diff --git a/app/Console/Commands/QueryDecipher.php b/app/Console/Commands/QueryDecipher.php
index 2f353df1..ba17ea48 100644
--- a/app/Console/Commands/QueryDecipher.php
+++ b/app/Console/Commands/QueryDecipher.php
@@ -44,7 +44,8 @@ public function handle()
try {
- $results = file_get_contents("https://decipher.sanger.ac.uk/files/downloads/HI_Predictions_Version3.bed.gz");
+ // $results = file_get_contents("https://decipher.sanger.ac.uk/files/downloads/HI_Predictions_Version3.bed.gz");
+ $results = file_get_contents("https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz");
} catch (\Exception $e) {
diff --git a/app/Console/Commands/UpdateLocations.php b/app/Console/Commands/UpdateLocations.php
index 29f1a403..0639eec3 100644
--- a/app/Console/Commands/UpdateLocations.php
+++ b/app/Console/Commands/UpdateLocations.php
@@ -89,7 +89,6 @@ public function handle()
if ($record !== null)
$record->update(['chr' => $chr, 'start37' => $start, 'stop37' => $stop, 'seqid37' => $parts[0]]);
-
}
fclose($handle);
@@ -101,7 +100,7 @@ public function handle()
}
// https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz
- $handle = fopen(base_path() . '/data/hg38/GCF_000001405.39_GRCh38.p13_genomic.gff', "r");
+ $handle = fopen(base_path() . '/data/hg38/GCF_000001405.40_GRCh38.p14_genomic.gff', "r");
if ($handle)
{
while (($line = fgets($handle)) !== false)
diff --git a/app/Console/Commands/UpdateMane.php b/app/Console/Commands/UpdateMane.php
index 1ac02e39..55b21b14 100644
--- a/app/Console/Commands/UpdateMane.php
+++ b/app/Console/Commands/UpdateMane.php
@@ -45,7 +45,7 @@ public function handle()
try {
- $results = file_get_contents("https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/MANE.GRCh38.v1.0.summary.txt.gz");
+ $results = file_get_contents("https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/MANE.GRCh38.v1.3.summary.txt.gz");
} catch (\Exception $e) {
diff --git a/data/hg38/GCF_000001405.40_GRCh38.p14_genomic.gff.gz b/data/hg38/GCF_000001405.40_GRCh38.p14_genomic.gff.gz
new file mode 100644
index 00000000..d454c4b7
Binary files /dev/null and b/data/hg38/GCF_000001405.40_GRCh38.p14_genomic.gff.gz differ
diff --git a/public/js/filters.js b/public/js/filters.js
index d850f375..d46b77ce 100644
--- a/public/js/filters.js
+++ b/public/js/filters.js
@@ -1 +1 @@
-!function(e){var t={};function o(a){if(t[a])return t[a].exports;var n=t[a]={i:a,l:!1,exports:{}};return e[a].call(n.exports,n,n.exports,o),n.l=!0,n.exports}o.m=e,o.c=t,o.d=function(e,t,a){o.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:a})},o.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},o.t=function(e,t){if(1&t&&(e=o(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var a=Object.create(null);if(o.r(a),Object.defineProperty(a,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var n in e)o.d(a,n,function(t){return e[t]}.bind(null,n));return a},o.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return o.d(t,"a",t),t},o.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},o.p="/",o(o.s=45)}({45:function(e,t,o){e.exports=o(46)},46:function(e,t){var o=[];function a(){$(".filter-container").html("");var e=$(".dosage-filter").filter((function(e){return $(this).hasClass("fa-toggle-on")}));if(e.length)e.each((function(){var e=$(this),t=$(''+e.data("badge")+"");$(".filter-container").append(t)}));else{var t=$('None');$(".filter-container").append(t)}}$((function(){a()})),$(".action-show-genes").on("click",(function(){var e=[];$(this).hasClass("btn-success")?($(this).removeClass("btn-success").addClass("btn-default active"),$(this).html("Genes: Off")):(e.push(0),e.push(3),$(this).addClass("btn-success").removeClass("btn-default active"),$(this).html("Genes: On")),$(".action-show-regions").hasClass("btn-success")&&e.push(1),f("geneswitch","type",e),r($table)})),$(".action-show-regions").on("click",(function(){var e=[];$(".action-show-genes").hasClass("btn-success")&&(e.push(0),e.push(3)),$(this).hasClass("btn-success")?($(this).removeClass("btn-success").addClass("btn-default active"),$(this).html("Regions: Off")):(e.push(1),$(this).addClass("btn-success").removeClass("btn-default active"),$(this).html("Regions: On")),f("geneswitch","type",e),r($table)})),$(".action-show-hiknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("haplo","haplo_assertion","3 (Sufficient Evidence)"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-hiknown-text").html("On")):(c("haplo"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-hiknown-text").html("Off")),r($table)})),$(".action-show-tsknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("triplo","triplo_assertion","3 (Sufficient Evidence)"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-tsknown-text").html("On")):(c("triplo"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-tsknown-text").html("Off")),r($table)})),$(".action-show-hitsknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("hits",["haplo_assertion","triplo_assertion"],["3 (Sufficient Evidence)","3 (Sufficient Evidence)"]),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-hitsknown-text").html("On")):(c("hits"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-hitsknown-text").html("Off")),r($table)})),$(".action-show-protein").