diff options
Diffstat (limited to 'bt2_inspect.cpp')
| -rw-r--r-- | bt2_inspect.cpp | 22 |
1 files changed, 11 insertions, 11 deletions
diff --git a/bt2_inspect.cpp b/bt2_inspect.cpp index d16a46c..92302c8 100644 --- a/bt2_inspect.cpp +++ b/bt2_inspect.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead <blangmea@jhsph.edu> + * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu> * * This file is part of Bowtie 2. * @@ -62,7 +62,7 @@ static struct option long_options[] = { * Print a summary usage message to the provided output stream. */ static void printUsage(ostream& out) { - out << "Bowtie 2 version " << string(BOWTIE2_VERSION) << " by Ben Langmead (blangmea@jhsph.edu)" << endl; + out << "Bowtie 2 version " << string(BOWTIE2_VERSION).c_str() << " by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)" << endl; out << "Usage: bowtie2-inspect [options]* <bt2_base>" << endl << " <bt2_base> bt2 filename minus trailing .1.bt2/.2.bt2" << endl @@ -142,19 +142,19 @@ static void print_fasta_record( const string& seq) { fout << ">"; - fout << defline << endl; + fout << defline.c_str() << endl; if(across > 0) { size_t i = 0; while (i + across < seq.length()) { - fout << seq.substr(i, across) << endl; + fout << seq.substr(i, across).c_str() << endl; i += across; } if (i < seq.length()) - fout << seq.substr(i) << endl; + fout << seq.substr(i).c_str() << endl; } else { - fout << seq << endl; + fout << seq.c_str() << endl; } } @@ -174,7 +174,7 @@ static void print_ref_sequence( int myacross = across > 0 ? across : 60; size_t incr = myacross * 1000; uint32_t *buf = new uint32_t[(incr + 128)/4]; - fout << ">" << name << "\n"; + fout << ">" << name.c_str() << "\n"; ASSERT_ONLY(SStringExpandable<uint32_t> destU32); for(size_t i = 0; i < len; i += incr) { size_t amt = min(incr, len-i); @@ -299,7 +299,7 @@ static void print_index_sequence_names(const string& fname, ostream& fout) EList<string> p_refnames; readEbwtRefnames(fname, p_refnames); for(size_t i = 0; i < p_refnames.size(); i++) { - cout << p_refnames[i] << endl; + cout << p_refnames[i].c_str() << endl; } } @@ -343,7 +343,7 @@ static void print_index_summary( assert_eq(ebwt.nPat(), p_refnames.size()); for(size_t i = 0; i < p_refnames.size(); i++) { cout << "Sequence-" << (i+1) - << '\t' << p_refnames[i] + << '\t' << p_refnames[i].c_str() << '\t' << (ebwt.plen()[i] + (color ? 1 : 0)) << endl; } @@ -451,8 +451,8 @@ int main(int argc, char **argv) { // Optionally summarize if(verbose) { - cout << "Input ebwt file: \"" << ebwtFile << "\"" << endl; - cout << "Output file: \"" << outfile << "\"" << endl; + cout << "Input ebwt file: \"" << ebwtFile.c_str() << "\"" << endl; + cout << "Output file: \"" << outfile.c_str() << "\"" << endl; cout << "Local endianness: " << (currentlyBigEndian()? "big":"little") << endl; #ifdef NDEBUG cout << "Assertions: disabled" << endl; |