read->dust(dust_threshold);}
+        if (rm_header) {read->rm_header();}
+        read->print(out_format);
+    }
+}
 
diff --git a/src/reads.cpp b/src/reads.cpp
index 6db96d9..40ca4f0 100644
--- a/src/reads.cpp
+++ b/src/reads.cpp
@@ -13,6 +13,11 @@
 #include <math.h>
 #endif
 
+#ifndef PTHREAD
+#define PTHREAD
+#include <pthread.h>
+#endif
+
 #include "reads.h"
 #include <unordered_map>
 #include <algorithm> 
diff --git a/src/reads.h b/src/reads.h
index 4d8b158..312e864 100644
--- a/src/reads.h
+++ b/src/reads.h
@@ -13,12 +13,19 @@
 #include <math.h>
 #endif
 
+#ifndef PTHREAD
+#define PTHREAD
+#include <pthread.h>
+#endif
+
 using namespace std;
 
 
 class single_read {
     public:
         single_read(istream &is);
+        single_read(void);
+        void set_inputs(istream &is);
         void set_outputs(ostream& bad_out_file, ostream& single_out_file, ostream& good_out_file);
         int read_read(void);
         void ns_max_n(int ns_max_n);
@@ -100,3 +107,5 @@ class pair_read {
 };                    
 
 string random_string( size_t length );
+
+

From 348cdf44d2dcd3c16b13a6e06eedf24187f56b67 Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Tue, 27 Feb 2018 03:44:41 +0000
Subject: [PATCH 2/7] added p_thread support

---
 src/Makefile.in |   3 +-
 src/README      |   2 +
 src/main.cpp    | 129 +++++++++++++++++++++++++++++++++++-------------
 src/reads.cpp   |  33 +++++++++++--
 src/reads.h     |   6 ++-
 5 files changed, 132 insertions(+), 41 deletions(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index 89e40ee..f827655 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -12,7 +12,7 @@ bindir = @bindir@
 srcdir = @srcdir@
 VPATH = @srcdir@
 
-CXXFLAGS = -std=c++11 -Wall -O3
+CXXFLAGS = -std=c++11 -Wall -O3 -pthread
 
 
 all: pprinseqc
@@ -41,6 +41,7 @@ test: all
 	
 test_single: all
 	./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single
+	
 
 install:
 	install -d $(DESTDIR)$(bindir)/bin
diff --git a/src/README b/src/README
index 0418fc1..89c9b08 100644
--- a/src/README
+++ b/src/README
@@ -6,6 +6,8 @@ CXXFLAGS = -std=c++11 -O2 -Wall
 CXXFLAGS = -std=c++11 -Wall
 CXXFLAGS = -std=c++11 -Wall -fno-omit-frame-pointer -ggdb
 
+CXXFLAGS = -std=c++11 -Wall -pthread
+
 sudo sh -c " echo 0 > /proc/sys/kernel/kptr_restrict"
 
 sudo perf record -g ./pprinseqc -fastq stenotrophomonas_R1.fastq -fastq2 stenotrophomonas_R2.fastq -min_len 5000 -ns_max_n 2
diff --git a/src/main.cpp b/src/main.cpp
index 3500bd7..ca51809 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -26,6 +26,9 @@ using namespace std;
 #endif
 
 
+pthread_mutex_t write_mutex=PTHREAD_MUTEX_INITIALIZER;
+pthread_mutex_t read_mutex=PTHREAD_MUTEX_INITIALIZER;
+pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
 
     char *forward_read_file = NULL;
     char *reverse_read_file = NULL;
@@ -61,6 +64,7 @@ using namespace std;
     int trim_tail_left=0;
     int trim_tail_right=0;
     int threads=5;
+    int ii=0;
 
     struct option longopts[] = {
         { "fastq"           , required_argument , NULL     ,  1 },
@@ -95,7 +99,13 @@ struct arg_struct {
     bloom_filter * filter;
 };
 
-void do_single (arg_struct * arguments);
+struct arg_struct_pair {
+    pair_read * read;
+    bloom_filter * filter;
+};
+
+void* do_single (void * arguments);
+void* do_pair (void* arguments);
 
 int main (int argc, char **argv)
 {
@@ -240,7 +250,7 @@ int main (int argc, char **argv)
         good_out_file_R1.open(out_name  + "_good_out." + out_ext);
     }
     
-    
+
     single_read read_f(inFile_f);
     single_read read_r(inFile_r);
     pair_read read_rf(inFile_f,inFile_r);
@@ -264,42 +274,54 @@ int main (int argc, char **argv)
         parameters.compute_optimal_parameters();
         filter  = new bloom_filter(parameters);
     }
-    // declare structure for the thread
-    arg_struct ttt;
-    ttt.read= & read_f;
-    ttt.filter= filter;
+ 
+ 
+    
+ 
+ 
+ 
     // main loop
     if (reverse_read_file) {
         ////////////////////////////////////////for pair end
-        while(read_rf.read_read()) {
-        //read_rf.read1->trim_qual_right("mean","lt",5,10,30);
-            if (trim_tail_left) {read_rf.trim_tail_left(trim_tail_left);}
-            if (trim_tail_right) {read_rf.trim_tail_right(trim_tail_right);}
-            if (trim_qual_right) {read_rf.trim_qual_right("mean","lt",trim_qual_step,trim_qual_window,trim_qual_right_threshold);}
-            if (trim_qual_left) {read_rf.trim_qual_left("mean","lt",trim_qual_step,trim_qual_window,trim_qual_left_threshold);}
-            if (ns_max_n > -1 ) {read_rf.ns_max_n(ns_max_n);}
-            if (min_qual_mean)  {read_rf.min_qual_mean(min_qual_mean);}
-            if (min_qual_score) { read_rf.min_qual_score(min_qual_score);}
-            if (noiupac) {read_rf.noiupac();}
-            if (min_len) {read_rf.min_len(min_len);}
-            if (max_len) {read_rf.max_len(max_len);}
-            if (max_gc < 100) {read_rf.max_gc(max_gc);}
-            if (min_gc > 0) {read_rf.min_gc(min_gc);}
-            if (derep) {
-                read_rf.set_read_status(filter->contains(read_rf.read1->seq_seq),filter->contains(read_rf.read2->seq_seq));
-                filter->insert(read_rf.read1->seq_seq);
-                filter->insert(read_rf.read2->seq_seq);
-            }
+        vector<pair_read> v2(threads);
+        vector<pthread_t> tthreads(threads);
+        vector<arg_struct_pair> ttt2(threads);
+        for (ii=0 ; ii<threads ; ii++){
+       // v[ii].set_inputs(inFile_f);
+            v2[ii].set_inputs(inFile_f,inFile_r);
+            v2[ii].set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1,bad_out_file_R2,single_out_file_R2,good_out_file_R2);
+            v2[ii].set_out_format(out_format);
+            ttt2[ii].read= & v2[ii];
+            ttt2[ii].filter= filter;
+            pthread_create(&tthreads[ii],NULL,do_pair, (void *) &ttt2[ii]); 
+        }
         
-            if (lc_entropy) {read_rf.entropy(entropy_threshold);}
-            if (lc_dust) {read_rf.dust(dust_threshold);}
-            if (rm_header) {read_rf.rm_header();}
-            read_rf.print();
-        } 
+        for (ii=0 ; ii<threads ; ii++){
+            pthread_join(tthreads[ii],NULL);   
+        }
+       
     /////////////////////////////////////////// for single end    
     } else {
-        do_single(& ttt);
-    }
+             //////////// pthreads magic
+        vector<single_read> v(threads,inFile_f);
+        vector<pthread_t> tthreads(threads);
+        vector<arg_struct> ttt(threads);
+       // declare structure for the thread
+        
+    
+    
+        for (ii=0 ; ii<threads ; ii++){
+       // v[ii].set_inputs(inFile_f);
+            v[ii].set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1);
+            ttt[ii].read= & v[ii];
+            ttt[ii].filter= filter;
+            pthread_create(&tthreads[ii],NULL,do_single, (void *) &ttt[ii]); 
+        }
+    
+        for (ii=0 ; ii<threads ; ii++){
+            pthread_join(tthreads[ii],NULL);   
+        }
+    } 
     
     inFile_f.close();
     if (reverse_read_file){ 
@@ -310,11 +332,11 @@ int main (int argc, char **argv)
 }
 
