Merge branch 'master' of https://github.com/imgag/ngs-bits

doc/tools/ExportcBioportal.md

@@ -1,5 +1,5 @@
 ### ExportcBioportal tool help
-	ExportcBioportal (2023_06-98-g044e3ed3)
+	ExportcBioportal (2023_09-38-ga9141a54)
 
 	Converts a FASTQ file to FASTA format.
 
@@ -12,6 +12,8 @@
 	Optional parameters:
 	  -test                  Uses the test database instead of on the production database.
 	                         Default value: 'false'
+	  -debug                 Provide additional debug output on stdout.
+	                         Default value: 'false'
 
 	Special parameters:
 	  --help                 Shows this help and exits.
@@ -20,6 +22,6 @@
 	  --tdx                  Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### ExportcBioportal changelog
-	ExportcBioportal 2023_06-98-g044e3ed3
+	ExportcBioportal 2023_09-38-ga9141a54
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/FastqCheckUMI.md

@@ -0,0 +1,25 @@
+### FastqCheckUMI tool help
+	FastqCheckUMI (2023_09-38-ga9141a54)
+
+	Returns the UMI info of a FastQ file on STDOUT.
+
+	Mandatory parameters:
+	  -in <file>   Input FASTQ file.
+
+	Optional parameters:
+	  -out <file>  Output file containing the result string. If unset, writes to STDOUT.
+	               Default value: ''
+	  -lines <int> Number of lines which should be checked. (default: 10)
+	               Default value: '10'
+
+	Special parameters:
+	  --help       Shows this help and exits.
+	  --version    Prints version and exits.
+	  --changelog  Prints changeloge and exits.
+	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
+
+### FastqCheckUMI changelog
+	FastqCheckUMI 2023_09-38-ga9141a54
+
+	2023-10-05 Initial commit.
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/VariantFilterAnnotations.md

@@ -1,5 +1,5 @@
 ### VariantFilterAnnotations tool help
-	VariantFilterAnnotations (2023_03-107-g2a1d2478)
+	VariantFilterAnnotations (2023_09-38-ga9141a54)
 
 	Filter a variant list in GSvar format based on variant annotations.
 
@@ -80,16 +80,15 @@
 	                                   Parameters:
 	                                     action - Action to perform [default=FILTER] [valid=REMOVE,FILTER]
 	Predicted pathogenic               Filter for variants predicted to be pathogenic.
-	                                   Pathogenicity predictions used by this filter are: phyloP, Sift, PolyPhen, CADD and REVEL.
+	                                   Pathogenicity predictions used by this filter are: phyloP, CADD, REVEL and AlphaMissense.
 	                                   Parameters:
 	                                     min - Minimum number of pathogenic predictions [default=1] [min=1]
 	                                     action - Action to perform [default=FILTER] [valid=KEEP,FILTER]
 	                                     skip_high_impact - Do not apply this filter to variants with impact 'HIGH'. [default=false]
+	                                     cutoff_phylop - Minimum phyloP score for a pathogenic prediction. The phyloP score is not used if set to -10.0. [default=1.6]
 	                                     cutoff_cadd - Minimum CADD score for a pathogenic prediction. The CADD score is not used if set to 0.0. [default=20] [min=0]
 	                                     cutoff_revel - Minimum REVEL score for a pathogenic prediction. The REVEL score is not used if set to 0.0. [default=0.9] [min=0] [max=1]
-	                                     cutoff_phylop - Minimum phyloP score for a pathogenic prediction. The phyloP score is not used if set to -10.0. [default=1.6]
-	                                     ignore_sift - Do not used the Sift score. If unset, Sift consequence 'D' is considered pathogenic. [default=false]
-	                                     ignore_polyphen - Do not used the PolyPhen score. If unset, PolyPhen consequence 'D' is considered pathogenic. [default=false]
+	                                     cutoff_alphamissense - Minimum AlphaMissense score for a pathogenic prediction. The AlphaMissense score is not used if set to 0.0. [default=0.564] [min=0] [max=1]
 	RNA ASE allele frequency           Filter based on the allele specific expression allele frequency.
 	                                   Parameters:
 	                                     min_af - Minimal expression allele frequency. [default=0] [min=0.0] [max=1.0]
@@ -143,8 +142,8 @@
 	                                     build - Genome build used for pseudoautosomal region coordinates [default=hg38] [valid=hg19,hg38]
 	Tumor zygosity                     Filter based on the zygosity of tumor-only samples. Filters out germline het/hom calls.
 	                                   Parameters:
-	                                     het_af_range - Consider allele frequencies of 50% ± het_af_range as heterozygous and thus as germline. [default=0] [min=0] [max=49.9]
-	                                     hom_af_range - Consider allele frequencies of 100% ± hom_af_range as homozygous and thus as germline. [default=0] [min=0] [max=99.9]
+	                                     het_af_range - Consider allele frequencies of 50% ± het_af_range as heterozygous and thus as germline. [default=0] [min=0] [max=49.9]
+	                                     hom_af_range - Consider allele frequencies of 100% ± hom_af_range as homozygous and thus as germline. [default=0] [min=0] [max=99.9]
 	Variant quality                    Filter for variant quality
 	                                   Parameters:
 	                                     qual - Minimum variant quality score (Phred) [default=250] [min=0]
@@ -175,7 +174,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VariantFilterAnnotations changelog
-	VariantFilterAnnotations 2023_03-107-g2a1d2478
+	VariantFilterAnnotations 2023_09-38-ga9141a54
 
