From ef85da16bf72901eb67771bb366299bbf85b1453 Mon Sep 17 00:00:00 2001 From: grenkoca Date: Tue, 13 Jul 2021 07:50:01 -0400 Subject: [PATCH 1/3] Closed parenthesis on line 52 in Makefile --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index bb4952b..1700f61 100644 --- a/Makefile +++ b/Makefile @@ -49,7 +49,7 @@ ifdef BOOST_ROOT LDFLAGS += -L$(BOOST_ROOT)/lib else ifdef BOOST_INCLUDE - CPPFLAGS += -I$(BOOST_INCLUDE + CPPFLAGS += -I$(BOOST_INCLUDE) endif ifdef BOOST_LIB From 4e227ee681c076ede8067e60e330a69d1eba105c Mon Sep 17 00:00:00 2001 From: grenkoca Date: Tue, 13 Jul 2021 08:34:56 -0400 Subject: [PATCH 2/3] declared substitution as separate variable to avoid erro with mistmatched types --- src/cta.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/cta.cpp b/src/cta.cpp index cefd9da..933103c 100644 --- a/src/cta.cpp +++ b/src/cta.cpp @@ -84,8 +84,9 @@ bool is_gzipped_filename(const std::string& filename) { } std::regex fastq_filename_re("\\.(fq|fastq)?(\\.gz)?$"); -std::string make_trimmed_filename(const std::string& filename) { - return std::regex_replace(filename, fastq_filename_re, ".trimmed.fq.gz"); +std::string make_trimmed_filename(const std::string filename) { + std::string substitution = ".trimmed.fq.gz"; + return std::regex_replace(filename, fastq_filename_re, substitution); } std::map nucleotide_complements = { From 288d1ce1bd7265192cc02627a3b268fbe4c27769 Mon Sep 17 00:00:00 2001 From: Caleb Grenko <33234745+grenkoca@users.noreply.github.com> Date: Tue, 13 Jul 2021 08:38:34 -0400 Subject: [PATCH 3/3] Create README.md Started readme: to be filled in by someone who actually knows what they're doing --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..a7a95b6 --- /dev/null +++ b/README.md @@ -0,0 +1,7 @@ +# cta +C++ implementation of Buenrostro adapter trimming + +Installation: +`make CPPFLAGS="-I/path/to/boost/include"` + +Where `/path/to/boost/include` is the folder containing header files for [Boost](https://www.boost.org/) (can be installed with `conda install -c conda-forge boost`, placing it in `~/conda/env/your_env/include`)