 
-void do_single (arg_struct * arguments) {
-    struct arg_struct *args = arguments;
+void* do_single (void * arguments) {
+    struct arg_struct *args = (arg_struct*) arguments;
     single_read * read=args->read;
     bloom_filter* filter=args->filter;
-    while( read->read_read()) {
+    while( read->read_read( &read_mutex)) {
         if (trim_tail_left) {read->trim_tail_left(trim_tail_left);}
         if (trim_tail_right) {read->trim_tail_right(trim_tail_right);}
         if (trim_qual_right) {read->trim_qual_right("mean","lt",trim_qual_step,trim_qual_window,trim_qual_right_threshold);}
@@ -336,7 +358,44 @@ void do_single (arg_struct * arguments) {
         if (lc_entropy) {read->entropy(entropy_threshold);}
         if (lc_dust) {read->dust(dust_threshold);}
         if (rm_header) {read->rm_header();}
+        pthread_mutex_lock(& write_mutex);
         read->print(out_format);
+        pthread_mutex_unlock(& write_mutex);
     }
+    pthread_exit(NULL);
+    
 }
 
+void* do_pair (void * arguments) {
+    struct arg_struct_pair *args = (arg_struct_pair*) arguments;
+    pair_read * read=args->read;
+    bloom_filter* filter=args->filter;
+    while(read->read_read(&read_mutex, &read_mutex2)) {
+        //read_rf.read1->trim_qual_right("mean","lt",5,10,30);
+            if (trim_tail_left) {read->trim_tail_left(trim_tail_left);}
+            if (trim_tail_right) {read->trim_tail_right(trim_tail_right);}
+            if (trim_qual_right) {read->trim_qual_right("mean","lt",trim_qual_step,trim_qual_window,trim_qual_right_threshold);}
+            if (trim_qual_left) {read->trim_qual_left("mean","lt",trim_qual_step,trim_qual_window,trim_qual_left_threshold);}
+            if (ns_max_n > -1 ) {read->ns_max_n(ns_max_n);}
+            if (min_qual_mean)  {read->min_qual_mean(min_qual_mean);}
+            if (min_qual_score) { read->min_qual_score(min_qual_score);}
+            if (noiupac) {read->noiupac();}
+            if (min_len) {read->min_len(min_len);}
+            if (max_len) {read->max_len(max_len);}
+            if (max_gc < 100) {read->max_gc(max_gc);}
+            if (min_gc > 0) {read->min_gc(min_gc);}
+            if (derep) {
+                read->set_read_status(filter->contains(read->read1->seq_seq),filter->contains(read->read2->seq_seq));
+                filter->insert(read->read1->seq_seq);
+                filter->insert(read->read2->seq_seq);
+            }
+        
+            if (lc_entropy) {read->entropy(entropy_threshold);}
+            if (lc_dust) {read->dust(dust_threshold);}
+            if (rm_header) {read->rm_header();}
+            pthread_mutex_lock(& write_mutex);
+            read->print();
+            pthread_mutex_unlock(& write_mutex);
+        } 
+    pthread_exit(NULL);
+}    
\ No newline at end of file
diff --git a/src/reads.cpp b/src/reads.cpp
index 40ca4f0..e22206a 100644
--- a/src/reads.cpp
+++ b/src/reads.cpp
@@ -27,6 +27,14 @@ using namespace std;
         single_read::single_read(istream &is): file1(is)  { 
             fastq_to_fasta.assign("^@");
         }
+        
+        single_read::single_read(void) : file1(cin){ // starndar input
+            fastq_to_fasta.assign("^@");
+        }
+        
+        void  single_read::set_inputs(istream &is) {
+            file1.rdbuf(is.rdbuf());
+        }
 
         void single_read::set_outputs(ostream& bad_out_file, ostream& single_out_file, ostream& good_out_file) {
             bad_out=bad_out_file.rdbuf();
@@ -34,14 +42,17 @@ using namespace std;
             good_out=good_out_file.rdbuf();
         }
 
-        int single_read::read_read(void) {
+        int single_read::read_read(pthread_mutex_t * read_mutex) {
         read_status=0;
+        pthread_mutex_lock(read_mutex);
             if (getline(file1,seq_name, '\n')) {
                 getline(file1, seq_seq, '\n');
                 getline(file1, seq_sep, '\n');
                 getline(file1, seq_qual, '\n');
+                pthread_mutex_unlock(read_mutex);
                 return 1;
             } else {
+                pthread_mutex_unlock(read_mutex);
                 return 0;
             }
         }
@@ -378,14 +389,30 @@ void single_read::trim_tail_right(int num) {
 
 //////////////////////////////////////////////////////////////////////////////
 
+
+
+/////////////////////////////////////////////////////////////////////////////
+
         pair_read::pair_read(istream &is1, istream &is2): file1(is1),file2(is2)  {
 
         read1= new single_read(file1);
         read2= new single_read(file2);
     }
+    
+    pair_read::pair_read(void):file1(cin),file2(cin) {
+        read1= new single_read(file1);
+        read2= new single_read(file2);
+    }    
+    
+    void  pair_read::set_inputs(istream &read_f,istream &read_r) {
+   //     read1->file1.rdbuf(read_f.rdbuf());
+    //    read2->file1.rdbuf(read_r.rdbuf());
+        read1->set_inputs(read_f);
+        read2->set_inputs(read_r);
+    }    
 
-    int pair_read::read_read(void) {
-        return read1->read_read() * read2->read_read();
+    int pair_read::read_read(pthread_mutex_t* read_mutex_1, pthread_mutex_t* read_mutex_2) {
+        return read1->read_read(read_mutex_1) * read2->read_read(read_mutex_2);
     }
 
 
diff --git a/src/reads.h b/src/reads.h
index 312e864..4cf61b0 100644
--- a/src/reads.h
+++ b/src/reads.h
@@ -27,7 +27,7 @@ class single_read {
         single_read(void);
         void set_inputs(istream &is);
         void set_outputs(ostream& bad_out_file, ostream& single_out_file, ostream& good_out_file);
-        int read_read(void);
+        int read_read(pthread_mutex_t * read_mutex);
         void ns_max_n(int ns_max_n);
       //  int max_n_p(int ns_max_p);
         void print(int out_form);
@@ -68,7 +68,9 @@ class single_read {
 class pair_read {
     public:
         pair_read(istream &is1, istream &is2);
-        int read_read(void);
+        pair_read(void);
+        void set_inputs(istream &read_f,istream &read_r);
+        int read_read(pthread_mutex_t* read_mutex_1, pthread_mutex_t* read_mutex_2);
         void print(void);
         void set_outputs(ostream& bad_out_file1, ostream& single_out_file1, ostream& good_out_file1,
                     ostream& bad_out_file2, ostream& single_out_file2, ostream& good_out_file2);

From 47d49f0543e6d3a8b9c951c293ff190a13513cd8 Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Tue, 27 Feb 2018 03:57:02 +0000
Subject: [PATCH 3/7] change comp code to test multicore

---
 src/Makefile.in | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index f827655..b5cc61a 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -24,8 +24,8 @@ comp: pprinseqc
 
 
 compp: pprinseqc
-	time ./prinseq-lite.pl -fastq test_F.fastq -fastq2 test_R.fastq -min_len 5 -out_good Test_good -out_bad Test_bad -no_qual_header -ns_max_n 2
-	time ./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -min_len 5 -ns_max_n 2
+	time -v ./prinseq-lite.pl -fastq stenotrophomonas_R1.fastq -fastq2 stenotrophomonas_R2.fastq -min_len 5 -out_good Test_good -out_bad Test_bad -no_qual_header -ns_max_n 2 
+	time -v ./pprinseqc -fastq stenotrophomonas_R1.fastq -fastq2 stenotrophomonas_R2.fastq -min_len 5 -ns_max_n 2 -out_name Test_time_ 
 
 pprinseqc: main.o reads.o
 	$(CXX) $(CXXFLAGS) -o pprinseqc main.o reads.o

From 10e3745eddffa8acc74407b5ff0aa11a12c80cb5 Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Thu, 1 Mar 2018 00:14:32 +0000
Subject: [PATCH 4/7] added support to read gz files