 	2018-07-30 Replaced command-line parameters by INI file and added many new filters.
 	2017-06-14 Refactoring of genotype-based filters: now also supports multi-sample filtering of affected and control samples.

src/GSvar/MainWindow.cpp

@@ -5896,7 +5896,7 @@ void MainWindow::on_actionImportSampleRelations_triggered()
 void MainWindow::on_actionImportSampleHpoTerms_triggered()
 {
 	importBatch("Import sample HPO terms",
-				"Batch import of sample HPO terms. Must contain the following tab-separated fields:<br><b>sample1</b>, <b>HPO term id, e.g. 'HP:0003002'</b>",
+				"Batch import of sample HPO terms. Must contain the following tab-separated fields:<br><b>sample1</b>, <b>HPO term id e.g. 'HP:0003002'</b>",
 				"sample_disease_info",
 				QStringList() << "sample_id" << "disease_info"
 				);

src/GSvar/VariantDetailsDockWidget.cpp

@@ -83,10 +83,9 @@ void VariantDetailsDockWidget::setLabelTooltips(const VariantList& vl)
 
 	//pathogenicity predictions
 	ui->label_phylop->setToolTip(vl.annotationDescriptionByName("phyloP").description());
-	ui->label_sift->setToolTip(vl.annotationDescriptionByName("Sift").description());
-	ui->label_polyphen->setToolTip(vl.annotationDescriptionByName("PolyPhen").description());
 	ui->label_cadd->setToolTip(vl.annotationDescriptionByName("CADD").description());
-	ui->label_revel->setToolTip(vl.annotationDescriptionByName("REVEL").description());
+	ui->label_revel->setToolTip(vl.annotationDescriptionByName("REVEL", false).description()); // optional
+	ui->label_alphamissense->setToolTip(vl.annotationDescriptionByName("AlphaMissense", false).description()); // optional (license and support of old
 
 	//splicing/regulatory
 	ui->label_maxentscan->setToolTip(vl.annotationDescriptionByName("MaxEntScan").description());
@@ -180,10 +179,9 @@ void VariantDetailsDockWidget::updateVariant(const VariantList& vl, int index)
 
 	//pathogenity predictions
 	setAnnotation(ui->phylop, vl, index, "phyloP");
-	setAnnotation(ui->sift, vl, index, "Sift");
-	setAnnotation(ui->polyphen, vl, index, "PolyPhen");
 	setAnnotation(ui->cadd, vl, index, "CADD");
 	setAnnotation(ui->revel, vl, index, "REVEL");
+	setAnnotation(ui->alphamissense, vl, index, "AlphaMissense");
 
 	//splicing/regulatory
 	setAnnotation(ui->maxentscan, vl, index, "MaxEntScan");
@@ -410,10 +408,6 @@ void VariantDetailsDockWidget::setAnnotation(QLabel* label, const VariantList& v
 				text = anno;
 			}
 		}
-		else if(name=="Sift" || name=="PolyPhen")
-		{
-			text = anno.replace("D", formatText("D", RED)).replace("P", formatText("P", ORANGE));
-		}
 		else if(name=="REVEL")
 		{
 			bool ok = true;
@@ -431,6 +425,23 @@ void VariantDetailsDockWidget::setAnnotation(QLabel* label, const VariantList& v
 				text = anno;
 			}
 		}
+		else if(name=="AlphaMissense")
+		{
+			bool ok = true;
+			double value = anno.toDouble(&ok);
+			if (ok && value>=0.564)
+			{
+				text = formatText(anno, RED);
+			}
+			else if (ok && value<=0.34)
+			{
+				text = formatText(anno, GREEN);
+			}
+			else
+			{
+				text = anno;
+			}
+		}
 		else if(name=="classification")
 		{
 			bool ok = true;