fix horrible bug, bump version number

Adrian-Cantu · Mar 4, 2018 · b42f49e · b42f49e
1 parent 102480c
commit b42f49e
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Showing 7 changed files with 47 additions and 50 deletions.
diff --git a/Makefile.in b/Makefile.in
@@ -21,8 +21,14 @@ 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 install-sh config.guess config.sub
+
+cleandist : FORCE
+	cd src && $(MAKE) clean
+	-rm -rf autom4te.cache 
 	-rm -f config.h config.log aclocal.m4 config.log config.status configure install-sh Makefile config.guess config.sub
 
+
 dist : $(distdir).tar.gz
 
 $(distdir).tar.gz : $(distdir)

diff --git 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], [0.9], [garbanyo@gmail.com])
+AC_INIT([pprinseqc], [0.9.1], [garbanyo@gmail.com])
 ##AM_INIT_AUTOMAKE
 AC_CONFIG_SRCDIR([src/main.cpp])
 AC_LANG([C++])

diff --git a/src/Makefile.in b/src/Makefile.in
@@ -28,7 +28,7 @@ compp: pprinseqc
 	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
+	$(CXX)  main.o reads.o  $(CXXFLAGS) -o pprinseqc
 
 main.o: main.cpp reads.h bloom_filter.hpp
 reads.o: reads.cpp reads.h 

diff --git a/src/main.cpp b/src/main.cpp
@@ -344,17 +344,7 @@ 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);
-
-    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_out_format(out_format);
-    } else {
-        read_f.set_outputs(*bad_out_file_R1,*bad_out_file_R1,*good_out_file_R1);
-    }
+
     bloom_parameters parameters;
     bloom_filter *filter=NULL;
     if (derep) {    
@@ -374,15 +364,15 @@ int main (int argc, char **argv)
     // main loop
     if (reverse_read_file) {
         ////////////////////////////////////////for pair end
-        vector<pair_read> v2(threads);
+        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];
+            v2[ii] = new pair_read(*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]); 
         }

diff --git a/src/reads.cpp b/src/reads.cpp
@@ -34,6 +34,7 @@ using namespace std;
 
         void  single_read::set_inputs(istream &is) {
             file1.rdbuf(is.rdbuf());
+           //is.rdbuf(file1.rdbuf());
         }
 
         void single_read::set_outputs(ostream& bad_out_file, ostream& single_out_file, ostream& good_out_file) {

diff --git a/src/test_F.fastq b/src/test_F.fastq
@@ -1,32 +1,32 @@
-@seq1
+@seq1_F
 CCCCCCCCCCCCCCC
-+seq1
++seq1_F
 ABCABCABCABCABC
-@seq2
+@seq2_F
 CGATCNATC
-+seq2
++seq2_F
 ABCABCABC
-@seq3
+@seq3_F
 TTNTTTT
-+seq3
++seq3_F
 ABCABCA
-@seq4
+@seq4_F
 CGATCAATC
-+seq4
++seq4_F
 ABCABCABC
-@seq5
+@seq5_F
 GUTTACTTGACCC
-+seq5
++seq5_F
 ABCABCABCABCC
-@seq6
+@seq6_F
 CCCCCCCCCCCCCCC
-+seq6
++seq6_F
 ABCABCABCABCABC
-@seq7
+@seq7_F
 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-+seq7
++seq7_F
 ABCABCABCABCABABCABCABCABCABABCABCABCABCABABCABCABCABC9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
-@seq8
+@seq8_F
 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-+seq8
++seq8_F
 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
diff --git a/src/test_R.fastq b/src/test_R.fastq
@@ -1,32 +1,32 @@
-@seq1
+@seq1_R
 CCCCCCCCCCCCCCC
-+seq1
++seq1_R
 ABCABCABCABCABC
-@seq2
+@seq2_R
 CGATCNATC
-+seq2
++seq2_R
 ABCABCABC
-@seq3
+@seq3_R
 TTTTTTT
-+seq3
++seq3_R
 ABCABCA
-@seq4
+@seq4_R
 CNGATCNNNATCTTTTTTTTT
-+seq4
++seq4_R
 ABCABCABCABC()()()))(
-@seq5
+@seq5_R
 GUTTACTTGACCC
-+seq5
++seq5_R
 ABCABCABCABCC
-@seq6
+@seq6_R
 CCCCCCCCCCCCCC
-+seq6
++seq6_R
 ABCABCABCABCAB
-@seq7
+@seq7_R
 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-+seq7
++seq7_R
 99999999999999999999999999999999999999999999999999999999999999999999999BCABCABCABCABABCABCABCABCABABCABCABCABCABABCABCABCABCABABCABCABCABCABABCABCABCABCABABCABCABC
-@seq8
+@seq8_R
 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGaAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-+seq8
++seq8_R
 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999