---
 README.md           |   1 +
 src/Makefile.in     |   5 ++-
 src/main.cpp        |  93 +++++++++++++++++++++++++++++++-------------
 src/test_F.fastq.gz | Bin 0 -> 151 bytes
 src/test_R.fastq.gz | Bin 0 -> 177 bytes
 5 files changed, 71 insertions(+), 28 deletions(-)
 create mode 100644 src/test_F.fastq.gz
 create mode 100644 src/test_R.fastq.gz

diff --git a/README.md b/README.md
index 7556401..0f9d266 100644
--- a/README.md
+++ b/README.md
@@ -11,4 +11,5 @@ parallel c prinseq
 1. automake
 2. g++
 3. make
+4. boost-devel
 
diff --git a/src/Makefile.in b/src/Makefile.in
index b5cc61a..09f1ba8 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -12,7 +12,7 @@ bindir = @bindir@
 srcdir = @srcdir@
 VPATH = @srcdir@
 
-CXXFLAGS = -std=c++11 -Wall -O3 -pthread
+CXXFLAGS = -std=c++11 -Wall -O3 -pthread -lboost_filesystem -lboost_system  -lboost_iostreams -lz
 
 
 all: pprinseqc
@@ -37,6 +37,9 @@ test: all
 	./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -out_format 1 -out_name Test_1 && \
 	./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -trim_qual_right=25 -out_name Test_2 && \
     ./pprinseqc -fastq test_F.fastq -fastq2 test_R.fastq -min_qual_mean 25 -ns_max_n 2 -out_name Test_3 && \
+    ./pprinseqc -fastq test_F.fastq.gz -fastq2 test_R.fastq.gz -out_format 1 -out_name Test_1Z && \
+	./pprinseqc -fastq test_F.fastq.gz -fastq2 test_R.fastq.gz -trim_qual_right=25 -out_name Test_2Z && \
+    ./pprinseqc -fastq test_F.fastq.gz -fastq2 test_R.fastq.gz -min_qual_mean 25 -ns_max_n 2 -out_name Test_3Z && \
 	echo "*** ALL TEST PASSED***"
 	
 test_single: all
diff --git a/src/main.cpp b/src/main.cpp
index ca51809..22e6238 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -25,6 +25,11 @@ using namespace std;
 #include <pthread.h>
 #endif
 
+#include <boost/iostreams/filtering_streambuf.hpp>
+#include <boost/iostreams/copy.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/filesystem.hpp>
+
 
 pthread_mutex_t write_mutex=PTHREAD_MUTEX_INITIALIZER;
 pthread_mutex_t read_mutex=PTHREAD_MUTEX_INITIALIZER;
@@ -32,8 +37,9 @@ pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
 
     char *forward_read_file = NULL;
     char *reverse_read_file = NULL;
+    boost::filesystem::path p1,p2;
     string out_ext="fastq";
-    int index;
+    int ii;
     int out_format=0; // 0 fastq, 1 fasta
     int min_qual_score=0;
     int ns_max_n=-1;
@@ -64,7 +70,8 @@ pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
     int trim_tail_left=0;
     int trim_tail_right=0;
     int threads=5;
-    int ii=0;
+
+    std::string line;
 
     struct option longopts[] = {
         { "fastq"           , required_argument , NULL     ,  1 },
@@ -115,9 +122,11 @@ int main (int argc, char **argv)
         switch (c) {
             case 1:
                 forward_read_file = optarg;
+                p1 = optarg;
                 break;
             case 2:
                 reverse_read_file = optarg;
+                p2=optarg;
                 break;
             case 3:
                 out_format = atoi(optarg);
@@ -202,31 +211,63 @@ int main (int argc, char **argv)
             default:
                 abort ();
         }
-
-    printf ("forward_read_file = %s ,reverse_read_file =%s\n ", forward_read_file, reverse_read_file);
+    
+/*    printf ("forward_read_file = %s ,reverse_read_file =%s\n ", forward_read_file, reverse_read_file);
     cout << "random string " << out_name << " out format " << out_format  << endl ;
     cout << "ns_max_n " << ns_max_n << endl ;
-    for (index = optind; index < argc; index++)
-        printf ("Non-option argument %s\n", argv[index]);
-
+    cout  <<  "  extension()----------: " << p1.extension() << '\n';
+    for (ii = optind; ii < argc; ii++)
+        printf ("Non-option argument %s\n", argv[ii]);
+*/
 
 
 /////////// open input files
-    ifstream inFile_f;
-    ifstream inFile_r;
-    inFile_f.open(forward_read_file);
-    if (!inFile_f) {
+
+    istream * inFile_r;
+    istream * inFile_f;
+    ifstream *file;
+    ifstream *file2;
+    boost::iostreams::filtering_streambuf<boost::iostreams::input> inbuf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::input> inbuf2;
+    
+
+    file = new ifstream(p1.native() , std::ios_base::in | std::ios_base::binary);
+    file2 = new ifstream(p2.native() , std::ios_base::in | std::ios_base::binary);
+    
+    if (!(*file)) {
         cerr << "Error: can not open " << forward_read_file  << endl ;
         return 1;
     }
     if (reverse_read_file) {
-        inFile_r.open(reverse_read_file);
-        if (!inFile_r) {
+        if (!(*file2)) {
             cerr << "Error: can not open " << reverse_read_file  << endl ;
             return 1;
         }
+    } 
+ 
+    
+    
+    if (p1.extension()==".gz") {
+        inbuf.push(boost::iostreams::gzip_decompressor());
     }    
-      
+    
+    
+    if (p2.extension()==".gz") {
+        inbuf2.push(boost::iostreams::gzip_decompressor());      
+    } 
+        
+
+    inbuf.push(*file);
+    inFile_f = new std::istream(&inbuf);
+    inbuf2.push(*file2);
+    inFile_r = new std::istream(&inbuf2);
+    
+ 
+
+//    while(std::getline(*inFile_f, line)) {
+//        std::cout << line << std::endl;
+//    }
+//    std::cout << "bla" << line << "bla" << std::endl;
 ////////// open and name oupput files
     ofstream bad_out_file_R1;
     ofstream single_out_file_R1;
@@ -251,9 +292,10 @@ int main (int argc, char **argv)
     }
     
 
-    single_read read_f(inFile_f);
-    single_read read_r(inFile_r);
-    pair_read read_rf(inFile_f,inFile_r);
+    single_read read_f(*inFile_f);
+    single_read read_r(*inFile_r);
+    pair_read read_rf(*inFile_f,*inFile_r);
+    
     if (reverse_read_file) {
         read_rf.set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1,
             bad_out_file_R2,single_out_file_R2,good_out_file_R2);
@@ -275,10 +317,7 @@ int main (int argc, char **argv)
         filter  = new bloom_filter(parameters);
     }
  
- 
-    
- 
- 
+
  
     // main loop
     if (reverse_read_file) {
@@ -288,14 +327,13 @@ int main (int argc, char **argv)
         vector<arg_struct_pair> ttt2(threads);
         for (ii=0 ; ii<threads ; ii++){
        // v[ii].set_inputs(inFile_f);
-            v2[ii].set_inputs(inFile_f,inFile_r);
+            v2[ii].set_inputs(*inFile_f,*inFile_r);
             v2[ii].set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1,bad_out_file_R2,single_out_file_R2,good_out_file_R2);
             v2[ii].set_out_format(out_format);
             ttt2[ii].read= & v2[ii];
             ttt2[ii].filter= filter;
             pthread_create(&tthreads[ii],NULL,do_pair, (void *) &ttt2[ii]); 
         }
-        
         for (ii=0 ; ii<threads ; ii++){
             pthread_join(tthreads[ii],NULL);   
         }
@@ -303,7 +341,7 @@ int main (int argc, char **argv)
     /////////////////////////////////////////// for single end    
     } else {
              //////////// pthreads magic
-        vector<single_read> v(threads,inFile_f);
+        vector<single_read> v(threads,*inFile_f);
         vector<pthread_t> tthreads(threads);
         vector<arg_struct> ttt(threads);
        // declare structure for the thread
@@ -322,12 +360,13 @@ int main (int argc, char **argv)
             pthread_join(tthreads[ii],NULL);   
         }
     } 
-    
-    inFile_f.close();
+
+//    inFile_f->close();
     if (reverse_read_file){ 
-        inFile_r.close(); 
+//        inFile_r->close(); 
         
