Split into files ; define modes & associated conda envs ; run on a single...

Split into files ; define modes & associated conda envs ; run on a single chromosome by keeping full initial BAM  ; functionnal until strandphaser

src/main.cpp

+/*
+ Copyright (C) 2017 Sascha Meiers
+ Distributed under the MIT software license, see the accompanying
+ file LICENSE.md or http://www.opensource.org/licenses/mit-license.php.
+ */
+
+#include <iostream>
+
+#include <htslib/sam.h>
+#include "version.hpp"
+#include "count.hpp"
+#include "segmentation.hpp"
+#include "simulate.hpp"
+#include "calc_bins.hpp"
+#include "sces.hpp"
+#include "ploidy.hpp"
+
+int main(int argc, char **argv)
+{
+
+    if (argc >= 2 && std::string(argv[1]) == "count") {
+        return main_count(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "simulate") {
+        return main_simulate(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "segment") {
+        return main_segment(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "makebins") {
+        return main_calc_bins(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "states") {
+        return main_strand_states(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "hmm") {
+        return main_hmm(argc-1, argv+1);
+
+    } else if (argc >= 2 && std::string(argv[1]) == "--version") {
+        std::cout << "Mosaicatcher " << STRINGIFYMACRO(MOSAIC_VERSION_MAJOR) ;
+        std::cout << "." << STRINGIFYMACRO(MOSAIC_VERSION_MINOR) << " (";
+		std::cout << STRINGIFYMACRO(MOSAIC_GIT_COMMIT_HASH) << "-";
+        std::cout << STRINGIFYMACRO(MOSAIC_GIT_BRANCH) << ")" << std::endl;
+        std::cout << "htslib " << STRINGIFYMACRO(HTSLIB_VERSION) << std::endl;
+        std::cout << "boost version " << STRINGIFYMACRO(BOOST_VERSION) << std::endl;
+        return 0;
+
+    } else {
+        std::cout << std::endl;
+        std::cout << "Mosaicatcher " << STRINGIFYMACRO(MOSAIC_VERSION_MAJOR);
+        std::cout << "." << STRINGIFYMACRO(MOSAIC_VERSION_MINOR) << std::endl;
+        std::cout << std::endl;
+        std::cout << "Usage:   " << argv[0] << " [--version] [--help] <command> [options]" << std::endl << std::endl;
+        std::cout << "Commands:" << std::endl;
+        std::cout << "    count       Count binned reads in Strand-seq cells" << std::endl;
+        //std::cout << "    hmm         Count binned reads in arbitrary ploidy" << std::endl;
+        std::cout << "    segment     Find a segmentation across binned counts" << std::endl;
+        std::cout << "    simulate    Simulate Strand-seq data" << std::endl;
+        std::cout << "    makebins    Create variable-width bins based on real data" << std::endl;
+        std::cout << "    states      Determine strand states including SCEs" << std::endl;
+        std::cout << std::endl;
+
+        if (argc >= 2 && std::string(argv[1]) == "--help") {
+            std::cout << "Mosaicatcher calls structural variants (SVs) in Strand-seq data." << std::endl;
+            std::cout << "It is currently under development." << std::endl;
+            std::cout << "This software comes with absolutely no warranty." << std::endl << std::endl;
+            return 0;
+        }
+    }
+    return 1;
+}
+

src/program_options.hpp

+/*
+ Copyright (C) 2017 Sascha Meiers
+ Distributed under the MIT software license, see the accompanying
+ file LICENSE.md or http://www.opensource.org/licenses/mit-license.php.
+ */
+
+#ifndef program_options_h
+#define program_options_h
+
+#include <fstream>
+#include <boost/program_options/errors.hpp>
+
+auto in_range = [](int min, int max, char const * const opt_name)
+{
+    using boost::program_options::validation_error;
+    // returns another lambda function
+    return [opt_name, min, max](unsigned short v)
+    {
+        if(v < min || v > max){
+            throw validation_error(validation_error::invalid_option_value,
+                                   opt_name,
+                                   std::to_string(v));
+        }
+    };
+};
+
+
+// opt::value<unsigned short>()->default_value(5)->notifier(in(0, 10, "my_opt"));
+
+template <typename TString>
+bool file_exists(TString const & fileName)
+{
+    std::ifstream infile(fileName);
+    return infile.good();
+}
+
+
+
+
+#endif

src/version.hpp.in

+#ifndef version_hpp
+#define version_hpp
+
+#define STRINGIFY(x) #x
+#define STRINGIFYMACRO(y) STRINGIFY(y)
+
+#define MOSAIC_VERSION_MAJOR @MOSAIC_VERSION_MAJOR@
+#define MOSAIC_VERSION_MINOR @MOSAIC_VERSION_MINOR@
+#define HTSLIB_VERSION @HTSLIB_VERSION@
+#define BOOST_VERSION @Boost_VERSION@
+#define MOSAIC_GIT_COMMIT_HASH @GIT_COMMIT_HASH@
+#define MOSAIC_GIT_BRANCH @GIT_BRANCH@
+
+#endif /* version_hpp */

workflow/.conda/environments.txt

+
+/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/41c386e2197cbc9beb30ca282d0aa485

workflow/envs/imagemagick.yaml

+name: plots
+channels:
+  - conda-forge
+dependencies:
+  - imagemagick