January 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Handle issues with invalid dicts received when from the tool shed api.
by commits-noreply＠bitbucket.org 09 Jan '14

09 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/61721f9eda65/ Changeset: 61721f9eda65 User: greg Date: 2014-01-09 03:15:31 Summary: Handle issues with invalid dicts received when from the tool shed api. Affected #: 1 file diff -r 70e221c1f38213b21c08ca44d9f92a892612d67b -r 61721f9eda65b1e7444264249815ad993e61fb27 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -469,7 +469,14 @@ def get_repository_dict( url, repository_dict ): error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] + if not isinstance( repository_dict, dict ): + error_message = 'Invalid repository_dict received: %s' % str( repository_dict ) + return None, error_message + repository_id = repository_dict.get( 'repository_id', None ) + if repository_id is None: + error_message = 'Invalid repository_dict does not contain a repository_id entry: %s' % str( repository_dict ) + return None, error_message + parts = [ 'api', 'repositories', repository_id ] api_url = get_api_url( base=url, parts=parts ) extended_dict, error_message = json_from_url( api_url ) if error_message: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional browser tests: update history options tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70e221c1f382/ Changeset: 70e221c1f382 User: carlfeberhard Date: 2014-01-08 23:47:26 Summary: Functional browser tests: update history options tests Affected #: 3 files diff -r 97d124fbe9fbbe2e7026b92db35e77e87e4ef435 -r 70e221c1f38213b21c08ca44d9f92a892612d67b test/casperjs/history-options-tests.js --- a/test/casperjs/history-options-tests.js +++ b/test/casperjs/history-options-tests.js @@ -114,8 +114,15 @@ this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); }); +}); + +spaceghost.then( function(){ // undelete the uploaded file - this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); + this.historyoptions.includeDeleted( function(){ + this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); + spaceghost.debug( 'undeleted' ); + }); + }); // ------------------------------------------------------------------- hidden hdas aren't shown @@ -132,10 +139,8 @@ this.historyoptions.collapseExpanded( function(){ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withHistoryPanel( function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); diff -r 97d124fbe9fbbe2e7026b92db35e77e87e4ef435 -r 70e221c1f38213b21c08ca44d9f92a892612d67b test/casperjs/modules/historyoptions.js --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -34,8 +34,11 @@ * @returns {Any} the return value of fn */ HistoryOptions.prototype.openMenu = function openMenu( fn ){ + return this.spaceghost.jumpToTop( function(){ - this.click( this.historyoptions.data.selectors.button ); + if( !spaceghost.visible( this.historyoptions.data.selectors.menu ) ){ + this.click( this.historyoptions.data.selectors.button ); + } return fn.call( this ); }); }; @@ -170,41 +173,32 @@ * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.includeDeleted = function includeDeleted( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, true ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeDeleted, true ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Deleted Datasets' to off * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.excludeDeleted = function excludeDeleted( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, false ); - //TODO:?? this puts in the history frame. Is that what we want? - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeDeleted, false ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Hidden Datasets' to on * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.includeHidden = function includeHidden( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, true ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeHidden, true ); + this.spaceghost.historypanel.waitForHdas( then ); }; /** set 'Include Hidden Datasets' to off * @param {Function} then casper step to run when option is set */ HistoryOptions.prototype.excludeHidden = function excludeHidden( then ){ - return this.spaceghost.then( function(){ - this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, false ); - this.historypanel.waitForHdas( then ); - }); + this.toggle( this.data.labels.options.includeHidden, false ); + this.spaceghost.historypanel.waitForHdas( then ); }; @@ -213,14 +207,14 @@ HistoryOptions.prototype.data = { selectors : { button : '#history-options-button', - buttonIcon : '#history-options-button span.fa-icon-cog', + buttonIcon : '#history-options-button span.fa-cog', menu : '#history-options-button-menu', optionXpathByLabelFn : function optionXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); }, optionIsOnXpathByLabelFn : function optionIsOnXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' - + '/span[@class="fa-icon-ok"]' ); + + '/span[@class="fa fa-check"]' ); } }, labels : { diff -r 97d124fbe9fbbe2e7026b92db35e77e87e4ef435 -r 70e221c1f38213b21c08ca44d9f92a892612d67b test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -271,7 +271,7 @@ */ HistoryPanel.prototype.undeleteHda = function undeleteHda( hdaSelector, whenUndeletedFn ){ this.spaceghost.historyoptions.includeDeleted( function(){ - this.click( hdaSelector + ' ' + this.historypanel.data.selectors.history.undeleteLink ); + this.click( hdaSelector + ' ' + this.historypanel.data.selectors.hda.undeleteLink ); this.historyoptions.excludeDeleted( function(){ this.info( 'hda undeleted: ' + hdaSelector ); if( utils.isFunction( whenUndeletedFn ) ){ whenUndeletedFn.call( this ); } @@ -338,7 +338,6 @@ annoArea : '.history-controls .annotation-display', emptyMsg : '.empty-history-message', hdaContainer: '.datasets-list' - //undeleteLink : '.historyItemUndelete', }, hda : { wrapper : { @@ -361,6 +360,9 @@ primaryActionButtons : '.dataset-actions .left', secondaryActionButtons : '.dataset-actions .right', + undeleteLink : '.dataset-undelete', + purgeLink : '.dataset-purge', + peek : '.dataset-peek' } }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Filter out deprecated repositories when resetting metadata on repositories in the tool shed - resetting metadata on deprecated repositories is essential only for ensuring reproducibility.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97d124fbe9fb/ Changeset: 97d124fbe9fb User: greg Date: 2014-01-08 22:26:51 Summary: Filter out deprecated repositories when resetting metadata on repositories in the tool shed - resetting metadata on deprecated repositories is essential only for ensuring reproducibility. Affected #: 1 file diff -r 626622be165b95acf40430ef309b92c1daa0b9ae -r 97d124fbe9fbbe2e7026b92db35e77e87e4ef435 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -865,9 +865,10 @@ def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=True ): """ - Return a query containing repositories for resetting metadata. This method is called from both the Tool Shed and Galaxy. The - my_writable parameter is ignored unless called from the Tool Shed, and the order parameter is used for displaying the list of - repositories ordered alphabetically for display on a page. When called from wither the Tool Shed or Galaxy API, order is False. + Return a query containing repositories for resetting metadata. This method is called from both the + Tool Shed and Galaxy. The my_writable parameter is ignored unless called from the Tool Shed, and the + order parameter is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from either the Tool Shed or Galaxy API, order is False. """ if trans.webapp.name == 'tool_shed': # When called from the Tool Shed API, the metadata is reset on all repositories of type tool_dependency_definition in addition @@ -876,7 +877,8 @@ username = trans.user.username clause_list = [] for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): # Always reset metadata on all repositories of type tool_dependency_definition. if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION: clause_list.append( trans.model.Repository.table.c.id == repository.id ) @@ -903,12 +905,14 @@ else: if order: return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ) \ .order_by( trans.model.Repository.table.c.name, trans.model.Repository.table.c.user_id ) else: return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ) else: # We're in Galaxy. if order: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional browser tests: update hda state tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/626622be165b/ Changeset: 626622be165b User: carlfeberhard Date: 2014-01-08 22:20:28 Summary: Functional browser tests: update hda state tests Affected #: 6 files diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -215,7 +215,8 @@ // return either: a single download icon-button (if there are no meta files) if( _.isEmpty( meta_files ) ){ return $([ - '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" class="icon-btn">', + '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" ', + 'class="icon-btn dataset-download-btn">', '<span class="fa fa-floppy-o"></span>', '</a>' ].join( '' ) ); @@ -239,7 +240,8 @@ '</div>', '<div class="icon-btn-group">', - '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" class="icon-btn">', + '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" ', + 'class="icon-btn dataset-download-btn">', '<span class="fa fa-floppy-o"></span>', // join these w/o whitespace or there'll be a gap when rendered '</a><a class="icon-btn popup" id="' + menuId + '">', @@ -257,6 +259,7 @@ // gen. safe to show in all cases return faIconButton({ title : _l( 'View details' ), + classes : 'dataset-params-btn', href : this.urls.show_params, target : this.linkTarget, faIcon : 'fa-info-circle' diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -72,7 +72,7 @@ var purged = this.model.get( 'purged' ), deleted = this.model.get( 'deleted' ), editBtnData = { - title : _l( 'Edit Attributes' ), + title : _l( 'Edit attributes' ), href : this.urls.edit, target : this.linkTarget, classes : 'dataset-edit' @@ -138,6 +138,7 @@ return faIconButton({ title : _l( 'View or report this error' ), href : this.urls.report_error, + classes : 'dataset-report-error-btn', target : this.linkTarget, faIcon : 'fa-bug' }); @@ -150,6 +151,7 @@ return faIconButton({ title : _l( 'Run this job again' ), href : this.urls.rerun, + classes : 'dataset-rerun-btn', target : this.linkTarget, faIcon : 'fa-refresh' }); @@ -189,6 +191,7 @@ var $icon = faIconButton({ title : _l( 'Visualize' ), + classes : 'dataset-visualize-btn', faIcon : 'fa-bar-chart-o' }); @@ -242,6 +245,7 @@ } var $icon = faIconButton({ title : _l( 'Visualize' ), + classes : 'dataset-visualize-btn', faIcon : 'fa-bar-chart-o' }); $icon.addClass( 'visualize-icon' ); // needed? @@ -364,8 +368,10 @@ // make the dbkey a link to editing if( this.model.get( 'metadata_dbkey' ) === '?' && !this.model.isDeletedOrPurged() ){ - $body.find( '.dataset-dbkey .value' ).replaceWith( - $( '<a target="' + this.linkTarget + '">?</a>' ).attr( 'href', this.urls.edit ) ); + var editableDbkey = $( '<a class="value">?</a>' ) + .attr( 'href', this.urls.edit ) + .attr( 'target', this.linkTarget ); + $body.find( '.dataset-dbkey .value' ).replaceWith( editableDbkey ); } }, diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(h){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var g=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);h.find(".dataset-dbkey .value").replaceWith(g)}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -56,7 +56,7 @@ filepathToUpload = '../../test-data/1.txt', testUploadInfo = {}, //TODO: get from the api module - that doesn't exist yet - summaryShouldBeArray = [ '10 lines', 'format: txt' ], + summaryShouldBeArray = [ '10 lines', 'format', 'txt' ], infoShouldBe = 'uploaded txt file', metadataFiles = null, peekShouldBeArray = []; @@ -104,13 +104,14 @@ if( expectedButtonData.hrefTpl ){ var href = buttonElement.attributes.href, - hrefShouldBe = utils.format( expectedButtonData.hrefTpl, hdaDbId ); + hrefShouldBe = ( expectedButtonData.hrefTpl.indexOf( '%s' ) !== -1 )? + ( utils.format( expectedButtonData.hrefTpl, hdaDbId ) ):( expectedButtonData.hrefTpl ); this.assertTextContains( href, hrefShouldBe, buttonName + ' has proper href (' + hrefShouldBe + '): ' + href ); } if( expectedButtonData.tooltip ){ - this.historypanel.hoverOver( btnSelector ); + this.hoverOver( btnSelector ); var tooltipText = expectedButtonData.tooltip; this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); this.test.assertSelectorHasText( tooltipSelector, tooltipText, @@ -159,7 +160,7 @@ this.test.assertSelectorHasText( dbkeySelector, dbkeySetTo, 'dbkey is specified: ' + dbkey.text ); this.test.assert( dbkey.nodeName === specifiedDbkeyNodeName, - 'dbkey has proper nodeName (' + specifiedDbkeyNodeName + '):' + dbkey.nodeName ); + 'dbkey has proper nodeName (' + specifiedDbkeyNodeName + '): ' + dbkey.nodeName ); // dbkey expected to be not set } else { @@ -305,7 +306,7 @@ // =================================================================== TESTS // ------------------------------------------------------------------- ok state -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; @@ -329,13 +330,10 @@ this.test.comment( 'clicking the hda title should expand its body' ); this.historypanel.thenExpandHda( uploadSelector, function(){ - // ugh. - this.jumpToHistory( function(){ - testExpandedBody.call( spaceghost, uploadSelector, - summaryShouldBeArray, infoShouldBe, false, metadataFiles ); - //testExpandedBody.call( spaceghost, uploadSelector, - // summaryShouldBeArray, infoShouldBe, false ); - }); + testExpandedBody.call( spaceghost, uploadSelector, + summaryShouldBeArray, infoShouldBe, false, metadataFiles ); + //testExpandedBody.call( spaceghost, uploadSelector, + // summaryShouldBeArray, infoShouldBe, false ); }); }); // restore to collapsed @@ -350,7 +348,7 @@ }); // ------------------------------------------------------------------- new state -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ // set state directly through model, wait for re-render //TODO: not ideal to test this this.evaluate( function(){ @@ -385,7 +383,7 @@ 'HDA body has text: ' + expectedBodyText ); }); - this.historypanel.then( function(){ + this.then( function(){ this.test.comment( 'a simulated error on a new dataset should appear in a message box' ); // datasets that error on fetching their data appear as 'new', so do this here // more of a unit test, but ok @@ -410,7 +408,7 @@ }); }); // restore state, collapse -spaceghost.withHistoryPanel( function revertStateAndCollapse(){ +spaceghost.then( function revertStateAndCollapse(){ var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.historypanel.thenCollapseHda( uploadSelector, function(){ diff -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c -r 626622be165b95acf40430ef309b92c1daa0b9ae test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -136,7 +136,7 @@ */ HistoryPanel.prototype._thenExpandOrCollapseHda = function _thenExpandOrCollapseHda( hdaSelector, then, desiredClosed ){ // using a step here (instead of a jump) bc we need the wait for function - this.then( function checkingHda(){ + this.spaceghost.then( function checkingHda(){ this.info( (( desiredClosed )?