     }  
+
     return 0;
 }
 
diff --git a/src/test_F.fastq.gz b/src/test_F.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..eae7df075b9bdadf73e4a4f7450a90c46c3b8bcc
GIT binary patch
literal 151
zcmV;I0BHXoiwFqI31M0Q19W9`bYDg;W?^%5aR75DPAxR#az+JQ+F(&fCud~D<p2~l
z;&OI(3~}}YVz4SBE>wAAu8<JF5Fh}{8pCA4awZVHjxfC@XnIY#+(Sb`9Gyc#+#O-A
zFhy|%M4cH{_nKjKuQ`_^6+j4W0oeWKXznMLXGu>04pWOE6Q&mEDP=GME&#*$dANiF
F003w?I8y)s

literal 0
HcmV?d00001

diff --git a/src/test_R.fastq.gz b/src/test_R.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..dab1b1ea62f54bf8d7c05f209fc4f900d24ad5ef
GIT binary patch
literal 177
zcmV;i08alOiwFn<EMZyz19W9`bYD^~W?^%5aR9wgyAFde4BYQah&u768?Fa$ncNTP
zzy~1yUurNy!fh9%&`UDJcPHC7F4J6sJ#e!sJ@|MrrfLNiQjY1Fs)FZh=mul!oi(lj
zM>EIOu6k59u3Hh-6GCCW7V=c3<Ph4YYn^`U-QmX?-NzcH>_O)tX$A+q7B+s5dmgwD
fDDTfQ9nNPeudmWSG97YddL{4%uey(+ngaj;Az)4$

literal 0
HcmV?d00001


From f0093f8303d99813be263b9dd9d349ac54b33783 Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Sat, 3 Mar 2018 19:43:15 +0000
Subject: [PATCH 5/7] added gzip write support

---
 src/Makefile.in |  4 ++-
 src/main.cpp    | 90 +++++++++++++++++++++++++++++++++++++------------
 2 files changed, 72 insertions(+), 22 deletions(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index 09f1ba8..6e80a84 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -43,7 +43,7 @@ test: all
 	echo "*** ALL TEST PASSED***"
 	
 test_single: all
-	./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single
+	./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single -out_gz
 	
 
 install:
@@ -59,6 +59,8 @@ clean:
 	-rm -f pprinseqc
 	-rm -f Test*fastq
 	-rm -f Test*fasta
+	-rm -f Test*fastq.gz
+	-rm -f Test*fasta.gz
 	-rm -f *.o
 	
 cc:
diff --git a/src/main.cpp b/src/main.cpp
index 22e6238..30f03a2 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -70,6 +70,7 @@ pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
     int trim_tail_left=0;
     int trim_tail_right=0;
     int threads=5;
+    int out_gz=0;
 
     std::string line;
 
@@ -98,6 +99,7 @@ pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
         { "rm_header"       , no_argument       , &rm_header, 1 },
         { "trim_tail_left"  , required_argument , NULL     , 20 },
         { "trim_tail_right" , required_argument , NULL     , 21 },
+        { "out_gz"          , no_argument       , &out_gz  ,  1 },
 {0,0,0,0}
     };    
     
@@ -269,26 +271,72 @@ int main (int argc, char **argv)
 //    }
 //    std::cout << "bla" << line << "bla" << std::endl;
 ////////// open and name oupput files
-    ofstream bad_out_file_R1;
-    ofstream single_out_file_R1;
-    ofstream good_out_file_R1;
-    ofstream bad_out_file_R2;
-    ofstream single_out_file_R2;
-    ofstream good_out_file_R2;
-
-    if (out_format == 1 ) { out_ext = "fasta";}
+    ofstream *tmp_bad_out_file_R1;
+    ofstream *tmp_single_out_file_R1;
+    ofstream *tmp_good_out_file_R1;
+    ofstream *tmp_bad_out_file_R2;
+    ofstream *tmp_single_out_file_R2;
+    ofstream *tmp_good_out_file_R2;
+    
+    ostream *bad_out_file_R1= NULL;
+    ostream *single_out_file_R1= NULL;
+    ostream *good_out_file_R1= NULL;
+    ostream *bad_out_file_R2= NULL;
+    ostream *single_out_file_R2= NULL;
+    ostream *good_out_file_R2= NULL;
     
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_bad_R1_buf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_bad_R2_buf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_single_R1_buf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_single_R2_buf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_good_R1_buf;
+    boost::iostreams::filtering_streambuf<boost::iostreams::output> out_good_R2_buf;
+    
+    if (out_format == 1 ) { out_ext = "fasta";}
+    if (out_gz == 1 ) { out_ext = out_ext + ".gz"; }
     
     if (reverse_read_file) {
-        bad_out_file_R1.open(out_name  + "_bad_out_R1." + out_ext );
-        single_out_file_R1.open(out_name  + "_single_out_R1." + out_ext  );
-        good_out_file_R1.open(out_name  + "_good_out_R1." + out_ext);
-        bad_out_file_R2.open(out_name  + "_bad_out_R2." + out_ext );
-        single_out_file_R2.open(out_name  + "_single_out_R2." + out_ext);
-        good_out_file_R2.open(out_name + "_good_out_R2."  + out_ext);
+        tmp_bad_out_file_R1= new std::ofstream(out_name  + "_bad_out_R1." + out_ext );
+        tmp_single_out_file_R1= new std::ofstream(out_name  + "_single_out_R1." + out_ext  );
+        tmp_good_out_file_R1= new std::ofstream(out_name  + "_good_out_R1." + out_ext);
+        tmp_bad_out_file_R2= new std::ofstream(out_name  + "_bad_out_R2." + out_ext );
+        tmp_single_out_file_R2= new std::ofstream(out_name  + "_single_out_R2." + out_ext);
+        tmp_good_out_file_R2= new std::ofstream(out_name + "_good_out_R2."  + out_ext);
+        if (out_gz) {
+            out_bad_R1_buf.push(boost::iostreams::gzip_compressor());
+            out_bad_R2_buf.push(boost::iostreams::gzip_compressor());
+            out_single_R1_buf.push(boost::iostreams::gzip_compressor());
+            out_single_R2_buf.push(boost::iostreams::gzip_compressor());
+            out_good_R1_buf.push(boost::iostreams::gzip_compressor());
+            out_good_R2_buf.push(boost::iostreams::gzip_compressor());
+        }
+        out_bad_R1_buf.push(*tmp_bad_out_file_R1);
+        out_bad_R2_buf.push(*tmp_bad_out_file_R2);
+        out_single_R1_buf.push(*tmp_single_out_file_R1);
+        out_single_R2_buf.push(*tmp_single_out_file_R2);
+        out_good_R1_buf.push(*tmp_good_out_file_R1);
+        out_good_R2_buf.push(*tmp_good_out_file_R2);
+        
+        bad_out_file_R1= new std::ostream(&out_bad_R1_buf);
+        bad_out_file_R2= new std::ostream(&out_bad_R2_buf);
+        single_out_file_R1= new std::ostream(&out_single_R1_buf);
+        single_out_file_R2= new std::ostream(&out_single_R2_buf);
+        good_out_file_R1= new std::ostream(&out_good_R1_buf);
+        good_out_file_R2= new std::ostream(&out_good_R2_buf);
+        
+        
     } else {
-        bad_out_file_R1.open(out_name  + "_bad_out." + out_ext );
-        good_out_file_R1.open(out_name  + "_good_out." + out_ext);
+        tmp_good_out_file_R1= new std::ofstream(out_name  + "_good_out." + out_ext);
+        tmp_bad_out_file_R1= new std::ofstream(out_name  + "_bad_out." + out_ext);
+        if (out_gz) {
+            out_good_R1_buf.push(boost::iostreams::gzip_compressor());
+            out_bad_R1_buf.push(boost::iostreams::gzip_compressor());
+        }
+        out_good_R1_buf.push(*tmp_good_out_file_R1);
+        out_bad_R1_buf.push(*tmp_bad_out_file_R1);
+        
+        good_out_file_R1= new std::ostream(&out_good_R1_buf);
+        bad_out_file_R1= new std::ostream(&out_bad_R1_buf);
     }
     
