From b42f49ec73a6f5c4953bf61233f400408b5bf87c Mon Sep 17 00:00:00 2001 From: Adrian Cantu Date: Sun, 4 Mar 2018 04:26:07 +0000 Subject: [PATCH] fix horrible bug, bump version number --- Makefile.in | 6 ++++++ configure.ac | 2 +- src/Makefile.in | 2 +- src/main.cpp | 22 ++++++---------------- src/reads.cpp | 1 + src/test_F.fastq | 32 ++++++++++++++++---------------- src/test_R.fastq | 32 ++++++++++++++++---------------- 7 files changed, 47 insertions(+), 50 deletions(-) diff --git a/Makefile.in b/Makefile.in index 9676e9d..52889ef 100644 --- 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 index 81cfe3d..a0bb2b2 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], [0.9], [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 index 3d1d9cd..2d2ed86 100644 --- 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 index 8497965..c74b2f2 100644 --- 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 v2(threads); + vector v2(threads); vector tthreads(threads); vector ttt2(threads); for (ii=0 ; 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 index e22206a..960e656 100644 --- 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 index 940115d..3dd1f79 100644 --- 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 index 89c4454..56046c6 100644 --- 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