( 'collapsing' ):( 'expanding' )) + ' hda: ' + hdaSelector ); // click to open if the body isn't visible and call wait to account for opening animation @@ -241,7 +241,7 @@ * @param {Function} timeoutFn function to be called if/when the deleted attempted times out (optional) */ HistoryPanel.prototype.deleteHda = function deleteHda( hdaSelector, whenDeletedFn, timeoutFn ){ - this.then( function deletingHda(){ + this.spaceghost.then( function deletingHda(){ var hdaId = this.getElementInfo( hdaSelector ).attributes.id, deleteIconSelector = '#' + hdaId + ' ' + this.historypanel.data.hdaTitleButtons['delete'].selector; this.click( deleteIconSelector ); @@ -286,39 +286,39 @@ hdaTitleButtons : { // mixing text and selectors here display : { - selector : '.icon-button.display', + selector : '.icon-btn.dataset-display', tooltip : 'View data', hrefTpl : '/datasets/%s/display', nodeName : 'a' }, edit : { - selector : '.icon-button.edit', - tooltip : 'Edit Attributes', + selector : '.icon-btn.dataset-edit', + tooltip : 'Edit attributes', hrefTpl : '/datasets/%s/edit', nodeName : 'a' }, 'delete' : { - selector : '.icon-button.delete', + selector : '.icon-btn.dataset-delete', tooltip : 'Delete', - hrefTpl : '/datasets/%s/delete_async', + hrefTpl : 'javascript:void(0);', nodeName : 'a' } }, hdaPrimaryActionButtons : { download : { - selector : '.icon-button.disk', + selector : '.icon-btn.dataset-download-btn', tooltip : 'Download', hrefTpl : '/datasets/%s/display?to_ext=', nodeName : 'a' }, info : { - selector : '.icon-button.information', + selector : '.icon-btn.dataset-params-btn', tooltip : 'View details', hrefTpl : '/datasets/%s/show_params', nodeName : 'a' }, rerun : { - selector : '.icon-button.arrow-circle', + selector : '.icon-btn.dataset-rerun-btn', tooltip : 'Run this job again', hrefTpl : '/tool_runner/rerun?id=%s', nodeName : 'a' @@ -354,12 +354,12 @@ title : '.dataset-title', titleButtonArea : '.dataset-primary-actions', summary : '.dataset-summary', - dbkey : '.dataset-dbkey', + dbkey : '.dataset-dbkey .value', info : '.dataset-info', body : '.dataset-body', - primaryActionButtons : 'div[id^="primary-actions"]', - secondaryActionButtons : 'div[id^="secondary-actions"]', + primaryActionButtons : '.dataset-actions .left', + secondaryActionButtons : '.dataset-actions .right', peek : '.dataset-peek' } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix the single broken tool shed functional test.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea6d81ebd300/ Changeset: ea6d81ebd300 User: greg Date: 2014-01-08 21:48:54 Summary: Fix the single broken tool shed functional test. Affected #: 1 file diff -r b315c617830932da07e9cd3247790d3d2d3486c7 -r ea6d81ebd3006f7aed499e80805d71842d6d8c1c test/tool_shed/functional/test_1160_circular_prior_installation_required.py --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -222,14 +222,16 @@ filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) + # TODO: Tweak the uninstall_repository method by pulling out the stuff that deactivates a repository + # instead of uninstalling it and create a new deactivate_repository method. self.uninstall_repository( filter_repository, remove_from_disk=False ) self.uninstall_repository( column_repository, remove_from_disk=False ) self.uninstall_repository( convert_repository, remove_from_disk=False ) - def test_0045_reinstall_filter_repository( self ): + def test_0045_reactivatel_filter_repository( self ): '''Reinstall the filtering_0160 repository.''' filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) - self.reinstall_repository( filter_repository ) + self.reactivate_repository( filter_repository ) strings_displayed = [ 'filtering_0160', "Galaxy's filtering tool for test 0160", 'user1', @@ -242,6 +244,7 @@ def test_0050_verify_reinstallation_order( self ): '''Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160.''' + # Fixme: this test is not covering any important behavior since repositories were only deactivated and not uninstalled. filter_repository = self.test_db_util.get_installed_repository_by_name_owner( filter_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Functional browser tests: update history panel tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b315c6178309/ Changeset: b315c6178309 User: carlfeberhard Date: 2014-01-08 21:41:32 Summary: Functional browser tests: update history panel tests Affected #: 3 files diff -r a7101734b29e8ff8aff0a8170bb8d0c5ec1a5455 -r b315c617830932da07e9cd3247790d3d2d3486c7 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -40,7 +40,7 @@ // selectors and labels var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, editableTextClass = spaceghost.data.selectors.editableText, - editableTextInput = spaceghost.data.selectors.editableTextInput, + editableTextInput = spaceghost.historypanel.data.selectors.history.nameEditableTextInput, nameSelector = spaceghost.historypanel.data.selectors.history.name, subtitleSelector = spaceghost.historypanel.data.selectors.history.subtitle, @@ -56,8 +56,7 @@ nameTooltip = spaceghost.historypanel.data.text.history.tooltips.name, refreshButtonSelector = 'a#history-refresh-button', - refreshButtonIconSelector = 'span.fa-icon-refresh', - refreshButtonHref = '/history', + refreshButtonIconSelector = 'span.fa-refresh', includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; @@ -76,9 +75,6 @@ // ------------------------------------------------------------------- check structure of empty history spaceghost.thenOpen( spaceghost.baseUrl ).historypanel.waitForHdas( function(){ this.test.comment( 'history panel with a new, empty history should be well formed' ); - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); this.test.assertExists( nameSelector, nameSelector + ' exists' ); @@ -103,11 +99,11 @@ }); // ------------------------------------------------------------------- name editing -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'history panel, editing the history name' ); this.test.comment( 'name should have a tooltip with proper info on name editing' ); - this.historypanel.hoverOver( nameSelector ); + this.hoverOver( nameSelector ); this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); // clear the tooltip @@ -116,6 +112,7 @@ this.test.comment( 'name should be create an input when clicked' ); this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); this.click( nameSelector ); + spaceghost.debug( editableTextInput ); this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); this.test.comment( 'name should be editable by entering keys and pressing enter' ); @@ -129,7 +126,7 @@ }); }); -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'name should revert if user clicks away while editing' ); this.click( nameSelector ); @@ -142,7 +139,7 @@ }); }); -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'name should revert if user hits ESC while editing' ); this.click( nameSelector ); @@ -168,7 +165,7 @@ testUploadInfo = _uploadInfo; }); -spaceghost.withHistoryPanel( function checkPanelStructure(){ +spaceghost.then( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); @@ -196,7 +193,7 @@ // ------------------------------------------------------------------- tags // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.withHistoryPanel( function openTags(){ +spaceghost.then( function openTags(){ this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); this.click( tagIconSelector ); @@ -204,7 +201,7 @@ this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); }); }); -spaceghost.withHistoryPanel( function closeAnnotation(){ +spaceghost.then( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); this.click( tagIconSelector ); @@ -216,7 +213,7 @@ // ------------------------------------------------------------------- annotation // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.withHistoryPanel( function openAnnotation(){ +spaceghost.then( function openAnnotation(){ this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); this.click( annoIconSelector ); @@ -224,7 +221,7 @@ this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); }); }); -spaceghost.withHistoryPanel( function closeAnnotation(){ +spaceghost.then( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); this.click( annoIconSelector ); @@ -240,12 +237,10 @@ this.test.assertExists( refreshButtonSelector, "Found refresh button" ); this.test.assertVisible( refreshButtonSelector, "Refresh button is visible" ); this.test.assertVisible( refreshButtonSelector + ' ' + refreshButtonIconSelector, "Refresh icon is visible" ); - this.test.assert( this.getElementAttribute( refreshButtonSelector, 'href' ) === refreshButtonHref, - "Refresh button has href: " + refreshButtonHref ); - this.assertNavigationRequested( refreshButtonHref, "History refreshed when clicking refresh icon", function(){ - this.click( refreshButtonSelector ); - }); + //this.assertNavigationRequested( refreshButtonHref, "History refreshed when clicking refresh icon", function(){ + // this.click( refreshButtonSelector ); + //}); }); // ------------------------------------------------------------------- hdas can be expanded by clicking on the hda name @@ -275,7 +270,7 @@ }); // ------------------------------------------------------------------- expanded hdas collapse by clicking name again -spaceghost.withHistoryPanel( function(){ +spaceghost.then( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; diff -r a7101734b29e8ff8aff0a8170bb8d0c5ec1a5455 -r b315c617830932da07e9cd3247790d3d2d3486c7 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -330,6 +330,7 @@ history : { title : '.history-title', name : '.history-title .history-name', + nameEditableTextInput : '.history-name input', subtitle : '.history-subtitle', tagIcon : '.history-secondary-actions .history-tag-btn', tagArea : '.history-controls .tags-display', diff -r a7101734b29e8ff8aff0a8170bb8d0c5ec1a5455 -r b315c617830932da07e9cd3247790d3d2d3486c7 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -559,7 +559,7 @@ SpaceGhost.prototype.hoverOver = function hoverOver( selector, whenHovering ){ var elementInfo = this.getElementInfo( selector ); this.page.sendEvent( 'mousemove', elementInfo.x + 1, elementInfo.y + 1 ); - whenHovering.call( this ); + if( whenHovering ){ whenHovering.call( this ); } return this; }; @@ -1107,7 +1107,6 @@ tooltipBalloon : '.tooltip', editableText : '.editable-text', - editableTextInput : 'input#renaming-active', messages : { all : '[class*="message"]', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for pruning content from the tool shed's repository dependencies container.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7101734b29e/ Changeset: a7101734b29e User: greg Date: 2014-01-08 21:27:25 Summary: Fix for pruning content from the tool shed's repository dependencies container. Affected #: 1 file diff -r 8ee5977b21731ee1815995bbcc290b09a46a13cc -r a7101734b29e8ff8aff0a8170bb8d0c5ec1a5455 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -744,7 +744,8 @@ lock.release() return containers_dict -def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None ): +def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, + exclude=None ): """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed.""" if exclude is None: exclude = [] @@ -806,11 +807,12 @@ containers_dict[ 'readme_files' ] = readme_files_root_folder if 'repository_dependencies' not in exclude: # Repository dependencies container. - folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( trans=trans, - folder_id=folder_id, - repository_dependencies=repository_dependencies, - label='Repository dependencies', - installed=False ) + folder_id, repository_dependencies_root_folder = \ + build_repository_dependencies_folder( trans=trans, + folder_id=folder_id, + repository_dependencies=repository_dependencies, + label='Repository dependencies', + installed=False ) if repository_dependencies_root_folder: containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Tool dependencies container. @@ -868,11 +870,13 @@ if metadata: if 'data_manager' not in exclude and 'data_manager' in metadata: data_managers = metadata['data_manager'].get( 'data_managers', None ) - folder_id, data_managers_root_folder = build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) + folder_id, data_managers_root_folder = \ + build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) containers_dict[ 'valid_data_managers' ] = data_managers_root_folder error_messages = metadata['data_manager'].get( 'error_messages', None ) data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) - folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) + folder_id, data_managers_root_folder = \ + build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder except Exception, e: log.exception( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) @@ -890,15 +894,22 @@ folder_id += 1 # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] - repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) + repository_dependencies_folder = Folder( id=folder_id, + key=repository_dependencies_folder_key, + label=label, + parent=repository_dependencies_root_folder ) del repository_dependencies[ 'root_key' ] - # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. - # We want the description value associated with the repository_dependencies_folder. + # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more + # repository_dependency keys. We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) del repository_dependencies[ 'description' ] repository_dependencies_folder, folder_id, repository_dependency_id = \ - populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ) + populate_repository_dependencies_container( trans, + repository_dependencies_folder, + repository_dependencies, + folder_id, + repository_dependency_id ) repository_dependencies_folder = prune_repository_dependencies( repository_dependencies_folder ) else: repository_dependencies_root_folder = None @@ -985,11 +996,13 @@ tools_root_folder = None return folder_id, tools_root_folder -def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False ): +def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, + new_install=False, reinstalling=False ): """Return a folder hierarchy containing tool dependencies.""" - # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, they