docu update for release 2023_06

README.md

@@ -15,7 +15,7 @@ Alternatively, *ngs-bits* can be built from sources. Use git to clone the most r
 
     > git clone --recursive https://github.com/imgag/ngs-bits.git
 	> cd ngs-bits
-	> git checkout 2023_03
+	> git checkout 2023_06
 	> git submodule update --recursive --init
 
 Depending on your operating system, building instructions vary slightly:
@@ -176,12 +176,20 @@ Changes of master since last release:
 * none so far
 
 
-Changes in release 2023_03:
+Changes in release 2023_06:
 
-* NGSDImportEnsembl: Update to support Ensembl 109
-* RnaQC: Added target region to support targeted transcriptomics experiments
+* new tools: GenesToTranscripts, NGSDImportSampleQC, GenesToTranscripts, TranscriptsToBed, NGSDExportGff.
+* BamToFastq: Added support for single-end.
+* MappingQC: Added support for read QC.
+* VcfToBedpe: Added support for Sniffles, cuteSV and dipdiff.
+* FastqExtract: Added parameter 'long_read'.
+* ReadQC: Added parameter 'long_read'.
+* NGSDExportSamples: added parameters 'run_after' and 'no_normal'.
+* NGSDExportAnnotationData: speed-up by parallelization.
 * NGSD
-	* Added `ncbi_id` to `gene` table
-	* Added `folder_override`to `processed_sample` table
+	* Added 'side' enum to 'sequencing_run' table
+	* Added 'germline_mosaic' to 'variant' table
+	* Added 'hpo_obsolete' table with obsolete HPO terms
+	* Refactoring of 'expression' and 'gene_expression' tables to speed-up queries
 
 For older changes see [releases](https://github.com/imgag/ngs-bits/releases).

doc/tools/NGSDExportGff.md

@@ -1,10 +1,10 @@
 ### NGSDExportGff tool help
-	NGSDExportGff (2023_03-107-g2a1d2478)
+	NGSDExportGff (2023_03-106-gdd541c02)
 
 	Writes all transcripts and exons of all genes to a gff3 file.
 
 	Mandatory parameters:
-	  -out <file>  The output file directory.
+	  -out <file>  The output GFF file.
 
 	Optional parameters:
 	  -test        Uses the test database instead of on the production database.
@@ -17,6 +17,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDExportGff changelog
-	NGSDExportGff 2023_03-107-g2a1d2478
+	NGSDExportGff 2023_03-106-gdd541c02
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

src/NGSDExportGff/main.cpp

@@ -18,7 +18,7 @@ class ConcreteTool
 	virtual void setup()
 	{
         setDescription("Writes all transcripts and exons of all genes to a gff3 file.");
-        addOutfile("out", "The output file directory.", false);
+		addOutfile("out", "The output GFF file.", false);
         addFlag("test", "Uses the test database instead of on the production database.");
 	}