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("protein","locus","protein-coding gene"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-protein-text").html("On")):(c("protein"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-protein-text").html("Off")),r($table)})),$(".action-show-pseudogenes").on("click",(function(){if($(this).hasClass("fa-toggle-on")){if(f("pseudogene","@filter",i),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-pseudogenes-text").html("Off"),$(".action-pseudogenes-badge").remove(),""==$(".filter-container").html()){var e=$('None');$(".filter-container").append(e)}}else c("pseudogene"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-pseudogenes-text").html("On");r($table)})),$(".action-show-completed").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("complete","@filter",l),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-completed-text").html("On")):(c("complete"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-completed-text").html("Off"),$(".action-completed-badge").remove()),r($table)})),$(".action-show-new").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("history",["thr","hhr"],[1,1]),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-new-text").html("On")):(c("history"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-new-text").html("Off"),$(".action-new-badge").remove()),r($table)}));var n=(new Date).getTime()-7776e6;function s(e,t){return Date.parse(e.rawdate)>n}function l(e,t){return"Complete"===e.workflow}function i(e,t){return 0==e.type||1==e.type}function f(e,t,a){var n={name:e,column:t,value:a,active:!0};c(e),o.push(n),console.log(o)}function c(e){var t=o.findIndex((function(t){return t.name==e}));-1!=t&&o.splice(t,1)}function r(e){e.bootstrapTable("filterBy",{},{filterAlgorithm:g}),a()}function g(e,t){for(var a=!0,n=0;nRecently Reviewed');$(".filter-container").append(e)}else if(c("recent"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-recent-text").html("Off"),$(".action-nine-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)})),$(".action-show-acmg59").on("click",(function(){if($(this).hasClass("fa-toggle-off")){f("acmg59","acmg59",!0),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-acmg59-text").html("On"),$(".action-af-badge").remove();var e=$('ACMG SF v3.1');$(".filter-container").append(e)}else if(c("acmg59"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-acmg59-text").html("Off"),$(".action-acmg-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)})),$(".action-show-follow").on("click",(function(){if($(this).hasClass("fa-toggle-off")){f("follow","followed",!0),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-follow-text").html("On"),$(".action-af-badge").remove();var e=$('Followed');$(".filter-container").append(e)}else if(c("follow"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-follow-text").html("Off"),$(".action-follow-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)}))}});
\ No newline at end of file
+!function(e){var t={};function o(a){if(t[a])return t[a].exports;var n=t[a]={i:a,l:!1,exports:{}};return e[a].call(n.exports,n,n.exports,o),n.l=!0,n.exports}o.m=e,o.c=t,o.d=function(e,t,a){o.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:a})},o.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},o.t=function(e,t){if(1&t&&(e=o(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var a=Object.create(null);if(o.r(a),Object.defineProperty(a,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var n in e)o.d(a,n,function(t){return e[t]}.bind(null,n));return a},o.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return o.d(t,"a",t),t},o.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},o.p="/",o(o.s=45)}({45:function(e,t,o){e.exports=o(46)},46:function(e,t){var o=[];function a(){$(".filter-container").html("");var e=$(".advanced-filter").filter((function(e){return $(this).hasClass("fa-toggle-on")}));if(e.length)e.each((function(){var e=$(this),t=$(''+e.data("badge")+"");$(".filter-container").append(t)}));else{var t=$('None');$(".filter-container").append(t)}}$((function(){a()})),$(".action-show-genes").on("click",(function(){var e=[];$(this).hasClass("btn-success")?($(this).removeClass("btn-success").addClass("btn-default active"),$(this).html("Genes: Off")):(e.push(0),e.push(3),$(this).addClass("btn-success").removeClass("btn-default active"),$(this).html("Genes: On")),$(".action-show-regions").hasClass("btn-success")&&e.push(1),f("geneswitch","type",e),r($table)})),$(".action-show-regions").on("click",(function(){var e=[];$(".action-show-genes").hasClass("btn-success")&&(e.push(0),e.push(3)),$(this).hasClass("btn-success")?($(this).removeClass("btn-success").addClass("btn-default active"),$(this).html("Regions: Off")):(e.push(1),$(this).addClass("btn-success").removeClass("btn-default active"),$(this).html("Regions: On")),f("geneswitch","type",e),r($table)})),$(".action-show-hiknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("haplo","haplo_assertion","3 (Sufficient Evidence)"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-hiknown-text").html("On")):(c("haplo"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-hiknown-text").html("Off")),r($table)})),$(".action-show-tsknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("triplo","triplo_assertion","3 (Sufficient Evidence)"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-tsknown-text").html("On")):(c("triplo"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-tsknown-text").html("Off")),r($table)})),$(".action-show-hitsknown").