are considered missing. The tool - # dependency status will be displayed only if a record exists for the tool dependency in the Galaxy database, but the tool dependency is not installed. - # The value for new_install will be True only if the associated repository in being installed for the first time. This value is used in setting the + # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, + # they are considered missing. The tool dependency status will be displayed only if a record exists for the tool + # dependency in the Galaxy database, but the tool dependency is not installed. The value for new_install will be + # True only if the associated repository in being installed for the first time. This value is used in setting the # container description. if tool_dependencies: tool_dependency_id = 0 @@ -1138,7 +1151,10 @@ else: containing_folder = tool_test_results_root_folder folder_id += 1 - test_environment_folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + test_environment_folder = Folder( id=folder_id, + key='test_environment', + label='Automated test environment', + parent=containing_folder ) containing_folder.folders.append( test_environment_folder ) try: architecture = test_environment_dict.get( 'architecture', '' ) @@ -1184,7 +1200,10 @@ passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if len( passed_tests_dicts ) > 0: folder_id += 1 - passed_tests_folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) + passed_tests_folder = Folder( id=folder_id, + key='passed_tests', + label='Tests that passed successfully', + parent=containing_folder ) containing_folder.folders.append( passed_tests_folder ) passed_test_id = 0 for passed_tests_dict in passed_tests_dicts: @@ -1395,7 +1414,8 @@ rd_tool_shed = str( repository_dependency_successful_installation_dict.get( 'tool_shed', '' ) ) rd_name = str( repository_dependency_successful_installation_dict.get( 'name', '' ) ) rd_owner = str( repository_dependency_successful_installation_dict.get( 'owner', '' ) ) - rd_changeset_revision = str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) + rd_changeset_revision = \ + str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) except Exception, e: rd_tool_shed = 'unknown' rd_name = 'unknown' @@ -1495,7 +1515,8 @@ # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other # entry that may be added in the future. - display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', 'not_tested', 'passed_tests', 'skipped_tests' ] + display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', + 'not_tested', 'passed_tests', 'skipped_tests' ] for k, v in tool_test_results_dict.items(): if k in display_entries: # We've discovered an entry that can be displayed, so see if it has a value since displaying @@ -1506,8 +1527,9 @@ def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): """ - Change any empty folders contained within the repository dependencies container into a repository dependency since it has no repository dependencies - of it's own. This method is not used (and may not be needed), but here it is just in case. + Change any empty folders contained within the repository dependencies container into a repository dependency + since it has no repository dependencies of it's own. This method is not used (and may not be needed), but here + it is just in case. """ if not folder.folders and not folder.repository_dependencies: repository_dependency_id += 1 @@ -1519,10 +1541,14 @@ return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) return folder, repository_dependency_id -def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td, key ): +def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td, key ): """Return a repository dependency label based on the repository dependency key.""" - if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ): + if key_is_current_repositorys_key( repository_name, + repository_owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, key ): label = 'Repository dependencies' else: if galaxy.util.asbool( prior_installation_required ): @@ -1533,8 +1559,8 @@ ( repository_name, changeset_revision, repository_owner, prior_installation_required_str ) return label -def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td ): +def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td ): """Assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported.""" return '%s%s%s%s%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ), STRSEP, @@ -1551,13 +1577,6 @@ def generate_tool_dependencies_key( name, version, type ): return '%s%s%s%s%s' % ( str( name ), STRSEP, str( version ), STRSEP, str( type ) ) -def get_folder( folder, key ): - if folder.key == key: - return folder - for sub_folder in folder.folders: - return get_folder( sub_folder, key ) - return None - def get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ): """Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page.""" # Default prior_installation_required and only_if_compiling_contained_td to False. @@ -1610,7 +1629,15 @@ # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions. return toolshed_base_url, repository_name, repository_owner, changeset_revision -def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): +def get_folder( folder, key ): + if folder.key == key: + return folder + for sub_folder in folder.folders: + return get_folder( sub_folder, key ) + return None + +def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, + repository_dependency_id, folder_keys ): repository_components_tuple = get_components_from_key( rd_key ) components_list = suc.extract_components_from_tuple( repository_components_tuple ) toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ] @@ -1713,11 +1740,21 @@ return True return False -def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ): - folder_keys = repository_dependencies.keys() +def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, + repository_dependency_id ): + folder_keys = [] + for key in repository_dependencies.keys(): + if key not in folder_keys: + folder_keys.append( key ) for key, value in repository_dependencies.items(): repository_dependencies_folder, folder_id, repository_dependency_id = \ - handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, key, value, folder_id, repository_dependency_id, folder_keys ) + handle_repository_dependencies_container_entry( trans, + repository_dependencies_folder, + key, + value, + folder_id, + repository_dependency_id, + folder_keys ) return repository_dependencies_folder, folder_id, repository_dependency_id def print_folders( pad, folder ): @@ -1731,19 +1768,22 @@ for sub_folder in folder.folders: print_folders( pad+5, sub_folder ) +def prune_folder( folder, repository_dependency ): + listified_repository_dependency = repository_dependency.listify + if is_subfolder_of( folder, listified_repository_dependency ): + folder.repository_dependencies.remove( repository_dependency ) + def prune_repository_dependencies( folder ): """ - Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be json-serialize-able), the - order in which the dictionary is processed to create the container sometimes results in repository dependency entries in a folder that also - includes the repository dependency as a sub-folder (if the repository dependency has it's own repository dependency). This method will remove - all repository dependencies from folder that are also sub-folders of folder. + Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be + json-serialize-able), the order in which the dictionary is processed to create the container sometimes results in + repository dependency entries in a folder that also includes the repository dependency as a sub-folder (if the + repository dependency has it's own repository dependency). This method will remove all repository dependencies from + folder that are also sub-folders of folder. """ repository_dependencies = [ rd for rd in folder.repository_dependencies ] for repository_dependency in repository_dependencies: - listified_repository_dependency = repository_dependency.listify - if is_subfolder_of( folder, listified_repository_dependency ): - repository_dependencies.remove( repository_dependency ) - folder.repository_dependencies = repository_dependencies + prune_folder( folder, repository_dependency ) for sub_folder in folder.folders: return prune_repository_dependencies( sub_folder ) return folder Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional browser tests: update anon history tests
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ee5977b2173/ Changeset: 8ee5977b2173 User: carlfeberhard Date: 2014-01-08 21:06:57 Summary: Functional browser tests: update anon history tests Affected #: 3 files diff -r 83cbc7f1768231d92ee26604d1b03b8650f020a6 -r 8ee5977b21731ee1815995bbcc290b09a46a13cc test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -54,7 +54,8 @@ anonNameTooltip = spaceghost.historypanel.data.text.anonymous.tooltips.name; var historyFrameInfo = {}, - filepathToUpload = '../../test-data/1.txt', + filenameToUpload = '1.txt', + filepathToUpload = '../../test-data/' + filenameToUpload, testUploadInfo = {}; @@ -71,10 +72,6 @@ spaceghost.historypanel.waitForHdas( function testPanelStructure(){ this.test.comment( 'history panel for anonymous user, new history' ); - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); this.test.assertExists( nameSelector, nameSelector + ' exists' ); this.test.assertVisible( nameSelector, 'History name is visible' ); @@ -96,11 +93,6 @@ this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, 'Message contains "' + emptyMsgStr + '"' ); - this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); - this.historypanel.hoverOver( nameSelector ); - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); - this.test.comment( 'name should NOT be editable when clicked by anon-user' ); this.assertDoesntHaveClass( nameSelector, editableTextClass, "Name field is not classed as editable text" ); this.click( nameSelector ); @@ -115,10 +107,11 @@ this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( _uploadInfo.hdaElement ) ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'state-ok' ) !== -1; this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.hdaElement.text ); testUploadInfo = _uploadInfo; }); + }); spaceghost.then( function testAnonUpload(){ this.test.comment( "empty should be NO LONGER be displayed" ); @@ -136,7 +129,7 @@ this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); this.historypanel.waitForHdas( function(){ - var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.hdaElement.text ); + var hdaInfo = this.historypanel.hdaElementInfoByTitle( filenameToUpload ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, diff -r 83cbc7f1768231d92ee26604d1b03b8650f020a6 -r 8ee5977b21731ee1815995bbcc290b09a46a13cc test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -33,33 +33,16 @@ // =================================================================== API (external) // ------------------------------------------------------------------- frame control -///** Is casper currently 'in' the history frame? -// * @returns {Boolean} +///** Hover over an element in the history panel. +// * @param {String} selector a css or xpath selector for an historyItemWrapper // */ -//HistoryPanel.prototype.inFrame = function inFrame(){ -// return ( ( this.spaceghost.page.frameName === this.spaceghost.data.selectors.frames.history ) -// && ( this.spaceghost.page.frameTitle === this.data.text.frameTitle ) ); +//HistoryPanel.prototype.hoverOver = function hoverOver( selector ){ +// var spaceghost = this.spaceghost, +// elementInfo = spaceghost.getElementInfo( selector ); +// spaceghost.page.sendEvent( 'mousemove', elementInfo.x + 1, elementInfo.y + 1 ); +// return spaceghost; //}; -/** Hover over an element in the history panel. - * @param {String} selector a css or xpath selector for an historyItemWrapper - */ -HistoryPanel.prototype.hoverOver = function hoverOver( selector ){ - var spaceghost = this.spaceghost, - historyFrameInfo = spaceghost.jumpToTop( function(){ - return spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); - }); - //spaceghost.debug( 'historyFrameInfo:\n' + spaceghost.jsonStr( historyFrameInfo ) ); - - spaceghost.jumpToHistory( function(){ - var elementInfo = spaceghost.getElementInfo( selector ), - newCoords = { x: ( historyFrameInfo.x + elementInfo.x ), - y: ( historyFrameInfo.y + elementInfo.y ) }; - spaceghost.page.sendEvent( 'mousemove', newCoords.x + 1, newCoords.y + 1 ); - }); - return spaceghost; -}; - // ------------------------------------------------------------------- hdas ///** Parse the hid and name from an HDA title. // * NOTE: if more than one is found, will return the first found. diff -r 83cbc7f1768231d92ee26604d1b03b8650f020a6 -r 8ee5977b21731ee1815995bbcc290b09a46a13cc test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -89,9 +89,11 @@ // click the upload tool spaceghost.thenOpen( spaceghost.baseUrl, function(){ // we can apprently click a tool label without expanding the tool container for it - this.click( xpath( '//a[contains(text(),"Upload File")]' ) ); - this.jumpToMain( function(){ - this.waitForSelector( 'body' ); + this.waitForSelector( '.toolMenu', function(){ + this.click( xpath( '//a[contains(text(),"Upload File")]' ) ); + this.jumpToMain( function(){ + this.waitForSelector( 'body' ); + }); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Allow specifying the functional tests' install_database_connection with an environment variable.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83cbc7f17682/ Changeset: 83cbc7f17682 User: inithello Date: 2014-01-08 20:50:19 Summary: Allow specifying the functional tests' install_database_connection with an environment variable. Affected #: 1 file diff -r 16495aaa26ea3d8feabcd25ee395608568156b6f -r 83cbc7f1768231d92ee26604d1b03b8650f020a6 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -313,6 +313,7 @@ file_path = os.path.join( galaxy_db_path, 'files' ) new_file_path = tempfile.mkdtemp( prefix='new_files_path_', dir=tempdir ) job_working_directory = tempfile.mkdtemp( prefix='job_working_directory_', dir=tempdir ) + install_database_connection = os.environ.get( 'GALAXY_TEST_INSTALL_DBURI', None ) if 'GALAXY_TEST_DBURI' in os.environ: database_connection = os.environ['GALAXY_TEST_DBURI'] else: @@ -372,6 +373,8 @@ user_library_import_dir=user_library_import_dir, master_api_key=master_api_key, ) + if install_database_connection is not None: + kwargs[ 'install_database_connection' ] = install_database_connection if psu_production: kwargs[ 'global_conf' ] = None if not database_connection.startswith( 'sqlite://' ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Remove files from test-data that are not referenced in any tool test definition or functional test script.