 
@@ -297,11 +345,11 @@ int main (int argc, char **argv)
     pair_read read_rf(*inFile_f,*inFile_r);
     
     if (reverse_read_file) {
-        read_rf.set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1,
-            bad_out_file_R2,single_out_file_R2,good_out_file_R2);
+        read_rf.set_outputs(*bad_out_file_R1,*single_out_file_R1,*good_out_file_R1,
+            *bad_out_file_R2,*single_out_file_R2,*good_out_file_R2);
         read_rf.set_out_format(out_format);
     } else {
-        read_f.set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1);
+        read_f.set_outputs(*bad_out_file_R1,*bad_out_file_R1,*good_out_file_R1);
     }
     bloom_parameters parameters;
     bloom_filter *filter=NULL;
@@ -328,7 +376,7 @@ int main (int argc, char **argv)
         for (ii=0 ; ii<threads ; ii++){
        // v[ii].set_inputs(inFile_f);
             v2[ii].set_inputs(*inFile_f,*inFile_r);
-            v2[ii].set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1,bad_out_file_R2,single_out_file_R2,good_out_file_R2);
+            v2[ii].set_outputs(*bad_out_file_R1,*single_out_file_R1,*good_out_file_R1,*bad_out_file_R2,*single_out_file_R2,*good_out_file_R2);
             v2[ii].set_out_format(out_format);
             ttt2[ii].read= & v2[ii];
             ttt2[ii].filter= filter;
@@ -350,7 +398,7 @@ int main (int argc, char **argv)
     
         for (ii=0 ; ii<threads ; ii++){
        // v[ii].set_inputs(inFile_f);
-            v[ii].set_outputs(bad_out_file_R1,single_out_file_R1,good_out_file_R1);
+            v[ii].set_outputs(*bad_out_file_R1,*bad_out_file_R1,*good_out_file_R1);
             ttt[ii].read= & v[ii];
             ttt[ii].filter= filter;
             pthread_create(&tthreads[ii],NULL,do_single, (void *) &ttt[ii]); 

From cd3cfb9a1f128f501e6968d01e156d10d6076c8a Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Sat, 3 Mar 2018 20:47:10 +0000
Subject: [PATCH 6/7] added boost macros and changed version number

---
 .gitignore                |   3 +-
 Makefile.in               |   7 +-
 configure.ac              |   5 +-
 m4/ax_boost_base.m4       | 301 ++++++++++++++++++++++++++++++++++++++
 m4/ax_boost_filesystem.m4 | 118 +++++++++++++++
 m4/ax_boost_iostreams.m4  | 116 +++++++++++++++
 6 files changed, 547 insertions(+), 3 deletions(-)
 create mode 100644 m4/ax_boost_base.m4
 create mode 100644 m4/ax_boost_filesystem.m4
 create mode 100644 m4/ax_boost_iostreams.m4

diff --git a/.gitignore b/.gitignore
index 6446e0a..2db5f96 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,7 +14,8 @@ pprinseqc*.tar.gz
 src/*.fastq
 !src/test_F.fastq
 !src/test_R.fastq
-
+config.guess
+config.sub
 
 # Prerequisites
 *.d
diff --git a/Makefile.in b/Makefile.in
index 8d2259c..9676e9d 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -13,6 +13,7 @@ bindir = @bindir@
 srcdir = @srcdir@
 VPATH = @srcdir@
 
+ACLOCAL_AMFLAGS = -I m4 --install
 
 all test install uninstall pprinseqc:
 	cd src && $(MAKE) $@
@@ -20,7 +21,7 @@ all test install uninstall pprinseqc:
 clean : FORCE
 	cd src && $(MAKE) $@
 	-rm -rf autom4te.cache 
-	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile
+	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile config.guess config.sub
 
 dist : $(distdir).tar.gz
 
@@ -35,12 +36,16 @@ $(distdir): FORCE
 	cp $(srcdir)/config.h.in $(distdir)
 	cp $(srcdir)/install-sh $(distdir)
 	cp $(srcdir)/Makefile.in $(distdir)
+	cp $(srcdir)/config.sub $(distdir)
+	cp $(srcdir)/config.guess $(distdir)
 	cp $(srcdir)/src/Makefile.in $(distdir)/src
 	cp $(srcdir)/src/main.cpp $(distdir)/src
 	cp $(srcdir)/src/reads.cpp $(distdir)/src
 	cp $(srcdir)/src/reads.h $(distdir)/src
 	cp $(srcdir)/src/test_F.fastq $(distdir)/src
 	cp $(srcdir)/src/test_R.fastq $(distdir)/src
+	cp $(srcdir)/src/test_F.fastq.gz $(distdir)/src
+	cp $(srcdir)/src/test_R.fastq.gz $(distdir)/src
 	cp $(srcdir)/src/bloom_filter.hpp $(distdir)/src
 	cp $(srcdir)/src/README $(distdir)/src
 
diff --git a/configure.ac b/configure.ac
index 26ef726..81cfe3d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([pprinseqc], [0.1], [garbanyo@gmail.com])
+AC_INIT([pprinseqc], [0.9], [garbanyo@gmail.com])
 ##AM_INIT_AUTOMAKE
 AC_CONFIG_SRCDIR([src/main.cpp])
 AC_LANG([C++])
@@ -15,6 +15,9 @@ AC_CONFIG_HEADERS([config.h])
 # Checks for programs.
 AC_PROG_CXX
 AC_PROG_INSTALL
+AX_BOOST_BASE([1.41], [], AC_MSG_ERROR([Could not find a useful version of boost]))
+AX_BOOST_FILESYSTEM
+AX_BOOST_IOSTREAMS
 