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("hits",["haplo_assertion","triplo_assertion"],["3 (Sufficient Evidence)","3 (Sufficient Evidence)"]),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-hitsknown-text").html("On")):(c("hits"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-hitsknown-text").html("Off")),r($table)})),$(".action-show-protein").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("protein","locus","protein-coding gene"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-protein-text").html("On")):(c("protein"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-protein-text").html("Off")),r($table)})),$(".action-show-pseudogenes").on("click",(function(){if($(this).hasClass("fa-toggle-on")){if(f("pseudogene","@filter",i),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-pseudogenes-text").html("Off"),$(".action-pseudogenes-badge").remove(),""==$(".filter-container").html()){var e=$('None');$(".filter-container").append(e)}}else c("pseudogene"),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-pseudogenes-text").html("On");r($table)})),$(".action-show-completed").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("complete","@filter",l),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-completed-text").html("On")):(c("complete"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-completed-text").html("Off"),$(".action-completed-badge").remove()),r($table)})),$(".action-show-new").on("click",(function(){$(this).hasClass("fa-toggle-off")?(f("history",["thr","hhr"],[1,1]),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-new-text").html("On")):(c("history"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-new-text").html("Off"),$(".action-new-badge").remove()),r($table)}));var n=(new Date).getTime()-7776e6;function s(e,t){return Date.parse(e.rawdate)>n}function l(e,t){return"Complete"===e.workflow}function i(e,t){return 0==e.type||1==e.type}function f(e,t,a){var n={name:e,column:t,value:a,active:!0};c(e),o.push(n)}function c(e){var t=o.findIndex((function(t){return t.name==e}));-1!=t&&o.splice(t,1)}function r(e){e.bootstrapTable("filterBy",{},{filterAlgorithm:g}),a()}function g(e,t){for(var a=!0,n=0;nRecently Reviewed');$(".filter-container").append(e)}else if(c("recent"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-recent-text").html("Off"),$(".action-nine-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)})),$(".action-show-acmg59").on("click",(function(){if($(this).hasClass("fa-toggle-off")){f("acmg59","acmg59",!0),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-acmg59-text").html("On"),$(".action-af-badge").remove();var e=$('ACMG SF v3.1');$(".filter-container").append(e)}else if(c("acmg59"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-acmg59-text").html("Off"),$(".action-acmg-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)})),$(".action-show-follow").on("click",(function(){if($(this).hasClass("fa-toggle-off")){f("follow","followed",!0),$(this).removeClass("fa-toggle-off").addClass("fa-toggle-on"),$(".action-show-follow-text").html("On"),$(".action-af-badge").remove();var e=$('Followed');$(".filter-container").append(e)}else if(c("follow"),$(this).removeClass("fa-toggle-on").addClass("fa-toggle-off"),$(".action-show-follow-text").html("Off"),$(".action-follow-badge").remove(),""==$(".filter-container").html()){e=$('None');$(".filter-container").append(e)}r($table)}))}});
\ No newline at end of file
diff --git a/resources/js/filters.js b/resources/js/filters.js
index b38a4a48..5f70d2ac 100644
--- a/resources/js/filters.js
+++ b/resources/js/filters.js
@@ -8,8 +8,8 @@ $(function() {
function createBadges()
{
$('.filter-container').html('');
- var dosageFilters = $('.dosage-filter');
- var enabledFilters = dosageFilters.filter( function (filter) {
+ var advancedFilters = $('.advanced-filter');
+ var enabledFilters = advancedFilters.filter( function (filter) {
return $(this).hasClass('fa-toggle-on')
});
@@ -22,7 +22,6 @@ function createBadges()
var newbadge = $('' + filterObj.data('badge') + '');
$('.filter-container').append(newbadge);
})
-
}
}
/**
@@ -475,7 +474,6 @@ function filter_push(name, column, value) {
filter_pop(name);
filterstack.push(o);
- console.log(filterstack);
}
diff --git a/resources/views/gene-dosage/panels/filter.blade.php b/resources/views/gene-dosage/panels/filter.blade.php
index a21ad866..5c2e0835 100644
--- a/resources/views/gene-dosage/panels/filter.blade.php
+++ b/resources/views/gene-dosage/panels/filter.blade.php
@@ -16,42 +16,42 @@
@@ -59,14 +59,14 @@
diff --git a/resources/views/gene/panels/filter.blade.php b/resources/views/gene/panels/filter.blade.php
index 3d870457..e2f530b7 100644
--- a/resources/views/gene/panels/filter.blade.php
+++ b/resources/views/gene/panels/filter.blade.php
@@ -16,7 +16,7 @@
@@ -26,7 +26,7 @@