by commits-noreply＠bitbucket.org 08 Jan '14

08 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16495aaa26ea/ Changeset: 16495aaa26ea User: inithello Date: 2014-01-08 20:15:53 Summary: Remove files from test-data that are not referenced in any tool test definition or functional test script. Affected #: 97 files diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/10.bed --- a/test-data/10.bed +++ /dev/null @@ -1,40 +0,0 @@ -chr6 41411592 41411644 CCDS4855.1_cds_0_0_chr6_41411593_f 0 + -chr6 41411802 41412144 CCDS4855.1_cds_1_0_chr6_41411803_f 0 + -chr6 41417509 41417645 CCDS4855.1_cds_2_0_chr6_41417510_f 0 + -chr6 41417751 41417865 CCDS4855.1_cds_3_0_chr6_41417752_f 0 + -chr6 41426393 41426580 CCDS4855.1_cds_4_0_chr6_41426394_f 0 + -chr6 41641476 41641680 CCDS4856.1_cds_0_0_chr6_41641477_f 0 + -chr6 41653701 41653797 CCDS4856.1_cds_1_0_chr6_41653702_f 0 + -chr6 41660484 41660607 CCDS4856.1_cds_2_0_chr6_41660485_f 0 + -chr6 41661146 41661233 CCDS4856.1_cds_3_0_chr6_41661147_f 0 + -chr6 41662724 41662872 CCDS4856.1_cds_4_0_chr6_41662725_f 0 + -chr6 73388638 73389036 CCDS4976.1_cds_0_0_chr6_73388639_f 0 + -chr6 73770351 73770442 CCDS4976.1_cds_1_0_chr6_73770352_f 0 + -chr6 73808379 73808506 CCDS4976.1_cds_2_0_chr6_73808380_f 0 + -chr6 73843765 73843941 CCDS4976.1_cds_3_0_chr6_73843766_f 0 + -chr6 73844205 73844331 CCDS4976.1_cds_4_0_chr6_73844206_f 0 + -chr6 73871700 73871811 CCDS4976.1_cds_5_0_chr6_73871701_f 0 + -chr6 73877751 73877847 CCDS4976.1_cds_6_0_chr6_73877752_f 0 + -chr6 73886926 73887021 CCDS4976.1_cds_7_0_chr6_73886927_f 0 + -chr6 73890929 73890956 CCDS4976.1_cds_8_0_chr6_73890930_f 0 + -chr6 73899864 73900085 CCDS4976.1_cds_9_0_chr6_73899865_f 0 + -chr6 108650846 108650942 CCDS5064.1_cds_2_0_chr6_108650847_r 0 - -chr6 108688656 108688818 CCDS5064.1_cds_3_0_chr6_108688657_r 0 - -chr6 108650133 108650217 CCDS5066.1_cds_0_0_chr6_108650134_r 0 - -chr6 108650846 108650942 CCDS5066.1_cds_1_0_chr6_108650847_r 0 - -chr6 108688656 108688818 CCDS5066.1_cds_2_0_chr6_108688657_r 0 - -chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + -chr6 108751721 108751945 CCDS5067.1_cds_1_0_chr6_108751722_f 0 + -chr6 108774884 108774936 CCDS5067.1_cds_2_0_chr6_108774885_f 0 + -chr6 108783550 108783652 CCDS5067.1_cds_3_0_chr6_108783551_f 0 + -chr6 108784586 108784717 CCDS5067.1_cds_4_0_chr6_108784587_f 0 + -chr6 132171024 132171108 CCDS5150.1_cds_0_0_chr6_132171025_f 0 + -chr6 132210608 132210681 CCDS5150.1_cds_1_0_chr6_132210609_f 0 + -chr6 132212822 132212939 CCDS5150.1_cds_2_0_chr6_132212823_f 0 + -chr6 132213974 132214100 CCDS5150.1_cds_3_0_chr6_132213975_f 0 + -chr6 132215007 132215068 CCDS5150.1_cds_4_0_chr6_132215008_f 0 + -chr6 132217758 132217856 CCDS5150.1_cds_5_0_chr6_132217759_f 0 + -chr6 132221500 132221580 CCDS5150.1_cds_6_0_chr6_132221501_f 0 + -chr6 132223219 132223339 CCDS5150.1_cds_7_0_chr6_132223220_f 0 + -chr6 132224427 132224537 CCDS5150.1_cds_8_0_chr6_132224428_f 0 + -chr6 132227338 132227404 CCDS5150.1_cds_9_0_chr6_132227339_f 0 + diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/11.bed --- a/test-data/11.bed +++ /dev/null @@ -1,427 +0,0 @@ -chr5 166353 209999 NM_001083010 0 + 166353 209999 0 5 210,339,51,123,87, 0,26271,31586,42829,43559, -chr5 244659 248480 NM_001033042 0 + 244662 248468 0 3 291,582,660, 0,309,3161, -chr5 244662 248480 NM_001109333 0 + 244662 248468 0 3 288,582,660, 0,306,3158, -chr5 257679 269976 NM_001103318 0 - 258411 269964 0 5 27,77,24,668,135, 0,280,458,724,12162, -chr5 258441 269974 NM_198766 0 - 258441 269964 0 2 632,131, 0,11402, -chr5 277474 309535 NM_057862 0 + 277474 309535 0 13 158,148,162,3,150,124,167,201,156,99,123,96,30, 0,1055,1523,1798,3825,6517,9117,10782,12086,16018,26986,30033,32031, -chr5 277474 309535 NM_166344 0 + 277474 309535 0 13 158,148,162,3,150,124,167,201,156,99,123,96,30, 0,1055,1523,1798,3825,6517,9117,10782,12086,16018,26986,30033,32031, -chr6 50942 51856 NM_146402 0 - 50942 51856 0 1 914, 0, -chr6 50942 51856 NM_001000918 0 - 50942 51856 0 1 914, 0, -chr6 50942 51856 NM_001000608 0 - 50942 51856 0 1 914, 0, -chr6 50942 51856 NM_001000579 0 - 50942 51856 0 1 914, 0, -chr6 249621 295948 NM_134068 0 + 249621 295868 0 7 40,83,50,75,168,77,127, 0,7258,30492,41232,43481,44143,46200, -chr6 249621 295948 NM_001108412 0 + 249621 295868 0 7 40,77,56,75,172,73,127, 0,7258,30486,41232,43481,44147,46200, -chr6 249621 293951 NM_001037955 0 + 249621 293951 0 6 40,83,50,75,168,187, 0,7258,30492,41232,43481,44143, -chr6 336770 354706 NM_001106108 0 + 338152 352598 0 12 33,222,187,89,145,108,354,116,141,14,97,79, 0,1376,3050,4076,5337,7057,9653,13247,15687,16408,17049,17857, -chr6 336770 354947 NM_013674 0 + 338152 352598 0 13 30,222,187,89,145,108,354,116,141,13,93,112,49, 0,1376,3050,4076,5337,7057,9653,13247,15687,16407,17050,17845,18128, -chr6 338179 352598 NM_204299 0 + 338179 352598 0 8 189,189,37,108,350,2,115,144, 0,1641,4036,5648,8244,8603,11836,14275, -chr6 338221 350100 NM_212879 0 + 338221 350100 0 4 147,165,175,36, 0,1599,8375,11843, -chr6 338228 346773 NM_204558 0 + 338228 346773 0 4 140,168,90,183, 0,1592,8192,8362, -chr6 430099 638147 NM_134414 0 - 431670 582818 0 31 24,94,63,59,123,56,142,117,67,4,58,60,81,62,121,166,59,123,126,119,103,80,145,81,125,101,5,135,177,163,42, 0,1571,3879,6028,12267,14545,47369,64075,68754,70102,70131,70854,71384,77684,78933,79444,79771,87420,91657,107369,112921,113762,113980,124998,132611,134330,144691,144727,147841,152601,208006, -chr6 431670 582863 NM_025588 0 - 431670 582818 0 29 94,63,59,120,59,142,117,67,4,58,60,81,62,121,166,59,123,2,126,119,103,80,145,81,125,111,129,177,163, 0,2308,4457,10696,12971,45798,62504,67183,68531,68560,69283,69813,76113,77362,77873,78200,85849,90025,90086,105798,111350,112191,112409,123427,131040,132759,143162,146270,151030, -chr6 431691 582818 NM_200604 0 - 431691 582818 0 24 72,57,60,123,56,142,84,57,58,128,66,123,101,97,3,85,142,81,4,121,98,122,175,120, 0,2286,4435,10675,12953,45777,62516,67171,76092,77337,78172,85828,105799,111333,112112,112169,112392,123406,130987,131023,132738,143148,146249,151007, -chr6 562714 582818 NM_001006376 0 - 562784 582818 0 6 123,99,7,125,177,120, 0,1723,9432,12120,15224,19984, -chr6 601113 601944 NM_153072 0 - 601113 601944 0 1 831, 0, -chr6 1257218 1259863 NM_008239 0 + 1257939 1259151 0 9 234,156,326,223,99,110,56,33,135, 0,715,1048,1473,1834,2043,2292,2441,2510, -chr6 1257933 1259371 NM_022858 0 + 1257984 1259151 0 6 156,326,104,108,99,61, 0,333,758,873,1119,1377, -chr6 1258056 1258782 NM_212907 0 + 1258056 1258782 0 3 33,318,67, 0,216,659, -chr6 1258293 1556225 NM_079772 0 + 1258293 1556225 0 2 42,237, 0,297695, -chr6 1334956 1340813 NM_010225 0 + 1335445 1340093 0 8 175,605,252,176,22,80,36,196, 0,489,1144,4973,5159,5480,5609,5661, -chr6 1335445 1340093 NM_001083815 0 + 1335445 1340093 0 6 358,48,9,138,69,153, 0,378,474,657,825,4495, -chr6 1340435 1557341 NM_131728 0 + 1555679 1557341 0 11 21,75,394,39,55,12,54,51,63,44,180, 0,215244,215402,215901,216003,216090,216159,216300,216417,216639,216726, -chr6 1457597 1460466 NM_001033909 0 - 1458931 1460466 0 9 149,19,33,200,94,320,18,819,668, 0,411,463,577,799,906,1298,1325,2201, -chr6 1457597 1460811 NM_001012181 0 - 1458931 1460523 0 11 149,19,33,200,94,320,18,819,521,206,184, 0,411,463,577,799,906,1298,1325,2201,2757,3030, -chr6 1458271 1460466 NM_023502 0 - 1458931 1460466 0 8 103,15,217,13,102,16,816,668, 0,162,198,426,450,582,654,1527, -chr6 1555161 1559122 NM_008592 0 + 1555679 1557341 0 18 51,62,33,127,466,245,213,164,309,39,19,18,202,377,201,19,190,110, 0,106,356,468,626,1137,1427,1691,1873,2193,2243,2301,2329,2558,3367,3578,3616,3851, -chr6 1555673 1557341 NM_131729 0 + 1555679 1557341 0 5 75,407,60,35,202, 0,165,921,1404,1466, -chr6 1555673 1557854 NM_001096377 0 + 1555679 1557341 0 9 83,438,39,49,57,36,62,180,39, 0,114,663,762,915,1179,1401,1488,2142, -chr6 1555673 1557854 NM_001088214 0 + 1555679 1557341 0 11 83,438,39,49,57,63,36,62,180,21,39, 0,114,663,762,915,1060,1179,1401,1488,1976,2142, -chr6 1555673 1557854 NM_001087468 0 + 1555679 1557341 0 11 83,387,39,49,57,63,36,62,180,21,39, 0,165,663,762,915,1060,1179,1401,1488,1976,2142, -chr6 1555673 1557854 NM_001007863 0 + 1555679 1557341 0 12 83,438,39,47,57,63,36,27,41,202,21,39, 0,114,663,764,915,1060,1179,1275,1401,1466,1976,2142, -chr6 1555805 1557904 NM_205006 0 + 1555805 1557281 0 10 18,424,73,94,56,32,30,51,21,63, 0,28,510,629,790,919,1048,1257,1455,2036, -chr6 1555910 1556198 NM_079188 0 + 1555910 1556198 0 2 196,81, 0,207, -chr6 1569136 2190658 NM_001039606 0 - 1569402 2190655 0 13 63,11,66,69,97,119,128,105,195,108,88,45,105, 0,95,263,569,102512,118564,306199,335963,336870,491869,493565,500783,621417, -chr6 1569399 2190598 NM_001092144 0 - 1569402 2190598 0 10 66,97,119,128,105,193,108,88,45,45, 0,102249,118301,305936,335700,336607,491604,493302,500520,621154, -chr6 1569399 2190658 NM_001080331 0 - 1569402 2190655 0 11 66,69,97,119,128,107,193,108,88,45,105, 0,306,102249,118301,305936,335700,336609,491606,493302,500520,621154, -chr6 1569399 2190598 NM_001086883 0 - 1569402 2190598 0 11 66,97,119,128,105,193,108,3,87,45,45, 0,102249,118301,305936,335700,336607,491604,493277,493303,500520,621154, -chr6 1569399 2190658 NM_146041 0 - 1569402 2190655 0 11 66,69,97,119,128,105,195,108,88,45,105, 0,306,102249,118301,305936,335700,336607,491606,493302,500520,621154, -chr6 1569402 2190598 NM_001037253 0 - 1569402 2190598 0 10 63,97,119,128,105,193,108,88,45,45, 0,102246,118298,305933,335697,336604,491601,493299,500517,621151, -chr6 1687699 2062789 NM_001102475 0 - 1687699 2062789 0 6 120,126,105,197,108,88, 0,187636,217398,218305,373306,375002, -chr6 1687699 2062789 NM_200489 0 - 1687699 2062789 0 6 120,126,105,197,106,87, 0,187636,217398,218305,373306,375003, -chr6 1687714 2069967 NM_135044 0 - 1687714 2069967 0 6 105,128,100,189,111,51, 0,187621,217385,218293,373286,382202, -chr6 1875335 2062789 NM_001083199 0 - 1875335 2062789 0 6 120,7,101,189,105,69, 0,22270,29763,30672,185665,187385, -chr6 1875335 2062789 NM_001083201 0 - 1875335 2062789 0 6 120,7,101,189,105,69, 0,22270,29763,30672,185665,187385, -chr6 1875335 2062789 NM_001083200 0 - 1875335 2062789 0 6 120,7,101,189,105,69, 0,22270,29763,30672,185665,187385, -chr6 1875335 2062789 NM_060705 0 - 1875335 2062789 0 6 120,6,102,189,105,69, 0,25822,29762,30672,185665,187385, -chr6 1875335 2062789 NM_069163 0 - 1875335 2062789 0 6 