Commit 24d0de86 authored by Dr. Carsten Kemena's avatar Dr. Carsten Kemena
Browse files

small fixes

parent 64d93a63
Pipeline #64074 failed with stage
in 1 second
......@@ -4,6 +4,7 @@ test library:
- master
script:
- git submodule init
- git submodule foreach git pull origin master
- git submodule update
- mkdir build
- cd build
......
[![coverage report](https://ebbgit.uni-muenster.de/domainWorld/RADIANT/badges/master/coverage.svg)](https://ebbgit.uni-muenster.de/domainWorld/RADIANT/commits/master)
RApid DomaIn ANnoTation
RApid DomaIn ANnoTation 0.9.3-beta
====
This program allows to generate a fast domain annotation of protein fasta sequences.
Requirements
------------
We try to keep the dependencies as little as possible. Current dependencies are:
- BioSeqDataLib (https://ebbgit.uni-muenster.de/domainWorld/BioSeqDataLib) (can be added via git submodule)
- boost (http://www.boost.org) (>= 1.56)
- gcc (>=5.0)
- BioSeqDataLib (https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib) (included as git submodule)
- boost (http://www.boost.org)
- compiler with c++17 and OpenMP support
Download
--------
```bash
git clone https://zivgitlab.uni-muenster.de/domain-world/RADIANT.git
cd RADIANT
git submodule init
git submodule update
```
Installation
------------
Change into the RADIANT directory and run the following commands:
```bash
mkdir build && cd build
cmake ..
make
```
Usage
-----
Please take a look at the file UserManual.pdf included in this program to get a detailed overview on how to install and run the program.
Problems, Bugs & Suggestions
----------------------------
We try our best not to have any bugs in the code, unfortunately some will
probably avoid us and will not be detected. If you encounter one, please be so kind and let us know. The
easiest way would be to use write an email to domainworld[ at ]uni-muenster.de.
Subproject commit 71e7fcd4d592ba6d21d56e1bb89470c21cb72dc6
Subproject commit 3c5e993380e23abb5b784ba37973b869a762db24
......@@ -29,28 +29,6 @@ write2file(std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short >
}
}
fout.close();
/*
std::ofstream fout(outDir, std::ios::out | std::ios::binary);
std::ofstream fout_index(outDir+".index", std::ios::out | std::ios::binary);
size_t val= database.size();
fout.write((char*)&val, sizeof(size_t));
for (auto it=database.begin(); it!=database.end(); ++it)
{
size_t val= it->second.size();
fout_index.write((char*)&it->first, sizeof(PrefixType));
auto x = fout.tellp();
fout_index.write((char*)&x, sizeof(std::streampos));
fout.write((char*)&val, sizeof(size_t));
for (auto it2=it->second.begin(); it2!=it->second.end(); ++it2)
{
fout.write((char*)&(it2->first), sizeof(CodedSuffix));
fout.write((char*)&(it2->second), sizeof(unsigned short));
}
}
fout.close();
fout_index.close();*/
}
......@@ -67,7 +45,7 @@ main(int argc, char const *argv[])
general.add_options()
("help,h", "Produces this help message")
("in,i", po::value<fs::path>(&inFile)->required()->value_name("FILE"), "The input file")
("out,o", po::value<fs::path>(&outDir)->required()->value_name("DIRECTORY"), "The prefix for the output files")
("out,o", po::value<fs::path>(&outDir)->required()->value_name("DIRECTORY"), "The directory for the output files")
("nThreads,t", po::value<size_t>(&nThreads)->default_value(1), "The number of threads to use")
;
......
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