diff --git a/Makefile b/Makefile index 3c10f9b..6e7916b 100755 --- a/Makefile +++ b/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 diff --git a/README.md b/README.md index 1b93084..bfab813 100755 --- a/README.md +++ b/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. diff --git a/SeqyClean_UserManual_v1.10.08.pdf b/SeqyClean_UserManual_v1.10.08.pdf new file mode 100644 index 0000000..f65656d Binary files /dev/null and b/SeqyClean_UserManual_v1.10.08.pdf differ diff --git a/nbproject/private/configurations.xml b/nbproject/private/configurations.xml index 2c09465..4d81562 100644 --- a/nbproject/private/configurations.xml +++ b/nbproject/private/configurations.xml @@ -2,10 +2,6 @@ - - - - Dictionary.cpp Dictionary.h diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml index 080e99f..2e6bca7 100644 --- a/nbproject/private/private.xml +++ b/nbproject/private/private.xml @@ -11,9 +11,7 @@ file:/Users/ilya/Projects/seqyclean/src/main.cpp - file:/Users/ilya/Projects/seqyclean/README.md file:/Users/ilya/Projects/seqyclean/src/Illumina_retro_compiler.cpp - file:/Users/ilya/Projects/seqyclean/src/Illumina.h diff --git a/src/Illumina_retro_compiler.cpp b/src/Illumina_retro_compiler.cpp index e2a7294..2b7d3b6 100644 --- a/src/Illumina_retro_compiler.cpp +++ b/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& 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(read->lclip); cur_rclip_pe1 += static_cast(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(read->lclip); cur_rclip_pe1 += static_cast(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(read->lclip); cur_rclip_pe1 += static_cast(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) { diff --git a/src/main.cpp b/src/main.cpp index 6bad88c..d7b91ae 100755 --- a/src/main.cpp +++ b/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; diff --git a/src/poly.c b/src/poly.c index ef4060c..61e0ce1 100755 --- a/src/poly.c +++ b/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; } }