120,7,101,189,105,69, 0,22270,29763,30672,185665,187385, -chr6 1875335 2062789 NM_069162 0 - 1875335 2062789 0 6 120,7,101,189,105,69, 0,22270,29763,30672,185665,187385, -chr6 2694368 2696147 NM_001109635 0 - 2694368 2694640 0 2 272,39, 0,1740, -chr6 2710646 2730977 NM_030215 0 + 2710855 2730515 0 13 162,126,267,36,183,192,250,220,156,80,280,28,312, 0,209,416,761,848,3277,4706,13859,17992,18910,19593,19966,20019, -chr6 2710661 2730977 NM_172332 0 + 2710855 2730515 0 13 147,126,267,36,180,192,244,220,156,80,282,75,312, 0,194,401,746,836,3262,4691,13844,17977,18895,19578,19903,20004, -chr6 2710699 2730985 NM_001103106 0 + 2710855 2730515 0 12 81,126,265,183,192,243,217,156,80,278,15,263, 0,156,363,795,3224,4653,13809,17939,18857,19540,19996,20023, -chr6 2711518 2730494 NM_001095718 0 + 2711518 2730494 0 8 159,192,189,93,43,156,80,255, 0,2405,3834,12993,13164,17120,18038,18721, -chr6 2711527 2730497 NM_212920 0 + 2711527 2730497 0 9 150,27,144,195,87,43,156,80,258, 0,2396,2444,3825,12984,13155,17111,18029,18712, -chr6 2714058 2730440 NM_208117 0 + 2714058 2730440 0 4 66,117,159,81, 0,1303,14579,16301, -chr6 2714067 2730434 NM_102275 0 + 2714067 2730434 0 6 48,108,157,80,66,78, 0,1285,14570,15489,16172,16289, -chr6 2778233 2785831 NM_001081947 0 - 2778840 2785819 0 12 21,51,48,79,34,407,168,143,115,132,6,181, 0,149,358,455,544,605,2855,3107,4881,5547,5734,7417, -chr6 2778816 2785825 NM_025429 0 - 2778840 2785819 0 6 429,168,143,118,138,174, 0,2272,2524,4298,4965,6835, -chr6 2778816 2785825 NM_173051 0 - 2778840 2785819 0 7 381,36,153,144,118,138,174, 0,393,2278,2523,4298,4965,6835, -chr6 2778834 2845766 NM_001086317 0 - 2778840 2845766 0 7 84,109,173,14,90,96,93, 0,126,56793,58358,59863,62454,66839, -chr6 2778834 2845766 NM_001011419 0 - 2778840 2845766 0 7 111,66,90,24,141,66,81, 0,123,2260,2389,2506,61787,66851, -chr6 2778834 2845778 NM_001109730 0 - 2778840 2845778 0 6 93,117,90,141,72,96, 0,120,2254,2506,4950,66848, -chr6 2778834 2785825 NM_001031642 0 - 2778840 2785819 0 6 411,159,141,120,138,174, 0,2254,2506,4278,4947,6817, -chr6 2778834 2845778 NM_001114010 0 - 2778840 2845778 0 6 93,117,90,141,72,96, 0,120,2254,2506,4950,66848, -chr6 2778837 2845844 NM_199941 0 - 2778840 2845724 0 5 90,102,141,72,162, 0,132,2503,4947,66845, -chr6 2778840 2845778 NM_001009892 0 - 2778840 2845778 0 6 87,120,159,141,108,96, 0,111,2248,2500,4953,66842, -chr6 2778840 2781484 NM_001095913 0 - 2778840 2781484 0 3 227,153,144, 0,2254,2500, -chr6 2778840 2845766 NM_001007931 0 - 2778840 2845766 0 7 78,109,173,13,90,111,93, 0,120,56787,58680,59857,62448,66833, -chr6 2778852 2783892 NM_001002653 0 - 2778852 2783892 0 4 171,147,87,111, 0,2272,2542,4929, -chr6 2778885 2785825 NM_173052 0 - 2778885 2785819 0 7 54,285,168,141,120,138,174, 0,75,2203,2455,4227,4896,6766, -chr6 2834393 2845859 NM_001075859 0 - 2835395 2845844 0 9 45,93,276,6,150,143,118,136,185, 0,1002,1134,2619,2678,4250,6230,6892,11281, -chr6 2835360 2845826 NM_011453 0 - 2835395 2845793 0 6 132,275,151,144,114,132, 0,170,1707,3286,5267,10334, -chr6 2835380 2845852 NM_001111256 0 - 2835395 2845844 0 6 425,154,143,118,136,178, 0,1687,3263,5243,5905,10294, -chr6 2835391 2845856 NM_011452 0 - 2835395 2845844 0 7 93,279,24,140,55,30,173, 0,133,1798,3255,5232,5907,10292, -chr6 2835392 2904496 NM_001009892 0 - 2835395 2904496 0 4 90,87,114,90, 0,58258,62911,69014, -chr6 2835392 2845850 NM_009256 0 - 2835395 2845844 0 8 114,284,120,101,120,30,69,165, 0,135,1701,3254,5229,5906,5963,10293, -chr6 2835392 2845850 NM_001007732 0 - 2835395 2845844 0 6 96,284,140,118,30,156, 0,135,3254,5231,5906,10302, -chr6 2835394 2845856 NM_011460 0 - 2835395 2845844 0 7 88,273,20,22,30,21,171, 0,136,1799,3252,5244,5913,10291, -chr6 2835394 2845856 NM_011456 0 - 2835395 2845844 0 5 88,276,57,21,171, 0,133,5226,5913,10291, -chr6 2835394 2845856 NM_183197 0 - 2835395 2845844 0 7 88,276,16,22,30,24,171, 0,133,1799,3252,5244,5913,10291, -chr6 2835395 2857297 NM_001012214 0 - 2835395 2857297 0 7 93,72,180,127,115,99,54, 0,135,228,3264,5228,5905,21848, -chr6 2835395 2845793 NM_001107351 0 - 2835395 2845724 0 5 108,284,22,120,110, 0,132,3251,5226,10288, -chr6 2835395 2845856 NM_011455 0 - 2835395 2845844 0 7 87,276,16,22,30,21,171, 0,132,1798,3251,5243,5912,10290, -chr6 2835395 2845772 NM_011454 0 - 2835395 2845772 0 6 93,72,180,124,99,96, 0,135,228,3265,5905,10281, -chr6 2835398 2838742 NM_201376 0 - 2835398 2838742 0 3 72,198,78, 0,126,3266, -chr6 2835407 2841328 NM_001002653 0 - 2835407 2841328 0 6 75,120,33,30,45,30, 0,123,1781,3236,3290,5891, -chr6 2893522 2904578 NM_001012214 0 - 2893530 2904565 0 8 104,81,41,159,117,3,116,178, 0,131,234,621,6303,7190,7237,10878, -chr6 2893523 2916412 NM_009254 0 - 2893530 2904565 0 8 409,158,45,118,3,119,174,51, 0,623,4790,6302,7158,7237,10872,22838, -chr6 2893527 2904578 NM_199085 0 - 2893530 2904565 0 8 207,183,156,143,118,4,119,178, 0,222,619,4749,6297,7160,7233,10873, -chr6 2893530 2904490 NM_001007931 0 - 2893530 2904490 0 4 399,135,90,93, 0,637,4800,10867, -chr6 2893530 2904490 NM_001086317 0 - 2893530 2904490 0 4 399,135,123,93, 0,637,4767,10867, -chr6 2893530 2904581 NM_011454 0 - 2893530 2904565 0 9 96,81,145,141,45,117,3,120,186, 0,123,226,626,4783,6295,7210,7229,10865, -chr6 2893530 2900870 NM_001007732 0 - 2893530 2900870 0 4 212,116,106,102, 0,4773,6294,7238, -chr6 2893530 2904496 NM_199941 0 - 2893530 2904448 0 5 87,84,39,114,90, 0,123,360,4773,10876, -chr6 2893530 2898417 NM_199936 0 - 2893530 2898417 0 4 204,93,30,75, 0,297,742,4812, -chr7 288282 304060 NM_030565 0 + 288282 304060 0 4 186,362,179,80, 0,243,2354,15698, -chr7 503910 525249 NM_001075231 0 - 506606 525164 0 13 57,24,27,104,61,18,29,68,71,120,190,99,148, 0,286,345,399,589,663,696,739,2682,3375,13061,19644,21191, -chr7 504512 527768 NM_012801 0 - 507277 525164 0 11 78,101,128,188,105,97,113,57,39,17,24, 0,90,2765,12459,14001,19044,20589,22046,22160,23051,23232, -chr7 504528 517160 NM_001087835 0 - 506603 517160 0 6 62,81,9,65,84,189, 0,95,2075,2095,2793,12443, -chr7 504530 525341 NM_008808 0 - 504726 525164 0 7 60,138,124,188,105,97,240, 0,72,2751,12441,13983,19026,20571, -chr7 507279 525263 NM_204306 0 - 507279 523653 0 4 126,189,99,33, 0,9692,16275,17951, -chr7 525038 960654 NM_214226 0 - 905083 960639 0 13 18,27,38,229,72,63,84,149,111,81,92,131,97, 0,670,380036,380157,380543,381226,381657,385250,386186,401092,407676,416498,435519, -chr7 556577 686890 NM_001033679 0 - 556592 686890 0 9 188,82,122,61,159,47,62,92,172, 0,974,28841,34093,45731,55778,56976,126814,130141, -chr7 556589 718597 NM_008923 0 - 556592 717668 0 11 176,82,122,61,159,47,62,92,171,203,17, 0,962,28829,34081,45719,55766,56964,126802,130129,160902,161991, -chr7 556589 717671 NM_001075201 0 - 556592 717668 0 11 176,82,120,2,61,159,47,62,92,171,180, 0,962,28829,34060,34081,45719,55766,56964,126802,130129,160902, -chr7 556592 717641 NM_001076623 0 - 556592 717641 0 10 171,84,122,61,159,45,64,92,171,150, 0,957,28826,34078,45716,55763,56959,126799,130126,160899, -chr7 556592 717629 NM_001014596 0 - 556592 717629 0 8 174,122,61,159,47,64,90,135, 0,28826,34078,45716,55763,56961,126801,160902, -chr7 556592 717629 NM_001014594 0 - 556592 717629 0 8 174,122,61,159,47,64,90,135, 0,28826,34078,45716,55763,56961,126801,160902, -chr7 556592 717629 NM_001014593 0 - 556592 717629 0 8 174,122,61,159,47,64,90,135, 0,28826,34078,45716,55763,56961,126801,160902, -chr7 556592 717644 NM_001017732 0 - 556592 717644 0 10 171,84,122,61,159,45,64,92,93,153, 0,957,28826,34078,45716,55763,56959,126799,130126,160899, -chrX 140917 155993 NM_207279 0 + 140917 155993 0 7 64,132,134,156,184,2,228, 0,4482,6392,7248,8784,8995,14848, -chrX 145398 155993 NM_001105044 0 + 145398 155993 0 5 140,127,156,184,230, 0,1918,2767,4303,10365, -chrX 219352 228428 NM_001079206 0 - 219352 228428 0 9 78,122,176,92,156,87,78,99,105, 0,157,2147,2689,6899,7556,8083,8619,8971, -chrX 511617 525371 NM_001079724 0 + 511632 525371 0 6 292,209,61,86,133,78, 0,3735,9938,10119,13508,13676, -chrX 511629 525371 NM_001039978 0 + 511632 525304 0 8 54,96,213,55,89,30,62,78, 0,90,3722,9929,10104,13496,13565,13664, -chr18 37500 39183 NM_168168 0 - 37500 39183 0 6 63,282,225,54,78,36, 0,90,405,660,786,1647, -chr18 148508 204624 NM_001038589 0 + 153306 201284 0 25 69,147,33,104,59,131,72,86,115,66,93,130,50,110,184,21,22,105,145,17,55,34,16,16,135, 0,4798,8278,21727,34333,38128,39107,39538,40693,44371,44589,46055,51471,51875,52624,52820,53149,53182,53300,53472,53692,55420,55803,55897,55981, -chr18 148508 204624 NM_021522 0 + 153306 201284 0 26 69,147,33,105,104,59,131,72,86,115,66,93,130,50,110,184,21,22,105,145,17,55,34,16,16,135, 0,4798,8278,20424,21727,34333,38128,39107,39538,40693,44371,44589,46055,51471,51875,52624,52820,53149,53182,53300,53472,53692,55420,55803,55897,55981, -chr18 148524 201889 NM_001075189 0 + 148698 201284 0 21 39,16,146,33,105,104,59,131,81,86,115,66,93,130,60,108,236,142,39,141,130, 0,174,4783,8262,20408,21711,34317,38112,39091,39522,40677,44355,44573,46039,51447,51861,52608,52861,53014,53082,53235, -chr18 148552 202219 NM_001045496 0 + 148698 201281 0 18 26,88,146,33,105,104,59,131,81,86,115,66,93,129,61,108,884,181, 0,74,4755,8234,20380,21683,34289,38084,39063,39494,40649,44327,44545,46011,51418,51833,52580,53486, -chr18 148631 201378 NM_001082257 0 + 153306 201284 0 16 39,147,33,105,104,59,131,82,77,115,66,93,129,61,106,248, 0,4675,8155,20301,21604,34210,38005,38984,39424,40570,44248,44466,45932,51339,51754,52499, -chr18 153299 201720 NM_001005641 0 + 153299 201284 0 16 156,111,104,59,131,72,65,115,63,3,93,108,105,3,153,18, 0,15627,16936,29542,33337,34316,34768,35902,39580,39684,39798,41264,47085,47735,47832,48403, -chr18 153300 201257 NM_199973 0 + 153300 201257 0 14 153,33,105,105,132,54,63,117,66,93,108,105,3,126, 0,3486,15632,16935,33335,34315,34767,35899,39579,39797,41263,47084,47775,47831, -chr18 153306 201790 NM_001008301 0 + 153306 201284 0 17 147,33,105,104,59,131,72,86,115,66,93,130,52,108,164,36,133, 0,3480,15626,16929,29535,33330,34309,34740,35895,39573,39791,41257,46673,47079,47826,48305,48351, -chr8 106109 107024 NM_146402 0 - 106109 107024 0 1 915, 0, -chr8 106109 107024 NM_001000918 0 - 106109 107024 0 1 915, 0, -chr8 106109 107024 NM_001000608 0 - 106109 107024 0 1 915, 0, -chr8 106109 107024 NM_001000579 0 - 106109 107024 0 1 915, 0, -chr8 106130 107024 NM_001000378 0 - 106130 107024 0 1 894, 0, -chr8 182889 