Skip to content
This repository has been archived by the owner on Apr 7, 2022. It is now read-only.

Feature/indel primer #37

Merged
merged 3 commits into from
May 4, 2021
Merged

Feature/indel primer #37

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
5d657fc
fix bam tracks loading
samwachspress May 4, 2021
5992127
remove variants
samwachspress May 4, 2021
4c09231
btn
samwachspress May 4, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
101 changes: 23 additions & 78 deletions base/templates/browser.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,18 +190,10 @@ <h5>Isotype (reference strain) <a href="{{ url_for('primary.help_item', filename
<div id="browser"></div>


<div class="row">
<div class="col-md-12 col-lg-12" style='text-align:center'>
<h3>Variants</h3>
</div> {# /col-lg-12 #}
</div> {# /row #}

<div class="row">
<div class="col-md-10">
<p><small><strong>A Maximum of 1000 variants or 100kb will be queried and returned</strong>. Heterozygous calls are likely errors. When rows are yellow, it indicates the entire variant failed QC.</small></p>
<small>Hovering over a failing genotype will list the filter applied. Genotypes are shown as follows:</small>
</div> {# /col-md-10 #}
<div class="col-md-2">
<div class="col-md-2 btn-mid-row">
<button id='download' class="btn btn-primary btn-block">Download</button>
</div> {# /col-md-10 #}
</div> {# /row #}
Expand Down Expand Up @@ -285,46 +277,14 @@ <h3>Variants</h3>
},
{{ strain }}_bam : {
id: "{{ strain.strain }}_bam",
name: "{{ strain.strain }}",
name: "{{ strain.strain }}_bam",
url: "//storage.googleapis.com/elegansvariation.org/bam/{{ strain }}.bam",
indexURL: "//storage.googleapis.com/elegansvariation.org/bam/{{ strain }}.bam.bai",
order: 100,
visibilityWindow: 20000,
searchable: false
},
{% endfor %}
"LOW": {
name: "LOW",
url: "//storage.googleapis.com/elegansvariation.org/releases/{{ DATASET_RELEASE }}/tracks/{{ DATASET_RELEASE }}.LOW.bed.gz",
order: 3,
color: "#33cc33",
displayMode: "EXPANDED",
height: 35
},
"MODERATE": {
name: "MODERATE",
url: "//storage.googleapis.com/elegansvariation.org/releases/{{ DATASET_RELEASE }}/tracks/{{ DATASET_RELEASE }}.MODERATE.bed.gz",
order: 4,
color: "#ffc500",
displayMode: "EXPANDED",
height: 35
},
"HIGH": {
name: "HIGH",
url: "//storage.googleapis.com/elegansvariation.org/releases/{{ DATASET_RELEASE }}/tracks/{{ DATASET_RELEASE }}.HIGH.bed.gz",
order: 5,
color: "#ff0000",
displayMode: "EXPANDED",
height: 35
},
"MODIFIER": {
name: "MODIFIER",
url: "//storage.googleapis.com/elegansvariation.org/releases/{{ DATASET_RELEASE }}/tracks/{{ DATASET_RELEASE }}.MODIFIER.bed.gz",
order: 5,
color: "#999999",
displayMode: "EXPANDED",
height: 35
},
"Variants": {
name: "Variants",
url: "//storage.googleapis.com/elegansvariation.org/releases/{{ DATASET_RELEASE }}/variation/WI.{{ DATASET_RELEASE }}.hard-filter.isotype.vcf.gz",
Expand Down Expand Up @@ -397,6 +357,24 @@ <h3>Variants</h3>
}
};

function reload_tracks() {
$('.track-select').each(function(i, obj) {
const track_name = $(this).attr("value");
if ($(this).prop("checked") == true){
if (!tracks.includes(track_name)) {
igv.getBrowser().loadTrack(trackset[track_name]);
tracks.push(track_name);
}
} else {
igv.getBrowser().removeTrackByName(track_name);
const i = tracks.indexOf(track_name);
if (i !== -1) {
tracks.splice(i, 1);
}
}
});
}

$(document).ready(function () {
var div = $("#browser")[0],
options = {
Expand All @@ -412,10 +390,7 @@ <h3>Variants</h3>
fastaURL: "//storage.googleapis.com/elegansvariation.org/browser_tracks/c_elegans.PRJNA13758.WS245.genomic.fa",
},
locus: "{{ region }}",
tracks: [
trackset["Genes"],
trackset["Transcripts"]
]
tracks: []
};
var browser = igv.createBrowser(div, options)
.then(function(browser) {
Expand All @@ -428,21 +403,7 @@ <h3>Variants</h3>

// Detect track changes
$(".track-select").on("change", function() {
$('.track-select').each(function(i, obj) {
const track_name = $(this).attr("value");
if ($(this).prop("checked") == true){
if (!tracks.includes(track_name)) {
igv.getBrowser().loadTrack(trackset[track_name]);
tracks.push(track_name);
}
} else {
igv.getBrowser().removeTrackByName(track_name);
const i = tracks.indexOf(track_name);
if (i !== -1) {
tracks.splice(i, 1);
}
}
});
reload_tracks();
});

});
Expand Down Expand Up @@ -522,16 +483,7 @@ <h3>Variants</h3>
end = region.split(":")[1].split("-")[1].replace(/,/g, "");
release = {{ DATASET_RELEASE }};

sample_tracks = []
$(".sample-track:checked").each(function() { sample_tracks.push(this.value) })

tracks = [];
$('.track-select').each(function(i, obj) {
if ($(this).prop("checked") == true) {
tracks.push($(this).attr("value"));
}
});

reload_tracks();
data = {'chrom': chrom,
'start': parseInt(start),
'end': parseInt(end),
Expand Down Expand Up @@ -662,18 +614,11 @@ <h5>Other</h5>
typingTimer = setTimeout(process_gene_search, doneTypingInterval);
})

$(".checkbox").on("click", function() {
setTimeout(refresh_variants, 200);
})

$(".igvNavigationSearchInput").on("input paste", function() {
refresh_variants();
});

$(".track-select").on("change", function() {
setTimeout(refresh_variants, 200);
});

$(".igvNavigationSearchInput").keypress(function(e) {
if(e.which == 13) {
setTimeout(refresh_variants, 200);
Expand Down