CHANGES

@@ -1317,3 +1317,7 @@ The layer in which a tile appears can now be forced using 'layer'.
   layer = i
   ...
   </plot>
+
+12 Nov 2017
+
+Fixed SVG stroke opacity bug that was inverting opacity.

data/karyotype/parse.karyotype

@@ -28,10 +28,10 @@ prefix="chr"
 fi
 
 # chromosomes
-cat $file | grep -v ^\# | tr A-Z a-z | sort +0 -1 +2rn -3 | sort -u -k 1,1 | sed 's/\t/ /g' | tr -s " " | sed 's/chr//' | awk '{print $1,$0}' | awk -v prefix=$2 '{print "chr -",prefix$2,$1,0,$4,"chr"$1}' | sort -n +3 -4 | sed 's/x/X/g' | sed 's/y/Y/g'
+cat $file | grep -v ^\# | grep -v _random | grep -v chrUn | tr A-Z a-z | sort +0 -1 +2rn -3 | sort -u -k 1,1 | sed 's/\t/ /g' | tr -s " " | sed 's/chr//' | awk '{print $1,$0}' | awk -v prefix=$2 '{print "chr -",prefix$2,$1,0,$4,"chr"$1}' | sort -n +3 -4 | sed 's/x/X/g' | sed 's/y/Y/g'
 
 # bands
-cat $file  | grep -v ^\# | tr A-Z a-z | sed 's/\t/ /g' | tr -s " " | sed "s/chr/$prefix/" | awk '{print $1,$0}' | sed 's/chr//' | awk '{print "band",$2,$5,$5,$3,$4,$6}' | sort +1 -2 +4n -5 | sed 's/x/X/g' | sed 's/y/Y/g'
+cat $file  | grep -v ^\# | grep -v _random | grep -v chrUn | tr A-Z a-z | sed 's/\t/ /g' | tr -s " " | sed "s/chr/$prefix/" | awk '{print $1,$0}' | sed 's/chr//' | awk '{print "band",$2,$5,$5,$3,$4,$6}' | sort +1 -2 +4n -5 | sed 's/x/X/g' | sed 's/y/Y/g'
 
 
 

debian/changelog

+circos (0.69.9+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Fri, 19 Jul 2019 19:48:22 +0200
+
 circos (0.69.6+dfsg-2) unstable; urgency=medium
 
   [ Dylan Aïssi ]

debian/compat

-11
+12

debian/control

@@ -4,8 +4,8 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper (>= 12~)
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/circos
 Vcs-Git: https://salsa.debian.org/med-team/circos.git
 Homepage: http://circos.ca/
@@ -29,7 +29,7 @@ Depends: ${misc:Depends},
          libset-intspan-perl,
          liblist-allutils-perl,
          libfile-basedir-perl,
-         perl (>= 5.15.3) | libmath-bigint-perl,
+         libmath-bigint-perl,
          libmath-vec-perl,
          libio-all-perl,
          libmath-vecstat-perl,

lib/Circos.pm

 package Circos;
 
-our $VERSION      = "0.69-6";
-our $VERSION_DATE = "31 July 2017";
+our $VERSION      = "0.69-8";
+our $VERSION_DATE = "15 Jun 2019";
 
 =pod
 
@@ -1352,7 +1352,7 @@ or a hashref of the configuration options.
 					my @bezier_points = bezier_points(@bezier_control_points);
 
