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Closed parenthesis on line 52 in Makefile #5

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Closed parenthesis on line 52 in Makefile #5

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ef85da1
Closed parenthesis on line 52 in Makefile
grenkoca Jul 13, 2021
4e227ee
declared substitution as separate variable to avoid erro with mistmat…
grenkoca Jul 13, 2021
288d1ce
Create README.md
grenkoca Jul 13, 2021
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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7 changes: 7 additions & 0 deletions README.md
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@@ -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`)
5 changes: 3 additions & 2 deletions src/cta.cpp
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Expand Up @@ -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<char, char> nucleotide_complements = {
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