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Fix issues with global filter #100

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Fix issues with global filter #100

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74c9fd3
Merge branch 'master' into fix-issues-with-global-filter
settatam Feb 14, 2024
3b4206f
update curation filters
settatam Feb 15, 2024
f84119f
Remove js alerts
settatam Feb 15, 2024
f49ba99
Change verbiage to ensure backward compat
settatam Feb 15, 2024
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3 changes: 2 additions & 1 deletion app/Console/Commands/QueryDecipher.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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) {

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3 changes: 1 addition & 2 deletions app/Console/Commands/UpdateLocations.php
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Expand Up @@ -89,7 +89,6 @@ public function handle()
if ($record !== null)
$record->update(['chr' => $chr, 'start37' => $start, 'stop37' => $stop, 'seqid37' => $parts[0]]);


}

fclose($handle);
Expand All @@ -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)
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2 changes: 1 addition & 1 deletion app/Console/Commands/UpdateMane.php
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Expand Up @@ -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) {

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Binary file added data/hg38/GCF_000001405.40_GRCh38.p14_genomic.gff.gz
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2 changes: 1 addition & 1 deletion public/js/filters.js
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6 changes: 2 additions & 4 deletions resources/js/filters.js
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Expand Up @@ -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')
});

Expand All @@ -22,7 +22,6 @@ function createBadges()
var newbadge = $('<span class="badge action-hi-badge bg-primary mr-1">' + filterObj.data('badge') + '</span>');
$('.filter-container').append(newbadge);
})

}
}
/**
Expand Down Expand Up @@ -475,7 +474,6 @@ function filter_push(name, column, value) {

filter_pop(name);
filterstack.push(o);
console.log(filterstack);
}


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