Merge branch 'release-v1.1.2'

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.10)
-project(kseq++ VERSION 1.1.1 LANGUAGES CXX)
+project(kseq++ VERSION 1.1.2 LANGUAGES CXX)
 
 #options
 option(BUILD_TESTING "Build test programs" OFF) # ignored by default

README.md

@@ -1,6 +1,6 @@
 kseq++
 ======
-kseq++ is a C++11 re-implementation of [kseq](https://github.com/attractivechaos/klib/blob/master/kseq.h)
+kseq++ is a C++11 re-implementation of [kseq](https://github.com/lh3/seqtk/blob/master/kseq.h)[.h](https://github.com/attractivechaos/klib/blob/master/kseq.h)
 by [Heng Li](https://github.com/lh3). The goal for re-implementation of `kseq` is
 providing better API and resource management while preserving its flexibility
 and performance. Like original kseq, this parser is based on generic stream
@@ -373,7 +373,7 @@ For this benchmark, I re-used sequence files from SeqKit benchmark:
 
 \* storing all records in `std::vector`.
 
-\*\* storing all records in `seqan::StringSet< seqan::CharString >`.
+\*\* storing all records in `seqan2::StringSet< seqan2::CharString >`.
 
 #### Writing all records
 

benchmark/kseq++_bench.cpp

@@ -121,10 +121,10 @@ main( int argc, char* argv[] )
  close( fd );
  }
  {
- seqan::SeqFileIn f;
- seqan::CharString name;
- seqan::CharString str;
- seqan::CharString qual;
+ seqan2::SeqFileIn f;
+ seqan2::CharString name;
+ seqan2::CharString str;
+ seqan2::CharString qual;
  open( f, argv[1] );
  t = clock();
  while ( !atEnd( f ) ) readRecord( name, str, qual, f );
@@ -201,11 +201,11 @@ main( int argc, char* argv[] )
  std::cerr << "[kseq++/read_all] " << std::setprecision(3) << d << " sec" << std::endl;
  gzclose( fp );
  }
- seqan::StringSet< seqan::CharString > names;
- seqan::StringSet< seqan::CharString > seqs;
- seqan::StringSet< seqan::CharString > quals;
+ seqan2::StringSet< seqan2::CharString > names;
+ seqan2::StringSet< seqan2::CharString > seqs;
+ seqan2::StringSet< seqan2::CharString > quals;
  {
- seqan::SeqFileIn i_file;
+ seqan2::SeqFileIn i_file;
  open( i_file, argv[1] );
  t = clock();
  readRecords( names, seqs, quals, i_file );
@@ -215,8 +215,8 @@ main( int argc, char* argv[] )
  }
  std::cerr << "=== WRITE TESTS ===" << std::endl;
  {
- seqan::SeqFileOut o_file;
- open( o_file, argv[2], seqan::FileOpenMode::OPEN_WRONLY );
+ seqan2::SeqFileOut o_file;
+ open( o_file, argv[2], seqan2::FileOpenMode::OPEN_WRONLY );
  t = clock();
  writeRecords( o_file, names, seqs, quals );
  close( o_file );

include/kseq++/kseq++.hpp

@@ -428,7 +428,7 @@ namespace klibpp {
  inline void
  worker_start( )
  {
- this->worker = std::thread( &KStream::writer, this );
+ this->worker = std::thread( [this](){ this->writer(); } );
  }
  };