 # Checks for libraries.
 
diff --git a/m4/ax_boost_base.m4 b/m4/ax_boost_base.m4
new file mode 100644
index 0000000..2bce519
--- /dev/null
+++ b/m4/ax_boost_base.m4
@@ -0,0 +1,301 @@
+# ===========================================================================
+#      https://www.gnu.org/software/autoconf-archive/ax_boost_base.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_BOOST_BASE([MINIMUM-VERSION], [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
+#
+# DESCRIPTION
+#
+#   Test for the Boost C++ libraries of a particular version (or newer)
+#
+#   If no path to the installed boost library is given the macro searchs
+#   under /usr, /usr/local, /opt and /opt/local and evaluates the
+#   $BOOST_ROOT environment variable. Further documentation is available at
+#   <http://randspringer.de/boost/index.html>.
+#
+#   This macro calls:
+#
+#     AC_SUBST(BOOST_CPPFLAGS) / AC_SUBST(BOOST_LDFLAGS)
+#
+#   And sets:
+#
+#     HAVE_BOOST
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Thomas Porschberg <thomas@randspringer.de>
+#   Copyright (c) 2009 Peter Adolphs
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 43
+
+# example boost program (need to pass version)
+m4_define([_AX_BOOST_BASE_PROGRAM],
+          [AC_LANG_PROGRAM([[
+#include <boost/version.hpp>
+]],[[
+(void) ((void)sizeof(char[1 - 2*!!((BOOST_VERSION) < ($1))]));
+]])])
+
+AC_DEFUN([AX_BOOST_BASE],
+[
+AC_ARG_WITH([boost],
+  [AS_HELP_STRING([--with-boost@<:@=ARG@:>@],
+    [use Boost library from a standard location (ARG=yes),
+     from the specified location (ARG=<path>),
+     or disable it (ARG=no)
+     @<:@ARG=yes@:>@ ])],
+    [
+     AS_CASE([$withval],
+       [no],[want_boost="no";_AX_BOOST_BASE_boost_path=""],
+       [yes],[want_boost="yes";_AX_BOOST_BASE_boost_path=""],
+       [want_boost="yes";_AX_BOOST_BASE_boost_path="$withval"])
+    ],
+    [want_boost="yes"])
+
+
+AC_ARG_WITH([boost-libdir],
+  [AS_HELP_STRING([--with-boost-libdir=LIB_DIR],
+    [Force given directory for boost libraries.
+     Note that this will override library path detection,
+     so use this parameter only if default library detection fails
+     and you know exactly where your boost libraries are located.])],
+  [
+   AS_IF([test -d "$withval"],
+         [_AX_BOOST_BASE_boost_lib_path="$withval"],
+    [AC_MSG_ERROR([--with-boost-libdir expected directory name])])
+  ],
+  [_AX_BOOST_BASE_boost_lib_path=""])
+
+BOOST_LDFLAGS=""
+BOOST_CPPFLAGS=""
+AS_IF([test "x$want_boost" = "xyes"],
+      [_AX_BOOST_BASE_RUNDETECT([$1],[$2],[$3])])
+AC_SUBST(BOOST_CPPFLAGS)
+AC_SUBST(BOOST_LDFLAGS)
+])
+
+
+# convert a version string in $2 to numeric and affect to polymorphic var $1
+AC_DEFUN([_AX_BOOST_BASE_TONUMERICVERSION],[
+  AS_IF([test "x$2" = "x"],[_AX_BOOST_BASE_TONUMERICVERSION_req="1.20.0"],[_AX_BOOST_BASE_TONUMERICVERSION_req="$2"])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_shorten=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '\([[0-9]]*\.[[0-9]]*\)'`
+  _AX_BOOST_BASE_TONUMERICVERSION_req_major=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '\([[0-9]]*\)'`
+  AS_IF([test "x$_AX_BOOST_BASE_TONUMERICVERSION_req_major" = "x"],
+        [AC_MSG_ERROR([You should at least specify libboost major version])])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_minor=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '[[0-9]]*\.\([[0-9]]*\)'`
+  AS_IF([test "x$_AX_BOOST_BASE_TONUMERICVERSION_req_minor" = "x"],
+        [_AX_BOOST_BASE_TONUMERICVERSION_req_minor="0"])
+  _AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
+  AS_IF([test "X$_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor" = "X"],
+        [_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor="0"])
+  _AX_BOOST_BASE_TONUMERICVERSION_RET=`expr $_AX_BOOST_BASE_TONUMERICVERSION_req_major \* 100000 \+  $_AX_BOOST_BASE_TONUMERICVERSION_req_minor \* 100 \+ $_AX_BOOST_BASE_TONUMERICVERSION_req_sub_minor`
+  AS_VAR_SET($1,$_AX_BOOST_BASE_TONUMERICVERSION_RET)
+])
+
+dnl Run the detection of boost should be run only if $want_boost
+AC_DEFUN([_AX_BOOST_BASE_RUNDETECT],[
+    _AX_BOOST_BASE_TONUMERICVERSION(WANT_BOOST_VERSION,[$1])
+    succeeded=no
+
+
+    AC_REQUIRE([AC_CANONICAL_HOST])
+    dnl On 64-bit systems check for system libraries in both lib64 and lib.
+    dnl The former is specified by FHS, but e.g. Debian does not adhere to
+    dnl this (as it rises problems for generic multi-arch support).
+    dnl The last entry in the list is chosen by default when no libraries
+    dnl are found, e.g. when only header-only libraries are installed!
+    AS_CASE([${host_cpu}],
+      [x86_64],[libsubdirs="lib64 libx32 lib lib64"],
+      [ppc64|s390x|sparc64|aarch64|ppc64le],[libsubdirs="lib64 lib lib64"],
+      [libsubdirs="lib"]
+    )
+
+    dnl allow for real multi-arch paths e.g. /usr/lib/x86_64-linux-gnu. Give
+    dnl them priority over the other paths since, if libs are found there, they
+    dnl are almost assuredly the ones desired.
+    AS_CASE([${host_cpu}],
+      [i?86],[multiarch_libsubdir="lib/i386-${host_os}"],
+      [multiarch_libsubdir="lib/${host_cpu}-${host_os}"]
+    )
+
+    dnl first we check the system location for boost libraries
+    dnl this location ist chosen if boost libraries are installed with the --layout=system option
+    dnl or if you install boost with RPM
+    AS_IF([test "x$_AX_BOOST_BASE_boost_path" != "x"],[
+        AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION) includes in "$_AX_BOOST_BASE_boost_path/include"])
+         AS_IF([test -d "$_AX_BOOST_BASE_boost_path/include" && test -r "$_AX_BOOST_BASE_boost_path/include"],[
+           AC_MSG_RESULT([yes])
+           BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path/include"
+           for _AX_BOOST_BASE_boost_path_tmp in $multiarch_libsubdir $libsubdirs; do
+                AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION) lib path in "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp"])
+                AS_IF([test -d "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp" && test -r "$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp" ],[
+                        AC_MSG_RESULT([yes])
+                        BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path/$_AX_BOOST_BASE_boost_path_tmp";
+                        break;
+                ],
+      [AC_MSG_RESULT([no])])
+           done],[
+      AC_MSG_RESULT([no])])
+    ],[
+        if test X"$cross_compiling" = Xyes; then
+            search_libsubdirs=$multiarch_libsubdir
+        else
+            search_libsubdirs="$multiarch_libsubdir $libsubdirs"
+        fi
+        for _AX_BOOST_BASE_boost_path_tmp in /usr /usr/local /opt /opt/local ; do
+            if test -d "$_AX_BOOST_BASE_boost_path_tmp/include/boost" && test -r "$_AX_BOOST_BASE_boost_path_tmp/include/boost" ; then
+                for libsubdir in $search_libsubdirs ; do
+                    if ls "$_AX_BOOST_BASE_boost_path_tmp/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                done
+                BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path_tmp/$libsubdir"
+                BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path_tmp/include"
+                break;
+            fi
+        done
+    ])
+
+    dnl overwrite ld flags if we have required special directory with
+    dnl --with-boost-libdir parameter
+    AS_IF([test "x$_AX_BOOST_BASE_boost_lib_path" != "x"],
+          [BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_lib_path"])
+
+    AC_MSG_CHECKING([for boostlib >= $1 ($WANT_BOOST_VERSION)])
+    CPPFLAGS_SAVED="$CPPFLAGS"
+    CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+    export CPPFLAGS
+
+    LDFLAGS_SAVED="$LDFLAGS"
+    LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+    export LDFLAGS
+
+    AC_REQUIRE([AC_PROG_CXX])
+    AC_LANG_PUSH(C++)
+        AC_COMPILE_IFELSE([_AX_BOOST_BASE_PROGRAM($WANT_BOOST_VERSION)],[
+        AC_MSG_RESULT(yes)
+    succeeded=yes
+    found_system=yes
+        ],[
+        ])
+    AC_LANG_POP([C++])
+
+
+
+    dnl if we found no boost with system layout we search for boost libraries
+    dnl built and installed without the --layout=system option or for a staged(not installed) version
+    if test "x$succeeded" != "xyes" ; then
+        CPPFLAGS="$CPPFLAGS_SAVED"
+        LDFLAGS="$LDFLAGS_SAVED"
+        BOOST_CPPFLAGS=
+        if test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+            BOOST_LDFLAGS=
+        fi
+        _version=0
+        if test -n "$_AX_BOOST_BASE_boost_path" ; then
+            if test -d "$_AX_BOOST_BASE_boost_path" && test -r "$_AX_BOOST_BASE_boost_path"; then
+                for i in `ls -d $_AX_BOOST_BASE_boost_path/include/boost-* 2>/dev/null`; do
+                    _version_tmp=`echo $i | sed "s#$_AX_BOOST_BASE_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+                    V_CHECK=`expr $_version_tmp \> $_version`
+                    if test "x$V_CHECK" = "x1" ; then
+                        _version=$_version_tmp
+                    fi
+                    VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+                    BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path/include/boost-$VERSION_UNDERSCORE"
+                done
+                dnl if nothing found search for layout used in Windows distributions
+                if test -z "$BOOST_CPPFLAGS"; then
+                    if test -d "$_AX_BOOST_BASE_boost_path/boost" && test -r "$_AX_BOOST_BASE_boost_path/boost"; then
+                        BOOST_CPPFLAGS="-I$_AX_BOOST_BASE_boost_path"
+                    fi
+                fi
+                dnl if we found something and BOOST_LDFLAGS was unset before
+                dnl (because "$_AX_BOOST_BASE_boost_lib_path" = ""), set it here.
+                if test -n "$BOOST_CPPFLAGS" && test -z "$BOOST_LDFLAGS"; then
+                    for libsubdir in $libsubdirs ; do
+                        if ls "$_AX_BOOST_BASE_boost_path/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                    done
+                    BOOST_LDFLAGS="-L$_AX_BOOST_BASE_boost_path/$libsubdir"
+                fi
+            fi
+        else
+            if test "x$cross_compiling" != "xyes" ; then
+                for _AX_BOOST_BASE_boost_path in /usr /usr/local /opt /opt/local ; do
+                    if test -d "$_AX_BOOST_BASE_boost_path" && test -r "$_AX_BOOST_BASE_boost_path" ; then
+                        for i in `ls -d $_AX_BOOST_BASE_boost_path/include/boost-* 2>/dev/null`; do
+                            _version_tmp=`echo $i | sed "s#$_AX_BOOST_BASE_boost_path##" | sed 's/\/include\/boost-//' | sed 's/_/./'`
+                            V_CHECK=`expr $_version_tmp \> $_version`
+                            if test "x$V_CHECK" = "x1" ; then
+                                _version=$_version_tmp
+                                best_path=$_AX_BOOST_BASE_boost_path
+                            fi
+                        done
+                    fi
+                done
+
+                VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
+                BOOST_CPPFLAGS="-I$best_path/include/boost-$VERSION_UNDERSCORE"
+                if test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+                    for libsubdir in $libsubdirs ; do
+                        if ls "$best_path/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                    done
