switch cerr

src/annotate.h

@@ -18,7 +18,6 @@
 #include <boost/iostreams/filter/gzip.hpp>
 #include <boost/icl/split_interval_map.hpp>
 #include <boost/filesystem.hpp>
-#include <boost/progress.hpp>
 
 #include "parsedb.h"
 #include "query.h"
@@ -122,7 +121,7 @@ namespace sansa
 
     // End
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Done." << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] Done." << std::endl;
     return 0;
   }
 
@@ -179,8 +178,9 @@ namespace sansa
 
     // Check command line arguments
     if ((vm.count("help")) || (!vm.count("input-file"))) {
-      std::cout << "Usage: sansa " << argv[0] << " [OPTIONS] input.bcf" << std::endl;
-      std::cout << visible_options << "\n";
+      std::cerr << std::endl;
+      std::cerr << "Usage: sansa " << argv[0] << " [OPTIONS] input.bcf" << std::endl;
+      std::cerr << visible_options << "\n";
       return -1;
     }
 
@@ -223,10 +223,10 @@ namespace sansa
 
     // Show cmd
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] ";
-    std::cout << "sansa ";
-    for(int i=0; i<argc; ++i) { std::cout << argv[i] << ' '; }
-    std::cout << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] ";
+    std::cerr << "sansa ";
+    for(int i=0; i<argc; ++i) { std::cerr << argv[i] << ' '; }
+    std::cerr << std::endl;
 
     return runAnnotate(c);
   }

src/bed.h

@@ -22,7 +22,7 @@ namespace sansa
   inline int32_t
   parseBEDAll(TConfig const& c, TGenomicRegions& overlappingRegions, TGeneIds& geneIds, TProteinCoding& pCoding) {
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "BED feature parsing" << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] " << "BED feature parsing" << std::endl;
 
     // Check gzip
     if (!is_gz(c.gtfFile)) {

src/gff3.h

@@ -107,7 +107,7 @@ namespace sansa
   inline int32_t
   parseGFF3All(TConfig const& c, TGenomicRegions& overlappingRegions, TGeneIds& geneIds, TProteinCoding& pCoding) {
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "GFF3 feature parsing" << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] " << "GFF3 feature parsing" << std::endl;
 
     // Check gzip
     if (!is_gz(c.gtfFile)) {

src/gtf.h

@@ -22,7 +22,7 @@ namespace sansa
   inline int32_t
   parseGTFAll(TConfig const& c, TGenomicRegions& overlappingRegions, TGeneIds& geneIds, TProteinCoding& pCoding) {
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "GTF feature parsing" << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] " << "GTF feature parsing" << std::endl;
 
     // Check gzip
     if (!is_gz(c.gtfFile)) {

src/parsedb.h

@@ -21,7 +21,7 @@ namespace sansa
   parseDB(TConfig& c, TSV& svs) {
 
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Parse SV annotation database" << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] Parse SV annotation database" << std::endl;
 
     // Load bcf file
     htsFile* ifile = bcf_open(c.db.string().c_str(), "r");
@@ -115,7 +115,7 @@ namespace sansa
 
     // Statistics
     now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Parsed " << svid << " out of " << sitecount << " VCF/BCF records." << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] Parsed " << svid << " out of " << sitecount << " VCF/BCF records." << std::endl;
 
     // Close output VCF
     bcf_hdr_destroy(hdr_out);

src/query.h

@@ -91,7 +91,7 @@ namespace sansa
   query(TConfig& c, TSV& svs, TGenomicRegions& gRegions, TGeneIds& geneIds) {
 
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Query input SVs" << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] Query input SVs" << std::endl;
 
     // Load bcf file
     htsFile* ifile = bcf_open(c.infile.string().c_str(), "r");
@@ -259,7 +259,7 @@ namespace sansa
 
     // Statistics
     now = boost::posix_time::second_clock::local_time();
-    std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Parsed " << parsedSV << " out of " << sitecount << " VCF/BCF records." << std::endl;
+    std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] Parsed " << parsedSV << " out of " << sitecount << " VCF/BCF records." << std::endl;
 
     // Close file handles
     dataOut.pop();

src/version.h

@@ -10,47 +10,47 @@ namespace sansa
   inline 
     void printTitle(std::string const& title) 
     {
-      std::cout << "**********************************************************************" << std::endl;
-      std::cout << "Program: Sansa" << std::endl;
-      std::cout << "This is free software, and you are welcome to redistribute it under" << std::endl;
-      std::cout << "certain conditions (BSD License); for license details use '-l'." << std::endl;
-      std::cout << "This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'." << std::endl;
-      std::cout <<  std::endl;
-      std::cout <<  title << " (Version: " << sansaVersionNumber << ")" << std::endl;
-      std::cout << "Contact: Tobias Rausch ([email protected])" << std::endl;
-      std::cout << "**********************************************************************" << std::endl;
-      std::cout << std::endl;
+      std::cerr << "**********************************************************************" << std::endl;
+      std::cerr << "Program: Sansa" << std::endl;
+      std::cerr << "This is free software, and you are welcome to redistribute it under" << std::endl;
+      std::cerr << "certain conditions (BSD License); for license details use '-l'." << std::endl;
+      std::cerr << "This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'." << std::endl;
+      std::cerr <<  std::endl;
+      std::cerr <<  title << " (Version: " << sansaVersionNumber << ")" << std::endl;
+      std::cerr << "Contact: Tobias Rausch ([email protected])" << std::endl;
+      std::cerr << "**********************************************************************" << std::endl;
+      std::cerr << std::endl;
     }
 
   inline
     void displayWarranty()
     {
-      std::cout << "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ";
-      std::cout << "THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR ";
-      std::cout << "CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, ";
-      std::cout << "PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, ";
-      std::cout << "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ";
-      std::cout << "ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." << std::endl;
-      std::cout << std::endl;
+      std::cerr << "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ";
+      std::cerr << "THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR ";
+      std::cerr << "CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, ";
+      std::cerr << "PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, ";
+      std::cerr << "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ";
+      std::cerr << "ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." << std::endl;
+      std::cerr << std::endl;
     }
 
   inline void
   bsd() {
-    std::cout << "Copyright (c) 2019 Sansa Project Authors (see AUTHORS file for details)." << std::endl;
-    std::cout << "All rights reserved." << std::endl;
-    std::cout << std::endl;
-    std::cout << "Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:" << std::endl;
-    std::cout << "    1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer." << std::endl;
-    std::cout << "    2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution." << std::endl;
-    std::cout << "    3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission." << std::endl;
-    std::cout << std::endl;
-    std::cout << "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ";
-    std::cout << "THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR ";
-    std::cout << "CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, ";
-    std::cout << "PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, ";
-    std::cout << "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ";
-    std::cout << "ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." << std::endl;
-    std::cout << std::endl;
+    std::cerr << "Copyright (c) 2019 Sansa Project Authors (see AUTHORS file for details)." << std::endl;
+    std::cerr << "All rights reserved." << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:" << std::endl;
+    std::cerr << "    1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer." << std::endl;
+    std::cerr << "    2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution." << std::endl;
+    std::cerr << "    3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission." << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ";
+    std::cerr << "THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR ";
+    std::cerr << "CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, ";
+    std::cerr << "PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, ";
+    std::cerr << "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ";
+    std::cerr << "ADVISED OF THE POSSIBILITY OF SUCH DAMAGE." << std::endl;
+    std::cerr << std::endl;
   }
 
 }