Merge branch 'release-v0.2.1'

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.10)
-project(kseq++ VERSION 0.2.0 LANGUAGES CXX)
+project(kseq++ VERSION 0.2.1 LANGUAGES CXX)
 
 # Finding dependencies.
 find_package(ZLIB REQUIRED)

README.md

@@ -181,6 +181,31 @@ There is no need to write `kend` to the stream if using `SeqStreamOut`.
 
 ---
 
+### Formatting
+
+The default behaviour is to write a record in FASTQ format if it has quality
+information. Otherwise, i.e. when the quality string is empty, the record will
+be written in FASTA format. So, the output might be a mixture of FASTQ and FASTA
+records. However, the output format can be forced by using `format::fasta` and
+`format::fastq` modifiers. For example:
+
+```c++
+out << format::fasta << fastq_record;
+out << another_record; // all other calls after this will also be in FASTA format.
+```
+
+will write a FASTQ record in FASTA format. These modifiers affect all writes
+after them until another modifier is used. The `format::mix` modifier reverts
+the behaviour to default.
+
+---
+**NOTE**
+
+Writing a FASTA record in FASTQ format throws an exception unless the record is
+empty (a record with empty sequence and quality string).
+
+---
+
 Benchmark
 ---------
 ### Datasets
@@ -201,7 +226,7 @@ For this benchmark, I re-used sequence files from SeqKit benchmark:
 - OS: Debian GNU/Linux 9.4 (stretch), Linux 4.9.91-1-amd64-smp
 - Compiler: GCC 6.3.0, compiled with optimisation level 3 (`-O3`)
 
-### Result
+### Result (for kseq++ v0.1.4)
 
 #### Reading all records
 

include/kseq++/config.hpp.in

@@ -19,9 +19,9 @@
 #ifndef KSEQPP_CONFIG_HPP__
 #define KSEQPP_CONFIG_HPP__
 
-#cmakedefine PROJECT_VERSION "@PROJECT_VERSION@"
-#cmakedefine PROJECT_VERSION_MAJOR "@PROJECT_VERSION_MAJOR@"
-#cmakedefine PROJECT_VERSION_MINOR "@PROJECT_VERSION_MINOR@"
-#cmakedefine PROJECT_VERSION_PATCH "@PROJECT_VERSION_PATCH@"
+#define KSEQPP_PROJECT_VERSION "@PROJECT_VERSION@"
+#define KSEQPP_PROJECT_VERSION_MAJOR "@PROJECT_VERSION_MAJOR@"
+#define KSEQPP_PROJECT_VERSION_MINOR "@PROJECT_VERSION_MINOR@"
+#define KSEQPP_PROJECT_VERSION_PATCH "@PROJECT_VERSION_PATCH@"
 
 #endif /* --- #ifndef KSEQPP_CONFIG_HPP__ --- */