Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
4 changed files
with
158 additions
and
16 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,25 @@ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| './_IndexedFileDriver' | ||
| './_MultiIndexedFileDriver' | ||
| ], | ||
| function( declare, IndexedFileDriver ) { | ||
| return declare( IndexedFileDriver, { | ||
| function( declare, MultiIndexedFileDriver ) { | ||
| return declare( MultiIndexedFileDriver, { | ||
| name: 'GFF3+Tabix', | ||
| storeType: 'JBrowse/Store/SeqFeature/GFF3Tabix', | ||
|
|
||
| fileExtension: 'gff3.gz', | ||
| fileConfKey: 'file', | ||
| fileUrlConfKey: 'urlTemplate', | ||
|
|
||
| indexExtension: 'gff3.gz.tbi', | ||
| indexConfKey: 'tbi', | ||
| indexUrlConfKey: 'tbiUrlTemplate' | ||
|
|
||
|
|
||
| indexType: [{ | ||
| ext: 'gff3.gz.tbi', | ||
| confKey: 'tbi', | ||
| urlConfKey: 'tbiUrlTemplate' | ||
| }, { | ||
| ext: 'gff3.gz.csi', | ||
| confKey: 'csi', | ||
| urlConfKey: 'csiUrlTemplate' | ||
| }] | ||
| }); | ||
|
|
||
| }); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,25 @@ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| './_IndexedFileDriver' | ||
| './_MultiIndexedFileDriver' | ||
| ], | ||
| function( declare, IndexedFileDriver ) { | ||
| return declare( IndexedFileDriver, { | ||
| function( declare, MultiIndexedFileDriver ) { | ||
| return declare( MultiIndexedFileDriver, { | ||
| name: 'VCF+Tabix', | ||
| storeType: 'JBrowse/Store/SeqFeature/VCFTabix', | ||
|
|
||
| fileExtension: 'vcf.gz', | ||
| fileConfKey: 'file', | ||
| fileUrlConfKey: 'urlTemplate', | ||
|
|
||
| indexExtension: 'vcf.gz.tbi', | ||
| indexConfKey: 'tbi', | ||
| indexUrlConfKey: 'tbiUrlTemplate' | ||
| indexTypes: [{ | ||
| ext: 'vcf.gz.tbi', | ||
| confKey: 'tbi', | ||
| urlConfKey: 'tbiUrlTemplate' | ||
| }, { | ||
| ext: 'vcf.gz.csi', | ||
| confKey: 'csi', | ||
| urlConfKey: 'csiUrlTemplate' | ||
| }] | ||
| }); | ||
|
|
||
| }); |
125 changes: 125 additions & 0 deletions
125
src/JBrowse/View/FileDialog/TrackList/_MultiIndexedFileDriver.js
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| define([ | ||
| 'dojo/_base/declare', | ||
| 'JBrowse/Util', | ||
| 'JBrowse/Model/FileBlob', | ||
| 'JBrowse/Model/XHRBlob' | ||
| ], | ||
| function( declare, Util, FileBlob, XHRBlob ) { | ||
| var uniqCounter = 0; | ||
| return declare( null, { | ||
|
|
||
| tryResource: function( configs, resource ) { | ||
| if( resource.type == this.fileExtension ) { | ||
| var basename = Util.basename( | ||
| resource.file ? resource.file.name : | ||
| resource.url ? resource.url : | ||
| '' | ||
| ); | ||
| if( !basename ) | ||
| return false; | ||
|
|
||
| // go through the configs and see if there is one for an index that seems to match | ||
| for( var n in configs ) { | ||
| var c = configs[n]; | ||
| for(const index in this.indexTypes) { | ||
| if( Util.basename( c[index.indexConfKey] ? c[index.indexConfKey ].url || c[index.indexConfKey].blob.name : c[index.indexUrlConfKey], '.'+index.indexExtension ) == basename ) { | ||
| // it's a match, put it in | ||
| c[this.fileConfKey] = this._makeBlob( resource ); | ||
| return true; | ||
| } | ||
| } | ||
| } | ||
| // go through again and look for index files that don't have the base extension in them | ||
