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|
--- a/src/lambda.cpp
+++ b/src/lambda.cpp
@@ -33,7 +33,7 @@
#include "holders.hpp"
#include "lambda.hpp"
-using namespace seqan;
+using namespace seqan2;
// inline BlastFormatFile
// _fileType(LambdaOptions const & options)
@@ -116,15 +116,15 @@
int main(int argc, char const ** argv)
{
// Parse the command line.
- seqan::ArgumentParser parser;
+ seqan2::ArgumentParser parser;
LambdaOptions options;
- seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+ seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
- if (res != seqan::ArgumentParser::PARSE_OK)
- return res == seqan::ArgumentParser::PARSE_ERROR;
+ if (res != seqan2::ArgumentParser::PARSE_OK)
+ return res == seqan2::ArgumentParser::PARSE_ERROR;
if (std::string(CMAKE_BUILD_TYPE) != "Release")
std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
--- a/src/lambda.hpp
+++ b/src/lambda.hpp
@@ -42,7 +42,7 @@
#include "match.hpp"
#include "misc.hpp"
-using namespace seqan;
+using namespace seqan2;
// ============================================================================
// Forwards
--- a/src/lambda_indexer.cpp
+++ b/src/lambda_indexer.cpp
@@ -30,7 +30,7 @@
#include "lambda_indexer.hpp"
-using namespace seqan;
+using namespace seqan2;
// ==========================================================================
// Forwards
@@ -72,15 +72,15 @@
int main(int argc, char const ** argv)
{
// Parse the command line.
- seqan::ArgumentParser parser;
+ seqan2::ArgumentParser parser;
LambdaIndexerOptions options;
- seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+ seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
- if (res != seqan::ArgumentParser::PARSE_OK)
- return res == seqan::ArgumentParser::PARSE_ERROR;
+ if (res != seqan2::ArgumentParser::PARSE_OK)
+ return res == seqan2::ArgumentParser::PARSE_ERROR;
if (std::string(CMAKE_BUILD_TYPE) != "Release")
std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
--- a/src/lambda_indexer.hpp
+++ b/src/lambda_indexer.hpp
@@ -37,7 +37,7 @@
#include "radix_inplace.h"
#include "lambda_indexer_misc.hpp"
-using namespace seqan;
+using namespace seqan2;
// --------------------------------------------------------------------------
// Function loadSubj()
--- a/src/match.hpp
+++ b/src/match.hpp
@@ -28,7 +28,7 @@
#include "options.hpp"
-using namespace seqan;
+using namespace seqan2;
//-----------------------------------------------------------------------------
// Finder
--- a/src/misc.hpp
+++ b/src/misc.hpp
@@ -33,7 +33,7 @@
#include "options.hpp"
-using namespace seqan;
+using namespace seqan2;
// ============================================================================
// Forwards
@@ -78,8 +78,8 @@
inline std::basic_ostream<char> &
operator<<(std::basic_ostream<char> & out,
const Iter<const String<SimpleType<unsigned char,TAlph>,
- seqan::Packed<> >,
- seqan::Packed<> > it)
+ seqan2::Packed<> >,
+ seqan2::Packed<> > it)
{
out << *it;
return out;
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -111,7 +111,7 @@
}
-using namespace seqan;
+using namespace seqan2;
// Index Specs
struct LambdaFMIndexConfig
--- a/src/output.hpp
+++ b/src/output.hpp
@@ -25,7 +25,7 @@
#include <seqan/blast.h>
#include <seqan/bam_io.h>
-using namespace seqan;
+using namespace seqan2;
template <typename TVoidSpec = void>
struct SamBamExtraTags
@@ -313,7 +313,7 @@
} else // SAM or BAM
{
open(globalHolder.outfileBam, toCString(options.output));
- auto & context = seqan::context(globalHolder.outfileBam);
+ auto & context = seqan2::context(globalHolder.outfileBam);
auto & subjSeqLengths = contigLengths(context);
auto & subjIds = contigNames(context);
@@ -407,7 +407,7 @@
{
// we only write the header records that we actually created ourselves
for (unsigned i = 0; i < length(header); ++i)
- write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
+ write(globalHolder.outfileBam.iter, header[i], seqan2::context(globalHolder.outfileBam), Sam());
}
else
{
|
