fix: Fix a domain error (issue 199)(v3.3.7)

changeLog.txt

@@ -10,8 +10,10 @@
 
 For more details, please see the README file.
 
-	- Include FranceGenRef benign SV annotation (856 WGS with ancestries in different regions of France)
-	WARNING: not supplied as part of the AnnotSV sources. Users need to request the FranceGenRef data dedicated to AnnotSV
+
+	- Fix a domain error (issue 199)
+	- Include code to allow FranceGenRef benign SV annotation (856 WGS with ancestries in different regions of France)
+	WARNING: not supplied as part of the AnnotSV sources. 
 	- Optimize access to the exomiser application properties file for use with singularity/bioconda
 	- Allow uppercase file extensions (".VCF", ".BED" or ".VCF.GZ") 
 	- Use the new format of the COSMIC data source 

share/tcl/AnnotSV/AnnotSV-pathogenicsv.tcl

@@ -710,8 +710,11 @@ proc poPathogenicSVannotation {SVchrom SVstart SVend} {
 		    if {[expr {$endP-$startP}] < $g_AnnotSV(SVminSize)} {continue}
 
 		    if {$SVtoAnn_end > $endP} {set po_end $endP} else {set po_end $SVtoAnn_end}
-		    if {$SVtoAnn_start > $startP} {set po_start $SVtoAnn_start} else {set po_start $startP}		    
-		    set percent [format "%.2f" [expr {($po_end-$po_start)*100.0/($endP-$startP)}]]
+		    if {$SVtoAnn_start > $startP} {set po_start $SVtoAnn_start} else {set po_start $startP}
+		    # Some pathogenic variant from dbvar (e.g. nssv17172411) are described with "$endP = $startP" (region size = 1)
+		    set length_endP_startP [expr {($endP-$startP)}]
+		    if {$length_endP_startP eq 0} {set length_endP_startP 1}
+		    set percent [format "%.2f" [expr {($po_end-$po_start)*100.0/$length_endP_startP}]]
 
 		    if {$percent == 100} {continue}