| basename = Util.basename( basename, '.'+this.fileExtension ); | ||
| for( var n in configs ) { | ||
| var c = configs[n]; | ||
| for(const index in this.indexTypes) { | ||
| if( Util.basename( c[index.indexConfKey] ? c[index.indexConfKey].url || c[index.indexConfKey].blob.name : c[index.indexUrlConfKey], '.'+index.indexExtension ) == basename ) { | ||
| // it's a match, put it in | ||
| c[this.fileConfKey] = this._makeBlob( resource ); | ||
| return true; | ||
| } | ||
| } | ||
|
|
||
| } | ||
|
|
||
| // otherwise make a new store config for it | ||
| var newName = this.name+'_'+basename+'_'+uniqCounter++; | ||
| configs[newName] = { | ||
| type: this.storeType, | ||
| name: newName, | ||
| fileBasename: basename | ||
| }; | ||
| configs[newName][this.fileConfKey] = this._makeBlob( resource ); | ||
|
|
||
| return true; | ||
| } else { | ||
| for(const index in this.indexTypes) { | ||
| if( resource.type == index.indexExtension ) { | ||
| var basename = Util.basename( | ||
| resource.file ? resource.file.name : | ||
| resource.url ? resource.url : | ||
| '' | ||
| , '.'+index.indexExtension | ||
| ); | ||
| if( !basename ) | ||
| return false; | ||
|
|
||
| // go through the configs and look for data files that match like zee.bam -> zee.bam.bai | ||
| for( var n in configs ) { | ||
| var c = configs[n]; | ||
| if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey].url || c[this.fileConfKey].blob.name : c[this.fileUrlConfKey] ) == basename ) { | ||
| // it's a match, put it in | ||
| c[index.indexConfKey] = this._makeBlob( resource ); | ||
| return true; | ||
| } | ||
| } | ||
| // go through again and look for data files that match like zee.bam -> zee.bai | ||
| for( var n in configs ) { | ||
| var c = configs[n]; | ||
| if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey].url || c[this.fileConfKey].blob.name : c[this.fileUrlConfKey], '.'+this.fileExtension ) == basename ) { | ||
| // it's a match, put it in | ||
| c[index.indexConfKey] = this._makeBlob( resource ); | ||
| return true; | ||
| } | ||
| } | ||
|
|
||
| // otherwise make a new store | ||
| var newName = this.name+'_'+Util.basename(basename,'.'+this.fileExtension)+'_'+uniqCounter++; | ||
| configs[newName] = { | ||
| name: newName, | ||
| type: this.storeType | ||
| }; | ||
|
|
||
| configs[newName][index.indexConfKey] = this._makeBlob( resource ); | ||
| return true; | ||
| } | ||
| } | ||
| } | ||
| return false; | ||
| }, | ||
|
|
||
| // try to merge any singleton file and index stores. currently can only do this if there is one of each | ||
| finalizeConfiguration: function( configs ) { | ||
|
|
||
| }, | ||
|
|
||
| _makeBlob: function( resource ) { | ||
| var r = resource.file ? new FileBlob( resource.file ) : | ||
| resource.url ? new XHRBlob( resource.url ) : | ||
| null; | ||
| if( ! r ) | ||
| throw 'unknown resource type'; | ||
| return r; | ||
|
|
||
| }, | ||
|
|
||
| confIsValid: function( conf ) { | ||
| var valid = false; | ||
| for(var i in this.indexTypes) { | ||
| valid |= (conf[this.fileConfKey] || conf[this.fileUrlConfKey]) && ( conf[index.indexConfKey] || conf[index.indexUrlConfKey] || conf[this.fileUrlConfKey] ); | ||
| } | ||
| return valid; | ||
| } | ||
| }); | ||
| }); |