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){ ...@@ -14,9 +14,9 @@ info['info']['info']['datasets'].forEach(function(dataset){
}); });
var referenceMap = { var referenceMap = {
'GRCh38': 'SEGMENTS_HG38', 'GRCh36': 'SEGMENTS_HG18',
'GRCh37': 'SEGMENTS_HG19', 'GRCh37': 'SEGMENTS_HG19',
'GRCh36': 'SEGMENTS_HG18' 'GRCh38': 'SEGMENTS_HG38'
}; };
//correspondence to arraymap class //correspondence to arraymap class
...@@ -26,8 +26,8 @@ var alternateBasesMap = { ...@@ -26,8 +26,8 @@ var alternateBasesMap = {
}; };
/* /*
By default doe Maximilien takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt By default doe Maximilian 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? TODO Should it be the same as Maximilian? Is it specified through the Beacon documentation?
*/ */
var defaultReference = 'GRCh37'; var defaultReference = 'GRCh37';
...@@ -64,6 +64,10 @@ function checkPreconditions(params) { ...@@ -64,6 +64,10 @@ function checkPreconditions(params) {
}; };
} }
/*
TODO: Change method for numeric test, since positions are 0-based.
*/
if (!Number(params.start)) { if (!Number(params.start)) {
return { return {
hasError: true, hasError: true,
......
...@@ -15,7 +15,7 @@ arrayMap.config(['$routeProvider', '$locationProvider', ...@@ -15,7 +15,7 @@ arrayMap.config(['$routeProvider', '$locationProvider',
arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope, $location) { arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope, $location) {
$scope.references = ['GRCh38','GRCh37','GRCh36']; $scope.references = ['GRCh36','GRCh37','GRCh38'];
$scope.config = { $scope.config = {
"referenceName": "2", "referenceName": "2",
...@@ -66,6 +66,9 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope ...@@ -66,6 +66,9 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
((conf.variantClass === "") ? "" : "&variantClass=" + conf.variantClass); ((conf.variantClass === "") ? "" : "&variantClass=" + conf.variantClass);
}; };
/*
TODO: Get datasets from beacon-info.js (or database query).
*/
$scope.datasets = [ $scope.datasets = [
{ {
...@@ -1681,4 +1684,3 @@ arrayMap.controller('DocumentationCtrl', ['$scope', '$http', function ($scope, $ ...@@ -1681,4 +1684,3 @@ arrayMap.controller('DocumentationCtrl', ['$scope', '$http', function ($scope, $
$scope.mkText = data; $scope.mkText = data;
}); });
}]); }]);
## Current implementation ## 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> <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"> <img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
...@@ -225,7 +226,7 @@ Open questions: ...@@ -225,7 +226,7 @@ Open questions:
2. use the property 'variants' to count the number of segments (for instance). - 9 March 2016 - APPROVED. 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. 3. ask the Beacon team if we can make this optional property.
4. ask the Beacon team if we can change the property name. 4. ask the Beacon team if we can change the property name.
-- --
...@@ -236,4 +237,4 @@ Open questions: ...@@ -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). 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 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 * 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) * 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
./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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