Flags -minoverlap and -alen are added back to options.

README.md

@@ -1,7 +1,7 @@
 # Description
 
 Program ```SeqyClean```
-Version: ```1.10.05 (2017-12-12)```
+Version: ```1.10.06 (2017-12-13)```
 
 Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
 

nbproject/configurations.xml

@@ -4,7 +4,6 @@
     <df root="." name="0">
       <df name="src">
         <in>Dictionary.cpp</in>
-        <in>Illumina.cpp</in>
         <in>Illumina_retro_compiler.cpp</in>
         <in>KMerRoutine.cpp</in>
         <in>MainPipeLine.cpp</in>
@@ -71,14 +70,6 @@
           </incDir>
         </ccTool>
       </item>
-      <item path="src/Illumina.cpp" ex="false" tool="1" flavor2="4">
-        <ccTool>
-          <incDir>
-            <pElem>src</pElem>
-            <pElem>.</pElem>
-          </incDir>
-        </ccTool>
-      </item>
       <item path="src/Illumina_retro_compiler.cpp" ex="false" tool="1" flavor2="0">
         <ccTool flags="1">
           <incDir>

nbproject/private/configurations.xml

@@ -9,7 +9,6 @@
       <df name="src">
         <in>Dictionary.cpp</in>
         <in>Dictionary.h</in>
-        <in>Illumina.cpp</in>
         <in>Illumina.h</in>
         <in>Illumina_retro_compiler.cpp</in>
         <in>KMerRoutine.cpp</in>
@@ -64,9 +63,9 @@
         <in>util.cpp</in>
         <in>util.h</in>
       </df>
-      <df name="test">
-      </df>
       <df name="test_data">
+        <df name="areads">
+        </df>
       </df>
     </df>
   </logicalFolder>
@@ -106,8 +105,6 @@
       </nativedebugger>
       <runprofile version="9">
         <runcommandpicklist>
-          <runcommandpicklistitem>bin/./seqyclean -U test_data/TestSRR_SE.fastq -o test/test -qual 24 24 -new2old -gz</runcommandpicklistitem>
-          <runcommandpicklistitem>bin/./seqyclean -1 test_data/TestSRR_PE1.fastq -2 test_data/TestSRR_PE2.fastq -o test/test -qual 24 24 -gz</runcommandpicklistitem>
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -qual 24 24 -gz</runcommandpicklistitem>
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -qual 24 24 -gz -no_adapter_trim</runcommandpicklistitem>
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -gz -no_adapter_trim</runcommandpicklistitem>
@@ -116,8 +113,10 @@
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -no_adapter_trim -ow -gz</runcommandpicklistitem>
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -overlap -ow -gz</runcommandpicklistitem>
           <runcommandpicklistitem>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -ow -gz</runcommandpicklistitem>
+          <runcommandpicklistitem>./bin/seqyclean -1 test_data/areads/frag_1.fastq -2 test_data/areads/frag_2.fastq -ow -o test/test -minlen 20 -minoverlap 20 -alen 30 -overlap -adp test_data/areads/adapters.fa </runcommandpicklistitem>
+          <runcommandpicklistitem>./bin/seqyclean -1 test_data/areads/frag_1.fastq -2 test_data/areads/frag_2.fastq -ow -o test/test -minlen 20 -minoverlap 20 -alen 30 -overlap -adp test_data/areads/adapters.fa</runcommandpicklistitem>
         </runcommandpicklist>
-        <runcommand>bin/./seqyclean -1 test_data/test_PE1.fastq.gz -2 test_data/test_PE2.fastq.gz -o test/test -ow -gz</runcommand>
+        <runcommand>./bin/seqyclean -1 test_data/areads/frag_1.fastq -2 test_data/areads/frag_2.fastq -ow -o test/test -minlen 20 -minoverlap 20 -alen 30 -overlap -adp test_data/areads/adapters.fa</runcommand>
         <rundir>.</rundir>
         <buildfirst>false</buildfirst>
         <terminal-type>0</terminal-type>

nbproject/private/private.xml

@@ -10,12 +10,9 @@
     <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
     <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
         <group>
-            <file>file:/Users/ilya/Projects/seqyclean/src/flash.h</file>
             <file>file:/Users/ilya/Projects/seqyclean/src/main.cpp</file>
             <file>file:/Users/ilya/Projects/seqyclean/src/Illumina_retro_compiler.cpp</file>
             <file>file:/Users/ilya/Projects/seqyclean/src/Illumina.h</file>
-            <file>file:/Users/ilya/Projects/seqyclean/src/flash.cpp</file>
-            <file>file:/Users/ilya/Projects/seqyclean/Makefile</file>
         </group>
     </open-files>
 </project-private>

src/Dictionary.cpp

@@ -1,5 +1,13 @@
 #include "Dictionary.h"
 
+/*i5 adapter*/
+ std::string tmpl_i5_1 = "AATGATACGGCGACCACCGAGATCTACAC";
+ std::string tmpl_i5_2;
+ /*i7 adapter*/
+ std::string tmpl_i7_1 = "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC";
+ std::string tmpl_i7_2; 
+
+
 /*Builds a new Vector Dictionary. Here it assumes that frequency is 1*/
 int BuildVectorDictionary(string filename) {
     string str;

src/Dictionary.h

@@ -1,3 +1,5 @@
+#pragma once
+
 #ifndef DICTIONARY_H
 #define	DICTIONARY_H
 
@@ -57,13 +59,7 @@ typedef struct {
    bool complement;
 } t_args;
 
- /*i5 adapter*/
- extern string tmpl_i5_1;
- extern string tmpl_i5_2;
- /*i7 adapter*/
- extern string tmpl_i7_1;
- extern string tmpl_i7_2; 
-
+
 /*Builds a new Vector Dictionary. Here it assumes that frequency is 1*/
 int BuildVectorDictionary(string filename);
 void ParseString(string str, int rec_id);