 					printdebug_group("bezier", "beziercontrols",int(@bezier_control_points), @bezier_control_points );
-
+          #printinfo(seek_parameter("color",@i_param_path_link),rgb_color_opacity(seek_parameter("color",@i_param_path_link)));
 					my $svg;
 					my $svg_attr = seek_parameter_glob("^svg.*",qr/^svg/,@i_param_path_link);
 					if ( $num_bezier_control_points == 10 && $SVG_MAKE ) {
@@ -1378,7 +1378,7 @@ or a hashref of the configuration options.
 													 qq{<path d="M %.1f,%.1f L $point_string " style="stroke-opacity: %f; stroke-width: %.1f; stroke: rgb(%d,%d,%d); fill: none" %s />},
 													 ( map { @$_ } @bezier_points[ 0, 1 ] ),
 													 ( map { @$_ } @bezier_points[ 2 .. @bezier_points - 1 ] ),
-													 rgb_color_opacity(seek_parameter("color",@i_param_path_link)),
+													 1-rgb_color_transparency(seek_parameter("color",@i_param_path_link)),
 													 unit_strip(seek_parameter("thickness", @i_param_path_link),"p"),
 													 rgb_color(seek_parameter("color", @i_param_path_link)),
 													 attr_string($svg_attr),
@@ -1389,7 +1389,7 @@ or a hashref of the configuration options.
 													 qq{<path d="M %.1f,%.1f C %s" style="stroke-opacity: %f; stroke-width: %.1f; stroke: rgb(%d,%d,%d); fill: none" %s />},
 													 @bezier_control_points[ 0, 1 ],
 													 $point_string,
-													 rgb_color_opacity(seek_parameter("color",@i_param_path_link)),
+													 1-rgb_color_transparency(seek_parameter("color",@i_param_path_link)),
 													 unit_strip(seek_parameter("thickness", @i_param_path_link),"p"),
 													 rgb_color(seek_parameter("color", @i_param_path_link)),
 													 attr_string($svg_attr),
@@ -1398,7 +1398,7 @@ or a hashref of the configuration options.
 						$svg = sprintf(
 													 qq{<path d="M %.1f,%.1f Q %.1f,%.1f %.1f,%.1f" style="stroke-opacity: %f; stroke-width: %.1f; stroke: rgb(%d,%d,%d); fill: none" %s />},
 													 @bezier_control_points,
-													 rgb_color_opacity(seek_parameter("color",@i_param_path_link)),
+													 1-rgb_color_transparency(seek_parameter("color",@i_param_path_link)),
 													 unit_strip(seek_parameter("thickness", @i_param_path_link),"p"),
 													 rgb_color(seek_parameter("color", @i_param_path_link)),
 													 attr_string($svg_attr),
@@ -6524,7 +6524,7 @@ sub ribbon {
 			$svg_colors .= sprintf( qq{ stroke: rgb(%d,%d,%d);}, rgb_color( $params{edgecolor} ) );
 			if ( rgb_color_opacity( $params{edgecolor} ) < 1 ) {
 				$svg_colors .= sprintf( qq{ stroke-opacity: %.3f;},
-																rgb_color_opacity( $params{edgecolor} ) );
+																1-rgb_color_opacity( $params{edgecolor} ) );
 			}
 		}
 
@@ -6543,7 +6543,7 @@ sub ribbon {
 			$svg_colors .= sprintf( qq{ fill: rgb(%d,%d,%d);}, rgb_color($svg_color) );
 			if ( rgb_color_opacity( $params{fillcolor} ) < 1 ) {
 				$svg_colors .= sprintf( qq{ opacity: %.3f;},
-																rgb_color_opacity( $params{fillcolor} ) );
+																1-rgb_color_opacity( $params{fillcolor} ) );
 			}
 		}
 		

lib/Circos/ColorTransform.pm

@@ -86,6 +86,9 @@ sub transform_color {
 		printinfo(@$rgb);
 		printinfo();
 	} elsif ($method =~ /wmmn/) {
+    if($rgb->[0] == 255 && $rgb->[1] == 255 && $rgb->[2] == 255) {
+      $rgb = [0,0,0];
+    } else {
       my $d1  = deltae([255,0,0],$rgb);
       my $d2  = deltae([0,255,0],$rgb);
       my @lch = rgb_to_lch(@$rgb);
@@ -99,6 +102,7 @@ sub transform_color {
         $lch[2] = 150;
       }
       $rgb = [lch_to_rgb(@lch)];
+    }
 	}
 	return $transform_table->{$name}{$method} = $rgb;
 }

lib/Circos/Colors.pm

@@ -106,6 +106,7 @@ sub allocate_colors {
   #   lch(l,c,h,a)
   #   hsv(h,s,v)
   #   hsv(h,s,v,a)
+  #   hex(59311c)
 	#
 	# resolution of name lookups or lists is deferred until later
 	

lib/Circos/SVG.pm

@@ -470,6 +470,7 @@ sub style {
 		my $sc = $params{color} || fetch_conf("default_color");
 		push @style, sprintf("stroke:rgb(%d,%d,%d)", rgb_color($sc));
 		if ( (my $op = rgb_color_opacity( $params{color} )) < 1 ) {
+      #printinfo($params{color},rgb_color_opacity($params{color}));
 	    push @style, sprintf("stroke-opacity:%.2f",$op);
 		}
 	}