A bug with both using polyat & qual is fixed. Version incremented.

Makefile

@@ -33,14 +33,7 @@ ifeq ($(PLATFORM),-DAPPLE)
 
     Illumina.o : 
 	$(CXX) $(CFLAGS) $(OPT) -c -o $(OBJ)Illumina.o $(SRC)Illumina_retro_compiler.cpp
-	#$(CXX) $(CFLAGS) ${PLATFORM} -O3 -c -o $(OBJ)Illumina.o $(SRC)Illumina_retro_compiler.cpp
-	#if [ "$(GCCVERSION)" > "4.2" ] ; then \
-        #    $(CXX) $(CFLAGS) -O3 -c -o $(OBJ)Illumina.o $(SRC)Illumina.cpp;\
-        #else \
-        #    $(CXX) $(CFLAGS) ${PLATFORM} -O3 -c -o $(OBJ)Illumina.o $(SRC)Illumina_retro_compiler.cpp ;\
-        #fi
 
-
     MainPipeLine.o :
 	$(CXX) $(CFLAGS) $(OPT) -c -o $(OBJ)MainPipeLine.o $(SRC)MainPipeLine.cpp 
 

README.md

@@ -1,7 +1,7 @@
 # Description
 
 Program ```SeqyClean```
-Version: ```1.10.07 (2017-12-14)```
+Version: ```1.10.08 (2017-10-15)```
 
 Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
 

nbproject/private/configurations.xml

@@ -2,10 +2,6 @@
 <configurationDescriptor version="100">
   <logicalFolder name="root" displayName="root" projectFiles="true" kind="ROOT">
     <df root="." name="0">
-      <df name="bin">
-      </df>
-      <df name="obj">
-      </df>
       <df name="src">
         <in>Dictionary.cpp</in>
         <in>Dictionary.h</in>

nbproject/private/private.xml

@@ -11,9 +11,7 @@
     <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
         <group>
             <file>file:/Users/ilya/Projects/seqyclean/src/main.cpp</file>
-            <file>file:/Users/ilya/Projects/seqyclean/README.md</file>
             <file>file:/Users/ilya/Projects/seqyclean/src/Illumina_retro_compiler.cpp</file>
-            <file>file:/Users/ilya/Projects/seqyclean/src/Illumina.h</file>
         </group>
     </open-files>
 </project-private>

src/Illumina_retro_compiler.cpp

@@ -73,8 +73,7 @@ double cur_lclip_pe1 = 0.0; double cur_rclip_pe1 = 0.0;
 double cur_lclip_pe2 = 0.0; double cur_rclip_pe2 = 0.0;
 
 //Dynamic Illumina: does not need space to store reads:
-void IlluminaDynamic()
-{
+void IlluminaDynamic() {
     cnt_avg_len1 = cnt_avg_len2 = 0;
     avg_len_pe1 = avg_len_pe2 = 0.0;
     cnt1_avg = cnt2_avg = 0;
@@ -107,8 +106,7 @@ void IlluminaDynamic()
     tmp_avg_right_clip_1 = 0; tmp_avg_left_clip_1 = 0;
     tmp_avg_right_clip_2 = 0; tmp_avg_left_clip_2 = 0;
 
-    if (detailed_report) 
-    {
+    if (detailed_report) {
         rep_file1.open(rep_file_name1.c_str(),ios::out);
         rep_file2.open(rep_file_name2.c_str(),ios::out);
     }
@@ -788,7 +786,7 @@ void IlluminaDynamicSE()
                     screen_duplicates(read, duplicates);
                 }
 
-                        
+
                 TrimIlluminaSE(read, true);
 
                 cnt+=1;
@@ -1331,6 +1329,7 @@ void ClearNNs( vector<Read*>& reads )
 int TrimIlluminaSE(Read* read, bool trim_adapter)
 {
     read->lclip = 0; read->rclip = read->read.length();
+    // std::cout << read->readID << " " << read->read.length() << " " << read->lclip << " " << read->rclip << "\n"; 
 
     if(contaminants_flag )
     {
@@ -1350,7 +1349,8 @@ int TrimIlluminaSE(Read* read, bool trim_adapter)
         cur_lclip_pe1 += static_cast<double>(read->lclip);
         cur_rclip_pe1 += static_cast<double>(read->read.length() - read->rclip);
     }
-
+
+
     // Trim quality
     //If quality trimming flag is set up -> perform the quality trimming before vector/contaminants/adaptors clipping.
     if( qual_trim_flag  ) {
@@ -1374,6 +1374,8 @@ int TrimIlluminaSE(Read* read, bool trim_adapter)
 
             cur_lclip_pe1 += static_cast<double>(read->lclip);
             cur_rclip_pe1 += static_cast<double>(read->read.length() - read->rclip);
+
+
             trim_read(read);
         }
     }
@@ -1403,7 +1405,7 @@ int TrimIlluminaSE(Read* read, bool trim_adapter)
     if(polyat_flag) {
         //Trim poly A/T:
         PolyAT_Trim(read); 
-        
+
         if( (read->rclip > read->poly_A_clip) && (read->poly_A_found)) {
             read->rclip = read->poly_A_clip;
             read->right_trimmed_by_polyat = 1;
@@ -1415,7 +1417,9 @@ int TrimIlluminaSE(Read* read, bool trim_adapter)
 
         cur_lclip_pe1 += static_cast<double>(read->lclip);
         cur_rclip_pe1 += static_cast<double>(read->read.length() - read->rclip);
+
         trim_read(read);
+
     }
 
 
@@ -1785,6 +1789,7 @@ void trim_read(Read *read)
     {
         read->discarded = true;
     }
+
 }
 
 void update_statistics(Read *read1, Read *read2) {

src/main.cpp

@@ -23,7 +23,7 @@
 
 using namespace std;
 
-std::string version = "1.10.07 (2017-12-14)";
+std::string version = "1.10.08 (2018-10-15)";
 
 /*Common parameters (default)*/
 short KMER_SIZE = 15;

src/poly.c

@@ -18,7 +18,7 @@ void PolyAT_Trim(Read* read)
     int left, right;
     left = right = 0;
 
-    if(qual_trim_flag) {
+    /*if(qual_trim_flag) {
         left = poly_at_left( (char*)read->read.substr( read->lucy_lclip, read->read.length() - read->lucy_lclip ).c_str(), read->lucy_rclip - read->lucy_lclip); 
         if (left) 
         {
@@ -44,6 +44,20 @@ void PolyAT_Trim(Read* read)
                 read->poly_A_clip = read->read.length()- right;
                 read->poly_A_found = true;
         }
+    }*/
+
+
+    left = poly_at_left( (char*)read->read.c_str(), read->read.length()); 
+    if (left) 
+    {
+        read->poly_T_clip = left;
+        read->poly_T_found = true;
+    }
+    right = poly_at_right((char*)read->read.c_str(), read->read.length());
+    if (right) 
+    {
+        read->poly_A_clip = read->read.length()- right;
+        read->poly_A_found = true;
     }
  }