186632 NM_001101948 0 + 182889 186331 0 3 138,1181,42, 0,2261,3701, -chr8 353069 409681 NM_001076211 0 + 353079 408804 0 13 139,5,104,50,92,95,188,176,144,101,41,64,57, 0,9643,18271,19816,22545,36919,38199,45306,49937,55645,56141,56474,56555, -chr8 353070 409568 NM_001014239 0 + 353079 408804 0 11 96,55,93,94,185,183,144,105,15,127,24, 0,19810,22544,36919,38198,45298,49936,55644,55928,56129,56474, -chr8 353070 409247 NM_025785 0 + 353079 408804 0 10 96,45,50,93,94,185,183,144,90,48, 0,18329,19815,22544,36919,38198,45298,49936,55644,56129, -chr8 353076 408802 NM_200917 0 + 353079 408802 0 8 72,53,91,3,93,166,165,36, 0,19804,22536,22730,36912,38190,45298,55690, -chr8 353079 408804 NM_001091583 0 + 353079 408804 0 8 75,92,94,167,168,3,144,90, 0,22535,36909,38204,45301,45481,49927,55635, -chr8 353079 408804 NM_001030531 0 + 353079 408804 0 8 75,92,94,165,168,3,144,90, 0,22535,36909,38206,45301,45481,49927,55635, -chr8 353079 408804 NM_205724 0 + 353079 408804 0 8 96,93,92,178,183,143,1,90, 0,22535,36910,38187,45289,49927,50121,55635, -chr8 432398 434597 NM_001016270 0 - 432398 434597 0 3 165,108,102, 0,222,2097, -chr8 6347230 6408177 NM_007426 0 - 6348029 6407863 0 13 56,68,163,137,161,3,99,108,238,122,156,294,27, 0,448,797,6630,11382,11807,12378,17562,18871,25253,30030,60345,60920, -chr8 6347561 6408088 NM_213808 0 - 6348029 6407863 0 13 103,90,12,163,137,161,102,131,232,122,156,293,36, 0,117,284,466,6299,11051,12044,17231,18546,24922,29699,60014,60491, -chr8 6347571 6407870 NM_001048126 0 - 6348029 6407863 0 10 193,161,137,161,102,128,231,122,156,295, 0,458,6289,11041,12034,17221,18537,24912,29689,60004, -chr8 6348027 6377416 NM_204817 0 - 6348029 6377416 0 8 163,135,163,39,111,232,122,156, 0,5833,10583,11641,16765,18080,24456,29233, -chr8 6553514 6604541 NM_026792 0 + 6553597 6602317 0 14 302,70,116,85,96,116,121,248,18,14,30,21,12,68, 0,16284,22125,23975,33070,39084,46464,48573,49608,49746,50411,50591,50912,50959, -chr8 6553583 6604589 NM_001075932 0 + 6553597 6602091 0 25 233,70,116,90,89,119,125,361,141,20,11,10,49,59,134,11,30,24,65,60,32,71,24,83,105, 0,16215,22056,23906,33006,39013,46395,48501,48892,49060,49093,49235,49266,49325,49419,49578,49646,49817,49895,50483,50555,50599,50698,50740,50901, -chr8 6553586 6602320 NM_001015964 0 + 6553597 6602317 0 8 234,117,69,81,117,126,2,226, 0,22052,23903,33003,39011,46392,46661,48508, -chr8 6553597 6600116 NM_001076745 0 + 6553597 6600116 0 5 216,125,69,84,138, 0,22033,23892,32992,46381, -chr8 6655497 6680552 NM_001033035 0 - 6656128 6680425 0 8 453,1211,113,170,210,185,184,185, 0,562,5240,11303,12955,14599,22151,24870, -chr8 6656095 6668591 NM_001012228 0 - 6656128 6668591 0 6 145,336,78,115,170,139, 0,573,1089,4640,10705,12357, -chr8 6656098 6680467 NM_001113350 0 - 6656128 6680425 0 11 132,48,246,78,48,57,174,206,185,164,109, 0,475,804,1086,4637,4695,10702,12358,13998,21550,24260, -chr8 6656098 6680467 NM_176951 0 - 6656128 6668591 0 11 132,48,246,78,48,57,174,206,185,164,167, 0,475,804,1086,4637,4695,10702,12358,13998,21550,24202, -chr8 9451477 9665182 NM_143153 0 + 9451477 9665182 0 13 55,221,96,60,186,126,165,220,110,189,96,191,160, 0,23601,148105,149630,150247,174353,176722,178307,178819,191466,204955,209674,213545, -chr8 9949466 10323440 NM_174114 0 + 9949466 10323232 0 8 112,69,121,104,107,223,20,50, 0,153286,190557,246988,265336,373601,373849,373924, -chr9 4803 15007 NM_001105406 0 - 4806 14999 0 9 139,67,160,208,131,137,147,112,157, 0,279,1105,2160,2545,2915,3224,3577,10047, -chr9 4806 15005 NM_001037757 0 - 4806 14999 0 9 105,72,160,195,132,141,147,112,155, 0,271,1102,2165,2537,2908,3221,3574,10044, -chr9 4806 15011 NM_026833 0 - 4806 14999 0 9 105,72,160,195,132,141,147,112,161, 0,271,1102,2165,2537,2908,3221,3574,10044, -chr9 4806 14963 NM_001016854 0 - 4806 14963 0 9 108,71,151,141,132,145,143,112,113, 0,272,1102,2213,2537,2908,3225,3574,10044, -chr9 4806 14972 NM_001110450 0 - 4806 14972 0 9 24,57,71,154,138,135,138,149,123, 0,39,272,1102,2216,2537,2911,3221,10043, -chr9 4806 14963 NM_001095143 0 - 4806 14963 0 10 108,71,154,141,132,145,47,75,112,113, 0,272,1102,2213,2537,2908,3225,3293,3574,10044, -chr9 4806 15005 NM_001006245 0 - 4806 14999 0 10 99,23,72,160,144,136,137,144,115,155, 0,108,271,1102,2216,2537,2912,3221,3571,10044, -chr9 24720 25860 NM_001034099 0 - 24720 25519 0 2 237,358, 0,782, -chr9 106063 108204 NM_001009014 0 - 106930 108119 0 1 2141, 0, -chr9 106541 107829 NM_008022 0 - 106861 107829 0 5 54,42,109,152,438, 0,320,524,664,850, -chr9 111094 169032 NM_001009106 0 - 111466 168969 0 15 479,130,66,69,52,57,45,86,48,38,60,92,97,87,217, 0,866,2122,2291,13884,25007,30939,33614,35385,41337,42883,50986,52175,54603,57721, -chr1 4555 14757 NM_001105406 0 - 4558 14749 0 9 139,67,159,208,131,137,147,112,157, 0,279,1103,2160,2545,2913,3222,3575,10045, -chr1 4558 14756 NM_001037757 0 - 4558 14749 0 9 105,72,159,195,132,141,147,112,156, 0,271,1100,2165,2537,2906,3219,3572,10042, -chr1 4558 14761 NM_026833 0 - 4558 14749 0 9 105,72,159,195,132,141,147,112,161, 0,271,1100,2165,2537,2906,3219,3572,10042, -chr1 4558 14713 NM_001016854 0 - 4558 14713 0 9 108,71,109,174,132,145,143,112,113, 0,272,1100,2180,2537,2906,3223,3572,10042, -chr1 4558 14722 NM_001110450 0 - 4558 14722 0 9 24,57,71,109,171,132,141,149,123, 0,39,272,1100,2183,2537,2906,3219,10041, -chr1 4558 14713 NM_001095143 0 - 4558 14713 0 10 108,71,109,174,132,145,47,75,112,113, 0,272,1100,2180,2537,2906,3223,3291,3572,10042, -chr1 4558 14755 NM_001006245 0 - 4558 14749 0 11 99,23,72,109,16,192,132,141,144,115,155, 0,108,271,1100,1237,2168,2537,2906,3219,3569,10042, -chr1 24800 25940 NM_001034099 0 - 24800 25599 0 2 237,358, 0,782, -chr1 42314 59841 NM_001000613 0 + 42314 59841 0 3 162,701,46, 0,10659,17481, -chr1 42314 53690 NM_001000367 0 + 42314 53690 0 2 157,722, 0,10654, -chr1 52812 53714 NM_146400 0 + 52812 53714 0 1 902, 0, -chr1 52812 53750 NM_001000369 0 + 52812 53750 0 1 938, 0, -chr1 52841 53716 NM_146381 0 + 52841 53716 0 1 875, 0, -chr1 58975 59845 NM_146404 0 + 58975 59845 0 1 870, 0, -chr1 357521 358436 NM_146402 0 + 357521 358436 0 1 915, 0, -chr1 357521 358436 NM_001000918 0 + 357521 358436 0 1 915, 0, -chr1 357521 358436 NM_001000608 0 + 357521 358436 0 1 915, 0, -chr1 357521 358436 NM_001000579 0 + 357521 358436 0 1 915, 0, -chr1 357521 358415 NM_001000378 0 + 357521 358415 0 1 894, 0, -chr1 357641 358418 NM_001000614 0 + 357641 358418 0 3 288,135,96, 0,519,681, -chr1 460879 461086 NM_001021076 0 + 460879 461086 0 2 81,57, 0,150, -chr1 556991 557841 NM_001097928 0 + 557841 557841 0 1 850, 0, -chr1 559052 559609 NM_001011372 0 + 559609 559609 0 3 36,339,86, 0,69,471, -chr1 610982 611897 NM_146402 0 - 610982 611897 0 1 915, 0, -chr1 610982 611897 NM_001000918 0 - 610982 611897 0 1 915, 0, -chr1 610982 611897 NM_001000608 0 - 610982 611897 0 1 915, 0, -chr1 610982 611897 NM_001000579 0 - 610982 611897 0 1 915, 0, -chr1 611003 611897 NM_001000378 0 - 611003 611897 0 1 894, 0, -chr1 851175 869345 NM_001030877 0 + 851184 869345 0 10 87,53,113,57,33,120,75,45,117,21, 0,5104,9839,15192,15300,16201,16479,16624,17762,18149, -chr1 864275 870039 NM_001110516 0 + 864275 869389 0 18 83,118,163,118,78,204,137,27,98,105,199,27,29,12,20,14,9,105, 0,262,2111,3103,3379,3545,3851,4001,4250,4668,4872,5087,5217,5334,5370,5406,5534,5659, -chr1 9713148 9756040 NM_001077784 0 - 9713152 9756040 0 18 145,24,186,66,146,174,201,117,139,160,123,2,249,186,150,208,197,124, 0,178,702,1327,2897,3468,4469,4983,5400,10590,13377,13736,13891,18957,19260,20969,24609,42768, -chr1 9832545 9860636 NM_023465 0 - 9833362 9854709 0 9 115,44,131,275,21,135,91,103,96, 0,126,189,363,648,741,21286,22068,27995, -chr2 208325 243115 NM_001034607 0 - 208810 243115 0 10 123,257,74,4,169,129,113,65,114,111, 0,420,11638,12016,12697,14775,15834,29212,31405,34679, -chr2 208766 243115 NM_013709 0 - 208810 243115 0 10 236,6,51,79,162,137,105,65,114,111, 0,5532,6104,11200,12263,14334,15401,28771,30964,34238, -chr2 208766 243115 NM_001108705 0 - 208810 243115 0 10 236,6,50,80,162,137,105,65,114,111, 0,5532,6104,11199,12263,14334,15401,28771,30964,34238, -chr2 208804 243113 NM_001093063 0 - 208810 243113 0 9 171,150,130,113,63,2,114,1,108, 0,12224,14295,15355,28733,30840,30926,34155,34201, -chr2 221028 243113 NM_001113912 0 - 221028 243113 0 8 150,130,113,63,2,114,1,108, 0,2071,3131,16509,18616,18702,21931,21977, -chr2 254952 267304 NM_001039291 0 + 254964 267304 0 6 55,56,116,60,106,78, 0,6913,7084,10189,12027,12274, -chr2 254958 267583 NM_173978 0 + 254964 267295 0 8 49,74,116,60,106,69,60,51, 0,6907,7233,10183,12021,12268,12449,12574, -chr2 254964 267570 NM_021262 0 + 254964 267304 0 9 43,74,114,62,106,78,24,25,48, 0,6901,7072,10175,12015,12262,12441,12476,12558, -chr2 261864 267295 NM_001085856 0 + 261864 267295 0 7 68,7,114,60,2,106,69, 0,95,172,3275,3367,5115,5362, -chr2 261864 268126 NM_001095294 0 + 262108 268126 0 6 69,105,60,108,62,15, 0,181,3275,5113,5362,6247, -chr2 261864 267292 NM_001005082 0 + 261864 267292 0 5 57,114,60,108,66, 0,327,3275,5113,5362, -chr2 261864 267295 NM_001114769 0 + 261864 267295 0 7 68,7,114,60,2,106,69, 0,95,327,3275,3367,5115,5362, -chr2 269765 276344 NM_001109372 0 - 273116 276344 0 6 89,66,48,59,79,57, 0,218,322,3351,6357,6522, -chr2 659629 667360 NM_001007748 0 - 659629 667345 0 5 45,94,55,118,66, 0,127,3178,5880,7665, -chr2 659753 667348 NM_001034793 0 - 659753 667345 0 4 97,55,121,60, 0,3054,5756,7535, -chr2 9641759 9688565 NM_013053 0 - 9642865 9688032 0 11 528,33,92,24,432,96,164,124,294,22,63, 0,544,591,700,734,3234,3985,7212,45979,46308,46743, -chr2 9641847 9688562 NM_001078127 0 - 9642865 9688032 0 7 454,572,96,164,123,294,48, 0,506,3146,3897,7125,45891,46667, -chr2 9641847 9688032 NM_001006415 0 - 9642865 9688032 0 10 375,17,66,217,155,96,162,2,124,294, 0,386,607,684,923,3146,3897,7050,7124,45891, -chr2 9641862 9688129 NM_011739 0 - 9642865 9688032 0 10 425,33,84,24,432,96,164,124,294,62, 0,441,488,597,631,3131,3882,7109,45876,46205, -chr2 9641899 9688032 NM_201513 0 - 9644993 9688032 0 6 46,99,159,114,3,294, 0,3094,3848,7079,45762,45839, -chr2 9642563 9688030 NM_001086903 0 - 9644993 9688030 0 9 68,21,48,24,96,168,108,3,292, 0,84,155,241,2430,3181,6421,45099,45175, -chr2 9642647 9688014 NM_001030399 0 - 9644993 9688014 0 10 21,89,24,96,2,166,117,3,51,192, 0,45,157,2346,2835,3099,6328,45015,45091,45175, -chr2 9642678 9688023 NM_201484 0 - 9644993 