+                    BOOST_LDFLAGS="-L$best_path/$libsubdir"
+                fi
+            fi
+
+            if test -n "$BOOST_ROOT" ; then
+                for libsubdir in $libsubdirs ; do
+                    if ls "$BOOST_ROOT/stage/$libsubdir/libboost_"* >/dev/null 2>&1 ; then break; fi
+                done
+                if test -d "$BOOST_ROOT" && test -r "$BOOST_ROOT" && test -d "$BOOST_ROOT/stage/$libsubdir" && test -r "$BOOST_ROOT/stage/$libsubdir"; then
+                    version_dir=`expr //$BOOST_ROOT : '.*/\(.*\)'`
+                    stage_version=`echo $version_dir | sed 's/boost_//' | sed 's/_/./g'`
+                        stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
+                    V_CHECK=`expr $stage_version_shorten \>\= $_version`
+                    if test "x$V_CHECK" = "x1" && test -z "$_AX_BOOST_BASE_boost_lib_path" ; then
+                        AC_MSG_NOTICE(We will use a staged boost library from $BOOST_ROOT)
+                        BOOST_CPPFLAGS="-I$BOOST_ROOT"
+                        BOOST_LDFLAGS="-L$BOOST_ROOT/stage/$libsubdir"
+                    fi
+                fi
+            fi
+        fi
+
+        CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+        export CPPFLAGS
+        LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+        export LDFLAGS
+
+        AC_LANG_PUSH(C++)
+            AC_COMPILE_IFELSE([_AX_BOOST_BASE_PROGRAM($WANT_BOOST_VERSION)],[
+            AC_MSG_RESULT(yes)
+        succeeded=yes
+        found_system=yes
+            ],[
+            ])
+        AC_LANG_POP([C++])
+    fi
+
+    if test "x$succeeded" != "xyes" ; then
+        if test "x$_version" = "x0" ; then
+            AC_MSG_NOTICE([[We could not detect the boost libraries (version $1 or higher). If you have a staged boost library (still not installed) please specify \$BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.]])
+        else
+            AC_MSG_NOTICE([Your boost libraries seems to old (version $_version).])
+        fi
+        # execute ACTION-IF-NOT-FOUND (if present):
+        ifelse([$3], , :, [$3])
+    else
+        AC_DEFINE(HAVE_BOOST,,[define if the Boost library is available])
+        # execute ACTION-IF-FOUND (if present):
+        ifelse([$2], , :, [$2])
+    fi
+
+    CPPFLAGS="$CPPFLAGS_SAVED"
+    LDFLAGS="$LDFLAGS_SAVED"
+
+])
diff --git a/m4/ax_boost_filesystem.m4 b/m4/ax_boost_filesystem.m4
new file mode 100644
index 0000000..c392f9d
--- /dev/null
+++ b/m4/ax_boost_filesystem.m4
@@ -0,0 +1,118 @@
+# ===========================================================================
+#   https://www.gnu.org/software/autoconf-archive/ax_boost_filesystem.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_BOOST_FILESYSTEM
+#
+# DESCRIPTION
+#
+#   Test for Filesystem library from the Boost C++ libraries. The macro
+#   requires a preceding call to AX_BOOST_BASE. Further documentation is
+#   available at <http://randspringer.de/boost/index.html>.
+#
+#   This macro calls:
+#
+#     AC_SUBST(BOOST_FILESYSTEM_LIB)
+#
+#   And sets:
+#
+#     HAVE_BOOST_FILESYSTEM
+#
+# LICENSE
+#
+#   Copyright (c) 2009 Thomas Porschberg <thomas@randspringer.de>
+#   Copyright (c) 2009 Michael Tindal
+#   Copyright (c) 2009 Roman Rybalko <libtorrent@romanr.info>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 27
+
+AC_DEFUN([AX_BOOST_FILESYSTEM],
+[
+	AC_ARG_WITH([boost-filesystem],
+	AS_HELP_STRING([--with-boost-filesystem@<:@=special-lib@:>@],
+                   [use the Filesystem library from boost - it is possible to specify a certain library for the linker
+                        e.g. --with-boost-filesystem=boost_filesystem-gcc-mt ]),
+        [
+        if test "$withval" = "no"; then
+			want_boost="no"
+        elif test "$withval" = "yes"; then
+            want_boost="yes"
+            ax_boost_user_filesystem_lib=""
+        else
+		    want_boost="yes"
+		ax_boost_user_filesystem_lib="$withval"
+		fi
+        ],
+        [want_boost="yes"]
+	)
+
+	if test "x$want_boost" = "xyes"; then
+        AC_REQUIRE([AC_PROG_CC])
+		CPPFLAGS_SAVED="$CPPFLAGS"
+		CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+		export CPPFLAGS
+
+		LDFLAGS_SAVED="$LDFLAGS"
+		LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+		export LDFLAGS
+
+		LIBS_SAVED=$LIBS
+		LIBS="$LIBS $BOOST_SYSTEM_LIB"
+		export LIBS
+
+        AC_CACHE_CHECK(whether the Boost::Filesystem library is available,
+					   ax_cv_boost_filesystem,
+        [AC_LANG_PUSH([C++])
+         AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <boost/filesystem/path.hpp>]],
+                                   [[using namespace boost::filesystem;
+                                   path my_path( "foo/bar/data.txt" );
+                                   return 0;]])],
+					       ax_cv_boost_filesystem=yes, ax_cv_boost_filesystem=no)
+         AC_LANG_POP([C++])
+		])
+		if test "x$ax_cv_boost_filesystem" = "xyes"; then
+			AC_DEFINE(HAVE_BOOST_FILESYSTEM,,[define if the Boost::Filesystem library is available])
+            BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
+            if test "x$ax_boost_user_filesystem_lib" = "x"; then
+                for libextension in `ls -r $BOOSTLIBDIR/libboost_filesystem* 2>/dev/null | sed 's,.*/lib,,' | sed 's,\..*,,'` ; do
+                     ax_lib=${libextension}
+				    AC_CHECK_LIB($ax_lib, exit,
+                                 [BOOST_FILESYSTEM_LIB="-l$ax_lib"; AC_SUBST(BOOST_FILESYSTEM_LIB) link_filesystem="yes"; break],
+                                 [link_filesystem="no"])
+				done
+                if test "x$link_filesystem" != "xyes"; then
+                for libextension in `ls -r $BOOSTLIBDIR/boost_filesystem* 2>/dev/null | sed 's,.*/,,' | sed -e 's,\..*,,'` ; do
+                     ax_lib=${libextension}
+				    AC_CHECK_LIB($ax_lib, exit,
+                                 [BOOST_FILESYSTEM_LIB="-l$ax_lib"; AC_SUBST(BOOST_FILESYSTEM_LIB) link_filesystem="yes"; break],
+                                 [link_filesystem="no"])
+				done
+		    fi
+            else
+               for ax_lib in $ax_boost_user_filesystem_lib boost_filesystem-$ax_boost_user_filesystem_lib; do
+				      AC_CHECK_LIB($ax_lib, exit,
+                                   [BOOST_FILESYSTEM_LIB="-l$ax_lib"; AC_SUBST(BOOST_FILESYSTEM_LIB) link_filesystem="yes"; break],
+                                   [link_filesystem="no"])
+                  done
+
+            fi
+            if test "x$ax_lib" = "x"; then
+                AC_MSG_ERROR(Could not find a version of the library!)
+            fi
+			if test "x$link_filesystem" != "xyes"; then
+				AC_MSG_ERROR(Could not link against $ax_lib !)
+			fi
+		fi
+
+		CPPFLAGS="$CPPFLAGS_SAVED"
+		LDFLAGS="$LDFLAGS_SAVED"
+		LIBS="$LIBS_SAVED"
+	fi
+])
diff --git a/m4/ax_boost_iostreams.m4 b/m4/ax_boost_iostreams.m4
new file mode 100644
index 0000000..8f27f85
--- /dev/null
+++ b/m4/ax_boost_iostreams.m4
@@ -0,0 +1,116 @@
+# ===========================================================================
+#    https://www.gnu.org/software/autoconf-archive/ax_boost_iostreams.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_BOOST_IOSTREAMS
+#
+# DESCRIPTION
+#
+#   Test for IOStreams library from the Boost C++ libraries. The macro
+#   requires a preceding call to AX_BOOST_BASE. Further documentation is
+#   available at <http://randspringer.de/boost/index.html>.
+#
+#   This macro calls:
+#
+#     AC_SUBST(BOOST_IOSTREAMS_LIB)
+#
+#   And sets:
+#
+#     HAVE_BOOST_IOSTREAMS
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Thomas Porschberg <thomas@randspringer.de>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 21
+
+AC_DEFUN([AX_BOOST_IOSTREAMS],
+[
+	AC_ARG_WITH([boost-iostreams],
+	AS_HELP_STRING([--with-boost-iostreams@<:@=special-lib@:>@],
+                   [use the IOStreams library from boost - it is possible to specify a certain library for the linker
+                        e.g. --with-boost-iostreams=boost_iostreams-gcc-mt-d-1_33_1 ]),
+        [
+        if test "$withval" = "no"; then
+			want_boost="no"
+        elif test "$withval" = "yes"; then
+            want_boost="yes"
+            ax_boost_user_iostreams_lib=""
+        else
+		    want_boost="yes"
+		ax_boost_user_iostreams_lib="$withval"
+		fi
+        ],
+        [want_boost="yes"]
+	)
+
+	if test "x$want_boost" = "xyes"; then
+        AC_REQUIRE([AC_PROG_CC])
+		CPPFLAGS_SAVED="$CPPFLAGS"
+		CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
+		export CPPFLAGS
+
+		LDFLAGS_SAVED="$LDFLAGS"
+		LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
+		export LDFLAGS
+
+        AC_CACHE_CHECK(whether the Boost::IOStreams library is available,
+					   ax_cv_boost_iostreams,
+        [AC_LANG_PUSH([C++])
+		 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <boost/iostreams/filtering_stream.hpp>
+											 @%:@include <boost/range/iterator_range.hpp>
+											]],
+                                  [[std::string  input = "Hello World!";
+								 namespace io = boost::iostreams;
+									 io::filtering_istream  in(boost::make_iterator_range(input));
+									 return 0;
+                                   ]])],
+                             ax_cv_boost_iostreams=yes, ax_cv_boost_iostreams=no)
+         AC_LANG_POP([C++])
+		])
+		if test "x$ax_cv_boost_iostreams" = "xyes"; then
+			AC_DEFINE(HAVE_BOOST_IOSTREAMS,,[define if the Boost::IOStreams library is available])
+            BOOSTLIBDIR=`echo $BOOST_LDFLAGS | sed -e 's/@<:@^\/@:>@*//'`
+            if test "x$ax_boost_user_iostreams_lib" = "x"; then
+                for libextension in `ls $BOOSTLIBDIR/libboost_iostreams*.so* $BOOSTLIBDIR/libboost_iostream*.dylib* $BOOSTLIBDIR/libboost_iostreams*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_iostreams.*\)\.so.*$;\1;' -e 's;^lib\(boost_iostream.*\)\.dylib.*$;\1;' -e 's;^lib\(boost_iostreams.*\)\.a.*$;\1;'` ; do
+                     ax_lib=${libextension}
+				    AC_CHECK_LIB($ax_lib, exit,
+                                 [BOOST_IOSTREAMS_LIB="-l$ax_lib"; AC_SUBST(BOOST_IOSTREAMS_LIB) link_iostreams="yes"; break],
+                                 [link_iostreams="no"])
+				done
+                if test "x$link_iostreams" != "xyes"; then
+                for libextension in `ls $BOOSTLIBDIR/boost_iostreams*.dll* $BOOSTLIBDIR/boost_iostreams*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_iostreams.*\)\.dll.*$;\1;' -e 's;^\(boost_iostreams.*\)\.a.*$;\1;'` ; do
+                     ax_lib=${libextension}
+				    AC_CHECK_LIB($ax_lib, exit,
+                                 [BOOST_IOSTREAMS_LIB="-l$ax_lib"; AC_SUBST(BOOST_IOSTREAMS_LIB) link_iostreams="yes"; break],
+                                 [link_iostreams="no"])
+				done
+                fi
+
+            else
+               for ax_lib in $ax_boost_user_iostreams_lib boost_iostreams-$ax_boost_user_iostreams_lib; do
+				      AC_CHECK_LIB($ax_lib, main,
+                                   [BOOST_IOSTREAMS_LIB="-l$ax_lib"; AC_SUBST(BOOST_IOSTREAMS_LIB) link_iostreams="yes"; break],
+                                   [link_iostreams="no"])
+                  done
+
+            fi
+            if test "x$ax_lib" = "x"; then
+                AC_MSG_ERROR(Could not find a version of the library!)
+            fi
+			if test "x$link_iostreams" != "xyes"; then
+				AC_MSG_ERROR(Could not link against $ax_lib !)
+			fi
+		fi
+
+		CPPFLAGS="$CPPFLAGS_SAVED"
+	LDFLAGS="$LDFLAGS_SAVED"
+	fi
+])

