Commit 0c03c9d8 authored by Michael Baudis's avatar Michael Baudis
Browse files

adding some TODO statements, speling

parent 432fa2fe
......@@ -14,9 +14,9 @@ info['info']['info']['datasets'].forEach(function(dataset){
});
var referenceMap = {
'GRCh38': 'SEGMENTS_HG38',
'GRCh36': 'SEGMENTS_HG18',
'GRCh37': 'SEGMENTS_HG19',
'GRCh36': 'SEGMENTS_HG18'
'GRCh38': 'SEGMENTS_HG38'
};
//correspondence to arraymap class
......@@ -26,8 +26,8 @@ var alternateBasesMap = {
};
/*
By default doe Maximilien takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt
TODO Should it be the same as Maximilen? Is it specified through the Beacon documentaiton?
By default doe Maximilian takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt
TODO Should it be the same as Maximilian? Is it specified through the Beacon documentation?
*/
var defaultReference = 'GRCh37';
......@@ -64,6 +64,10 @@ function checkPreconditions(params) {
};
}
/*
TODO: Change method for numeric test, since positions are 0-based.
*/
if (!Number(params.start)) {
return {
hasError: true,
......
......@@ -15,7 +15,7 @@ arrayMap.config(['$routeProvider', '$locationProvider',
arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope, $location) {
$scope.references = ['GRCh38','GRCh37','GRCh36'];
$scope.references = ['GRCh36','GRCh37','GRCh38'];
$scope.config = {
"referenceName": "2",
......@@ -66,6 +66,9 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
((conf.variantClass === "") ? "" : "&variantClass=" + conf.variantClass);
};
/*
TODO: Get datasets from beacon-info.js (or database query).
*/
$scope.datasets = [
{
......@@ -1681,4 +1684,3 @@ arrayMap.controller('DocumentationCtrl', ['$scope', '$http', function ($scope, $
$scope.mkText = data;
});
}]);
## Current implementation
This beacon queries 20K samples coming from ArrayMap from here:
This beacon queries <60k samples from arrayMap, containing genomic copy number aberration data from cancer samples and associated control experiments.
<a href="http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata">http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata</a>
<img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
......@@ -225,7 +226,7 @@ Open questions:
2. use the property 'variants' to count the number of segments (for instance). - 9 March 2016 - APPROVED.
3. ask the Beacon team if we can make this optional property.
4. ask the Beacon team if we can change the property name.
--
......@@ -236,4 +237,4 @@ Open questions:
4. ask the Beacon team if they can replace the property type by a list of strings (instead of a string).
5. clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)- OK
* It's basically a range. See example and our interpretation here: https://github.com/samtools/hts-specs/issues/132
* For arrayMap, we need to define that interval for POS and END position. Michael suggested something like 0.5 * average probe distance (would be in order of kB)
\ No newline at end of file
* For arrayMap, we need to define that interval for POS and END position. Michael suggested something like 0.5 * average probe distance (would be in order of kB)
./runquery.sh get-datasets.js | grep -E '[\"\{\}\;]|\[|\]' > /Library/WebServer/Documents/ga4gh-arraymap/beacon-app/arraymap-beacon/v0.4/beacon-info.js
./runquery.sh build-info.js | grep -E '[\"\{\}\;]|\[|\]' > /Library/WebServer/Documents/ga4gh-arraymap/beacon-app/arraymap-beacon/v0.4/beacon-info.js
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