9688023 0 7 18,31,99,159,3,123,285, 0,126,2315,3069,6269,6294,45060, -chr2 9642865 9688032 NM_001082168 0 - 9642865 9688032 0 5 60,96,164,124,294, 0,2128,2879,6106,44873, -chr2 9644993 9688005 NM_111119 0 - 9644993 9688005 0 6 99,96,81,48,102,30, 0,754,3979,42757,42835,42982, -chr2 9644993 9688008 NM_001074599 0 - 9644993 9688008 0 5 99,96,81,108,33, 0,754,3979,42835,42982, -chr3 4378854 4434809 NM_138159 0 - 4378854 4434809 0 3 84,117,105, 0,54954,55850, -chr3 8750426 8762720 NM_019155 0 + 8750562 8762553 0 4 71,127,434,33, 0,123,11785,12261, -chr3 8750480 8762964 NM_001046558 0 + 8750562 8762553 0 5 196,353,33,190,60, 0,11731,12147,12209,12424, -chr3 8750562 8762550 NM_001037149 0 + 8750562 8762550 0 2 114,339, 0,11649, -chr3 8750598 8762547 NM_204370 0 + 8750598 8762547 0 2 78,336, 0,11613, -chr3 8762209 8762553 NM_205738 0 + 8762209 8762553 0 1 344, 0, -chr3 8765961 8784877 NM_001081147 0 - 8769662 8784873 0 6 27,11,110,14,277,926, 0,581,748,3510,3672,17990, -chr3 8769144 8784877 NM_214027 0 - 8769677 8784873 0 6 33,78,21,45,251,926, 0,125,324,389,515,14807, -chr3 8769536 8785009 NM_174134 0 - 8769662 8784873 0 4 42,250,982,57, 0,124,14415,15416, -chr3 8769579 8784873 NM_001044732 0 - 8769662 8784873 0 2 331,922, 0,14372, -chr3 8769660 8784873 NM_001009752 0 - 8769662 8784873 0 2 250,922, 0,14291, -chr3 8769665 8784871 NM_012871 0 - 8769665 8784871 0 2 245,920, 0,14286, -chr3 8769674 8784798 NM_001031569 0 - 8769674 8784798 0 3 236,157,633, 0,14277,14491, -chr3 8769841 8784636 NM_001110125 0 - 8769841 8784636 0 4 51,120,150,147, 0,14132,14408,14648, -chr3 8897812 8980074 NM_001035295 0 - 8898040 8980069 0 15 72,109,65,35,43,15,61,77,185,100,338,71,62,82,56, 0,222,9260,17768,17851,17904,31183,32515,54742,58425,60338,66091,67380,77791,82206, -chr3 8898017 8980084 NM_001077673 0 - 8898040 8980069 0 15 115,64,32,87,65,77,185,102,102,75,69,3,60,90,66, 0,9054,17560,21096,30974,32310,54537,58220,60252,60389,65885,67132,67175,77578,82001, -chr3 8898040 8975687 NM_021385 0 - 8898040 8975687 0 13 92,102,62,58,79,185,102,132,82,68,3,60,92, 0,17576,21102,30955,32285,54514,58197,60199,60366,65863,67109,67152,77555, -chr3 8928993 8975679 NM_001030603 0 - 8928993 8975679 0 6 54,187,104,71,60,84, 0,23562,27247,34909,36199,46602, -chr3 8997279 9266289 NM_080448 0 - 9002202 9265635 0 44 364,90,59,111,92,84,113,65,27,30,31,191,127,175,14,31,73,22,78,391,521,328,150,181,80,228,104,135,78,61,103,28,85,198,102,222,129,186,63,163,193,210,154,204, 0,397,503,615,796,951,1083,1220,1329,1393,1456,1497,1698,1844,2045,2074,2179,2883,3773,4044,4816,9916,12310,13747,29712,32712,33143,35001,44665,46339,52054,57467,66795,72431,75637,77655,79635,83800,99429,124084,144129,268289,268515,268806, -chr3 9002505 9265635 NM_001048235 0 - 9002505 9265635 0 18 114,171,195,1,35,128,79,84,198,87,3,234,129,57,87,162,194,67, 0,8520,27518,27814,27915,29782,39439,61570,67205,70411,72384,72417,74409,78574,78673,118858,138902,263063, -chr3 9009583 9265638 NM_001030604 0 - 9009585 9265635 0 22 156,182,3,75,237,2,99,134,78,61,103,26,87,198,102,222,129,187,62,163,193,70, 0,1443,17393,17412,20399,20690,20839,22698,32361,34035,39750,45163,54489,60127,63333,65351,67331,71496,87126,111780,131825,255985, -chr3 9381716 9401345 NM_001038062 0 + 9381752 9401345 0 9 288,78,477,131,70,116,111,124,138, 0,1875,6027,9483,12786,15470,18166,19179,19491, -chr3 9381857 9401384 NM_008188 0 + 9381857 9401360 0 9 147,78,477,131,70,117,103,124,177, 0,1734,5886,9342,12645,15329,18033,19038,19350, -chr3 9381863 9401303 NM_001089394 0 + 9381863 9401303 0 8 72,78,135,128,67,98,120,100, 0,1728,6222,9336,12636,18032,19032,19340, -chr3 9414379 9494818 NM_001106614 0 + 9450154 9492775 0 34 111,151,187,225,188,111,152,59,179,243,149,118,110,253,84,258,321,243,130,248,469,304,134,89,966,195,11,16,48,13,435,101,113,403, 0,131,31127,32131,35674,36144,36638,37128,38032,42760,43897,44432,45612,47352,47961,49354,49990,50692,56043,66729,72763,75538,76753,77372,77787,78790,79023,79064,79101,79159,79297,79749,79871,80036, -chr3 9414587 9494818 NM_028385 0 + 9445622 9492775 0 29 74,187,106,152,59,179,243,149,118,110,253,84,258,321,243,130,248,469,304,134,89,966,199,16,190,245,101,146,404, 0,30919,35941,36430,36920,37824,42552,43689,44224,45404,47144,47753,49146,49782,50484,55835,66521,72555,75330,76545,77164,77579,78578,78856,79071,79279,79541,79658,79827, -chr3 9515045 9570536 NM_177763 0 - 9518894 9569363 0 14 179,13,42,18,228,100,9,11,21,74,104,237,412,150, 0,341,2206,2520,2654,2934,3104,3169,3273,3308,3846,7605,53912,55341, -chr3 9515054 9570497 NM_001076226 0 - 9518893 9569363 0 17 190,111,54,62,39,41,38,9,204,115,57,14,36,213,237,412,129, 0,227,351,426,628,791,2167,2325,2641,2872,3367,3598,3640,3728,7596,53903,55314, -chr3 9518415 9808170 NM_001094246 0 - 9797040 9808150 0 9 24,196,183,110,104,142,106,251,227, 0,278625,282299,283584,285274,285467,287777,287981,289528, -chr3 9518884 9570470 NM_181387 0 - 9518894 9569363 0 4 111,237,412,87, 0,3766,50073,51499, -chr3 9522651 9569363 NM_001102981 0 - 9522651 9569363 0 2 236,406, 0,46306, -chr3 9617391 9620710 NM_133578 0 + 9617394 9619412 0 10 64,69,59,252,241,186,121,42,24,76, 0,103,301,1007,1601,1883,2078,2568,3164,3243, -chr3 9666216 9719066 NM_026849 0 + 9666267 9718657 0 23 210,150,108,76,62,122,76,69,75,48,92,77,37,53,61,134,180,157,231,63,24,37,78, 0,4088,12735,19186,19899,21516,23152,27786,28451,33645,35046,35355,35678,38288,39161,39416,40431,48178,52258,52534,52617,52679,52772, -chr3 9666248 9719076 NM_001100364 0 + 9666267 9718657 0 21 178,149,109,76,61,123,74,71,75,65,88,77,37,71,59,139,180,228,49,66,215, 0,4056,12702,19154,19867,21483,23120,27752,28419,33613,35018,35323,35646,38256,39131,39379,40399,52225,52462,52538,52613, -chr3 9666267 9719066 NM_001107880 0 + 9666267 9718657 0 23 159,149,109,76,57,127,74,71,75,48,92,77,37,53,61,131,180,157,230,27,24,23,78, 0,4037,12683,19135,19848,21460,23101,27733,28400,33594,34995,35304,35627,38237,39110,39368,40380,48127,52207,52450,52597,52642,52721, -chr3 9670304 9718633 NM_001097244 0 + 9670304 9718633 0 16 129,108,78,120,73,71,75,45,81,77,37,54,80,92,33,159, 0,8647,15098,17425,19065,23696,24363,29557,30969,31267,31590,34200,36434,44081,44202,48170, -chr3 9670304 9718633 NM_001096415 0 + 9670304 9718633 0 14 129,109,78,120,65,79,75,45,81,77,39,52,81,141, 0,8646,15098,17425,19065,23688,24363,29557,30969,31267,31590,34202,36434,48188, -chr3 9720490 9746428 NM_170673 0 + 9720680 9746376 0 21 47,98,40,47,104,37,79,64,104,105,42,76,54,62,47,182,128,103,58,74,238, 0,160,780,942,1084,1657,2178,8734,8918,9168,11107,11482,11666,12167,13251,14222,14668,22142,22858,23306,25700, -chr3 9720627 9746588 NM_001099195 0 + 9720680 9746376 0 20 121,41,47,104,37,77,64,104,42,76,54,62,47,182,128,103,56,76,311,59, 0,643,805,947,1520,2043,8597,8781,10970,11345,11529,12030,13114,14085,14531,22005,22721,23167,25563,25902, -chr3 9720657 9746586 NM_001024982 0 + 9720680 9746376 0 23 91,40,47,104,37,79,64,104,105,42,76,54,62,45,184,128,103,58,74,209,38,21,24, 0,613,775,917,1490,2011,8567,8751,9001,10940,11315,11499,12000,13084,14053,14501,21975,22691,23139,25533,25813,25874,25905, -chr3 9720707 9746328 NM_001102940 0 + 9720707 9746328 0 20 39,40,23,111,77,64,105,105,41,79,50,63,47,182,116,100,55,3,74,138, 0,561,722,861,1963,8517,8701,8952,10891,11265,11452,11949,13034,14005,14463,21925,22641,22784,23089,25483, -chr3 9750803 9764039 NM_001112997 0 + 9750824 9764033 0 13 617,160,140,147,264,168,58,128,149,112,99,155,190, 0,6656,7180,7905,8824,9496,9724,10104,10887,11453,11712,12180,13046, -chr3 9750812 9764557 NM_030178 0 + 9750824 9764033 0 16 611,787,136,163,132,129,310,320,285,148,358,155,189,189,57,131, 0,4870,5694,6650,7179,7896,8815,9453,10095,10879,11444,12171,13037,13252,13469,13614, -chr3 9750817 9760455 NM_201016 0 + 9750824 9760455 0 11 172,57,15,777,133,149,144,129,42,189,90, 0,287,1784,4857,5691,6644,7162,7891,8810,8882,9548, -chr3 9750824 9764033 NM_001031464 0 + 9750824 9764033 0 15 597,789,134,155,134,129,280,228,66,283,148,137,119,155,184, 0,4856,5684,6638,7165,7884,8803,9451,9697,10085,10867,11432,11671,12159,13025, -chr3 9766985 9774086 NM_001080285 0 + 9766985 9773834 0 9 122,248,180,182,153,48,97,88,48, 0,643,1468,4402,6169,6467,6759,6917,7053, -chr3 9766988 9774087 NM_010957 0 + 9766988 9773834 0 8 119,248,182,180,151,50,111,55, 0,640,1465,4401,6166,6462,6756,7044, -chr3 9767000 9773852 NM_030870 0 + 9767000 9773834 0 7 107,248,182,180,151,50,108, 0,628,1453,4389,6154,6450,6744, -chr3 9774031 9786558 NM_134468 0 - 9774232 9784433 0 15 83,10,22,73,118,88,79,113,76,127,139,75,132,115,43, 0,106,135,201,381,2140,2324,3308,4113,4283,5566,5791,8411,10319,12484, -chr3 9774031 9786580 NM_133926 0 - 9774243 9784433 0 13 83,62,118,88,79,113,76,127,139,75,132,115,65, 0,212,381,2140,2324,3308,4113,4283,5566,5791,8411,10319,12484, -chr3 9774038 9786586 NM_001076868 0 - 9774222 9784433 0 13 60,161,118,88,79,113,76,127,139,75,131,116,71, 0,106,374,2133,2317,3301,4106,4276,5559,5784,8404,10311,12477, -chr3 9774449 9784403 NM_001086810 0 - 9774449 9784403 0 9 81,96,111,77,127,139,75,132,53, 0,1722,2891,3694,3865,5148,5373,7993,9901, -chr3 9774449 9784403 NM_001088849 0 - 9774449 9784403 0 9 81,96,111,77,127,139,75,131,54, 0,1722,2891,3694,3865,5148,5373,7993,9900, -chr3 9774449 9784403 NM_001016269 0 - 9774449 9784403 0 9 81,96,111,77,127,139,75,132,53, 0,1722,2891,3694,3865,5148,5373,7993,9901, -chr3 9776171 9779735 NM_199966 0 - 9776171 9779735 0 5 96,112,76,127,138, 0,1169,1973,2143,3426, -chr3 9776171 9779890 NM_166764 0 - 9776171 9779830 0 7 60,111,77,28,87,139,68, 0,1169,1972,2143,2183,3426,3651, -chr3 9776171 9779890 NM_166762 0 - 9776171 9779890 0 7 60,111,77,28,87,139,68, 0,1169,1972,2143,2183,3426,3651, -chr3 9776171 9779890 NM_166761 0 - 9776171 9779890 0 7 60,111,77,28,87,139,68, 0,1169,1972,2143,2183,3426,3651, -chr3 9776174 9782573 NM_001080658 0 - 9776174 9782573 0 9 93,73,109,78,31,78,138,76,131, 0,189,1167,1968,2140,2189,3423,3647,6268, -chr3 9777340 9779735 NM_067738 0 - 9777340 9779735 0 5 112,76,28,88,137, 0,804,974,1014,2258, -chr3 9796660 9809103 NM_133932 0 - 9797040 9808150 0 10 64,196,186,110,104,142,106,251,222,138, 0,377,4051,5339,7029,7222,9532,9736,11283,12305, -chr3 9796660 9809188 NM_001025734 0 - 9797040 9808150 0 10 99,196,188,110,104,142,106,251,222,223, 0,375,4049,5339,7029,7222,9532,9736,11283,12305, -chr3 9796671 9808179 NM_001024511 0 - 9797040 