From 3dbdb7e372d2c87f85a219c607c55c666c5440ac Mon Sep 17 00:00:00 2001
From: Adrian Cantu <garbanyo@gmail.com>
Date: Sat, 3 Mar 2018 21:05:01 +0000
Subject: [PATCH 7/7] added therads option

---
 src/Makefile.in | 5 ++++-
 src/main.cpp    | 4 ++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index 6e80a84..3d1d9cd 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -43,7 +43,10 @@ test: all
 	echo "*** ALL TEST PASSED***"
 	
 test_single: all
-	./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single -out_gz
+	time -v ./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single_t1 -out_gz -threads 1
+	time -v ./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single_t2 -out_gz -threads 2
+	time -v ./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single_t5 -out_gz -threads 5
+	time -v ./pprinseqc -fastq stenotrophomonas_R1.fastq -min_len 5000 -derep -out_name Test_1_Single_t10 -out_gz -threads 10
 	
 
 install:
diff --git a/src/main.cpp b/src/main.cpp
index 30f03a2..8497965 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -100,6 +100,7 @@ pthread_mutex_t read_mutex2=PTHREAD_MUTEX_INITIALIZER;
         { "trim_tail_left"  , required_argument , NULL     , 20 },
         { "trim_tail_right" , required_argument , NULL     , 21 },
         { "out_gz"          , no_argument       , &out_gz  ,  1 },
+        { "threads"         , required_argument , NULL     , 22 },
 {0,0,0,0}
     };    
     
@@ -199,6 +200,9 @@ int main (int argc, char **argv)
             case 21: 
                 trim_tail_right=atoi(optarg);
                 break;
+            case 22: 
+                threads=atoi(optarg);
+                break;
             case 0:
                 // getopt set a variable
                 break;