9808150 0 13 60,33,72,57,24,207,186,110,104,142,106,251,236, 0,97,139,231,304,355,4040,5328,7018,7211,9521,9725,11272, -chr3 9797040 9808150 NM_001086443 0 - 9797040 9808150 0 8 196,183,110,104,142,106,251,207, 0,3674,4959,6649,6842,9152,9356,10903, -chr3 9797040 9808150 NM_001008039 0 - 9797040 9808150 0 8 196,183,110,104,142,106,251,207, 0,3674,4959,6649,6842,9152,9356,10903, -chr3 9797040 9808150 NM_199926 0 - 9797040 9808150 0 9 193,1,94,66,105,81,106,254,195, 0,3113,3672,5003,6649,6903,9152,9356,10915, -chr3 9809725 9823808 NM_001106615 0 + 9820656 9823107 0 10 82,119,112,96,171,422,105,34,38,69, 0,4617,7143,8619,10801,13226,13662,13891,13967,14014, -chr3 9809728 9823776 NM_026552 0 + 9809805 9820697 0 11 79,119,112,96,171,239,159,15,27,39,33, 0,4614,7140,8616,10798,13224,13495,13665,13737,13948,14015, -chr3 9814341 9823190 NM_001076163 0 + 9814341 9822899 0 6 120,112,96,171,74,208, 0,2527,4003,6185,8552,8641, -chr3 9814342 9820697 NM_001004844 0 + 9814342 9820697 0 4 119,112,96,171, 0,2526,4002,6184, -chr3 9814342 9820697 NM_001094487 0 + 9814342 9820697 0 4 119,112,96,171, 0,2526,4002,6184, -chr3 9814342 9820697 NM_001003762 0 + 9814342 9820697 0 4 119,112,96,171, 0,2526,4002,6184, -chr3 9814342 9820697 NM_205537 0 + 9814342 9820697 0 4 115,116,96,171, 0,2522,4002,6184, -chr3 9814345 9820694 NM_001046984 0 + 9814345 9820694 0 5 116,112,93,3,168, 0,2523,3999,4122,6181, -chr3 9814345 9820694 NM_135152 0 + 9814345 9820694 0 4 111,111,96,168, 0,2524,3999,6181, -chr3 9814345 9820694 NM_065619 0 + 9814345 9820694 0 4 114,93,6,168, 0,3996,4689,6181, -chr3 9814348 9820694 NM_001032572 0 + 9814348 9820694 0 5 111,6,108,96,168, 0,391,2524,3996,6178, -chr3 9814348 9820694 NM_001058427 0 + 9814348 9820694 0 2 108,168, 0,6178, -chr3 9818341 9820682 NM_001019540 0 + 9818341 9820682 0 3 96,3,156, 0,132,2185, -chr3 9820526 9820682 NM_208665 0 + 9820526 9820682 0 1 156, 0, -chr3 9829629 9846079 NM_001045305 0 + 9829629 9846079 0 6 72,135,111,239,94,282, 0,3128,12894,14053,16011,16168, -chr3 9919581 9932470 NM_001004091 0 + 9919616 9932470 0 13 114,136,134,75,67,176,48,46,155,53,95,243,220, 0,3832,4063,5335,6319,7967,8229,8357,8545,11649,11781,12349,12669, -chr3 9919617 9932470 NM_001034031 0 + 9924979 9932470 0 15 78,81,135,75,67,176,48,46,155,5,64,52,95,236,220, 0,3797,4026,5299,6283,7931,8193,8321,8509,9433,11027,11614,11745,12313,12633, -chr3 9919617 9932470 NM_001034029 0 + 9924979 9932470 0 15 78,81,135,75,67,176,48,46,155,5,64,52,95,236,220, 0,3797,4026,5299,6283,7931,8193,8321,8509,9433,11027,11614,11745,12313,12633, -chr3 9933933 9945699 NM_001075178 0 + 9933999 9945326 0 12 173,154,75,110,112,45,140,60,55,179,63,33, 0,672,1085,1250,3241,3675,6631,6982,10916,11055,11330,11733, -chr3 9933940 9950128 NM_134159 0 + 9933999 9950128 0 13 163,22,155,111,110,64,195,42,122,41,86,261,205, 0,456,666,1242,3234,6974,11032,11335,12772,13644,15351,15695,15983, -chr3 9950555 9961708 NM_001014851 0 + 9951158 9961263 0 16 14,193,83,111,92,177,96,84,96,135,226,70,76,22,74,39, 0,548,963,3690,4143,6978,7239,8941,9205,9509,10493,10791,10883,10978,11018,11114, -chr3 9951059 9961709 NM_133930 0 + 9951122 9961263 0 15 237,83,108,95,2,175,96,84,94,137,363,13,10,20,42, 0,459,3186,3636,3768,6476,6735,8437,8701,9003,9989,10486,10520,10548,10608, -chr3 9951065 9961709 NM_001024783 0 + 9951122 9961263 0 14 231,83,105,98,2,175,96,84,94,137,363,29,13,107, 0,453,3180,3627,3762,6470,6729,8431,8695,8997,9983,10419,10514,10537, -chr3 9962910 9968919 NM_172487 0 - 9962910 9966799 0 9 90,1673,44,79,16,174,78,179,54, 0,102,2531,2595,2984,3020,3473,3760,5955, -chr3 9965282 9968895 NM_001075177 0 - 9965416 9966799 0 11 21,39,7,181,481,237,27,255,34,35,30, 0,38,101,134,502,1007,1256,1319,3461,3510,3583, -chr3 9965379 9969084 NM_001109350 0 - 9965379 9966799 0 8 18,177,375,45,174,12,179,66, 0,37,433,841,920,1119,1291,3639, -chr3 9979444 10003361 NM_001008355 0 - 9980752 10003345 0 17 25,55,144,21,60,14,14,42,55,129,83,80,78,111,92,58,171, 0,148,269,524,570,1025,1049,1152,1237,1308,6958,7821,10867,11619,14198,14628,23746, -chr3 9979449 10003357 NM_175101 0 - 9980752 10003345 0 15 25,55,72,60,154,27,162,129,83,80,78,111,92,58,167, 0,143,264,348,480,1065,1123,1303,6953,7816,10862,11614,14193,14623,23741, -chr3 9980463 10003354 NM_001035056 0 - 9980752 10003345 0 8 418,83,80,82,105,94,58,164, 0,5939,6802,9848,10604,13177,13609,22727, -chr3 9980746 10003345 NM_213505 0 - 9980752 10003345 0 9 131,4,81,82,78,109,94,58,155, 0,5630,5656,6517,9565,10317,12894,13326,22444, -chr3 9980747 10003345 NM_001016907 0 - 9980752 10003345 0 8 134,83,80,78,111,92,58,155, 0,5655,6518,9564,10316,12895,13325,22443, -chr3 9980794 10003345 NM_001009987 0 - 9980794 10003345 0 9 84,3,83,80,78,111,92,60,99, 0,5584,5608,6471,9517,10269,12848,13278,22452, -chr3 9980848 10003345 NM_001094319 0 - 9980848 10003345 0 8 33,83,80,78,111,92,58,155, 0,5554,6417,9463,10215,12794,13224,22342, -chr3 9986402 10003333 NM_135600 0 - 9986402 10003333 0 5 51,75,77,97,99, 0,873,3914,4665,16832, -chr3 9986402 10003336 NM_001086769 0 - 9986402 10003336 0 7 83,80,78,109,94,60,108, 0,863,3909,4661,7238,7670,16826, -chr3 9986402 10003336 NM_001095221 0 - 9986402 10003336 0 7 83,80,78,111,92,60,117, 0,863,3909,4661,7240,7670,16817, -chr3 9987275 10003330 NM_070174 0 - 9987275 10003330 0 5 76,2,69,105,114, 0,3024,3044,3793,15941, -chr16 48338 55019 NM_001002228 0 - 48338 55013 0 18 420,154,106,71,95,64,101,163,2,72,112,254,125,151,36,214,50,87, 0,633,908,1083,1391,1875,2098,2779,2958,3047,3244,3457,4434,4634,4806,5246,6358,6594, -chr16 69582 75762 NM_010822 0 + 69582 75762 0 3 117,203,365, 0,3468,5815, -chr16 69582 75761 NM_012601 0 + 69582 75761 0 3 117,203,364, 0,3468,5815, -chr16 73047 75620 NM_001017178 0 + 73047 75620 0 2 210,117, 0,2456, -chr16 73050 75614 NM_001082850 0 + 73050 75614 0 2 210,111, 0,2453, -chr16 73089 75551 NM_001042153 0 + 73089 75551 0 4 162,4,54,45, 0,186,2318,2417, -chr16 73089 75551 NM_001041368 0 + 73089 75551 0 4 162,4,54,45, 0,186,2318,2417, -chr16 76684 128271 NM_001034936 0 - 79698 128266 0 13 185,196,202,130,107,157,138,81,154,73,132,66,127, 0,2012,3014,5909,6532,11458,13685,23838,25936,30615,32438,43836,51460, -chr16 76694 128271 NM_181569 0 - 76703 128266 0 13 175,192,188,130,107,157,138,81,153,73,132,66,127, 0,2002,3018,5899,6522,11448,13675,23828,25927,30605,32428,43826,51450, -chr16 76703 128257 NM_001102803 0 - 76703 128257 0 14 168,114,2,73,69,129,105,159,139,80,147,79,119,81, 0,2069,2827,3007,3122,5890,6512,11436,13665,23819,25924,30596,32431,51473, -chr16 76703 128257 NM_001089801 0 - 76703 128257 0 15 168,114,2,73,69,129,105,159,139,80,147,79,120,45,81, 0,2069,2903,3007,3122,5890,6512,11436,13665,23819,25924,30596,32431,36802,51473, -chr16 76718 128254 NM_001025534 0 - 76718 128254 0 13 151,192,55,96,117,102,150,139,71,157,72,117,111, 0,1978,2992,3080,5893,6509,11430,13650,23804,25905,30587,32421,51425, -chr16 76718 128254 NM_001040371 0 - 76718 128254 0 13 151,192,55,96,117,103,149,139,71,157,72,117,111, 0,1978,2992,3080,5893,6509,11431,13650,23804,25905,30587,32421,51425, -chr16 142908 144402 NM_010405 0 + 142908 144399 0 3 95,205,132, 0,982,1362, -chr16 142909 144399 NM_001114542 0 + 142909 144399 0 3 94,205,129, 0,981,1361, -chr16 142950 144095 NM_131257 0 + 142950 144095 0 3 54,27,105, 0,956,1040, -chr16 142950 144095 NM_001033093 0 + 142950 144095 0 3 54,28,105, 0,956,1040, -chr16 143888 144396 NM_001004374 0 + 143888 144396 0 2 207,126, 0,382, -chr16 143888 144399 NM_001086277 0 + 143888 144399 0 2 207,129, 0,382, -chr16 182937 219363 NM_213685 0 - 182937 217340 0 8 72,174,144,111,99,99,11,84, 0,6127,13066,15140,27711,34304,35267,36342, -chr16 182937 219345 NM_001002116 0 - 182937 219339 0 8 78,2,175,144,102,99,95,67, 0,6098,6126,13066,15149,27711,34304,36341, -chr16 182946 219311 NM_001108893 0 - 189082 198185 0 9 69,150,17,143,111,97,97,4,28, 0,6115,6274,13058,15131,27702,34294,36000,36337, -chr16 189073 217313 NM_140734 0 - 189073 217313 0 4 162,102,81,72, 0,9013,21593,28168, -chr16 244377 255022 NM_001009701 0 + 244413 255022 0 11 294,118,192,131,132,31,152,76,132,85,212, 0,5104,5591,7006,7715,8052,8873,9322,9638,10254,10433, -chr16 244383 256830 NM_001075318 0 + 244413 256817 0 12 108,151,86,193,122,34,22,96,160,51,209,14, 0,147,5099,5584,7000,7794,7955,8048,9629,10246,10429,12433, -chr16 244389 255022 NM_207217 0 + 244413 255022 0 11 282,118,113,118,133,20,36,78,158,85,212, 0,5092,5579,6968,7702,8115,8875,9308,9626,10242,10421, -chr16 259277 265501 NM_001081069 0 - 259277 265501 0 14 102,7,80,139,85,124,109,63,84,75,59,52,108,101, 0,136,228,1245,1466,1703,1929,2121,4198,4485,4766,4937,5699,6123, -chr16 259331 265499 NM_001111161 0 - 260975 265499 0 6 54,120,93,60,108,99, 0,1644,1878,4712,5645,6069, -chr16 270478 272821 NM_001108269 0 + 270681 272815 0 8 56,33,73,173,85,80,55,206, 0,100,203,1268,1546,1819,1998,2137, -chr16 270578 272821 NM_008113 0 + 270681 272815 0 7 33,73,173,85,80,55,206, 0,103,1168,1446,1719,1898,2037, -chr16 270681 272827 NM_001076286 0 + 270681 272815 0 6 73,180,84,80,53,214, 0,1065,1344,1616,1795,1932, -chr16 273114 276925 NM_001081070 0 + 273179 276925 0 12 45,30,108,203,134,142,117,126,189,123,182,90, 0,65,146,1273,1541,1760,1970,2198,2392,3237,3440,3721, -chr16 273247 276739 NM_001098861 0 + 273247 276739 0 9 122,207,134,138,102,126,198,121,185, 0,1140,1412,1631,1840,2065,2259,3106,3307, -chr16 274387 277196 NM_001105775 0 + 274387 277166 0 10 207,130,142,117,122,202,121,182,85,39, 0,272,487,697,925,1115,1966,2167,2451,2770, -chr16 277441 342636 NM_009733 0 - 278122 337026 0 16 84,45,74,27,127,168,108,173,150,408,39,138,97,141,960,36, 0,106,204,594,681,1999,3749,6047,9614,10352,10772,16863,22532,27102,58707,65159, -chr16 277449 337108 NM_024405 0 - 278122 337041 0 13 43,71,74,127,168,173,150,408,39,138,97,141,960, 0,59,196,673,1991,6039,9606,10344,10764,16855,22524,27094,58699, -chr16 278122 336996 NM_131503 0 - 278122 336996 0 8 125,133,138,114,135,96,135,723, 0,1316,5401,9896,16185,21851,26420,58151, -chr16 278122 337008 NM_001095782 0 - 278122 337008 0 12 125,135,109,173,156,24,105,135,96,142,35,735, 0,1316,3067,5366,8951,9766,9902,16185,21851,26420,58026,58151, -chr16 278122 337008 NM_001088405 0 - 278122 337008 0 11 125,135,108,156,24,111,135,96,142,35,735, 0,1316,5431,8951,9766,9896,16185,21851,26420,58026,58151, -chr16 278122 337029 NM_204944 0 - 278122 337026 0 13 125,148,174,105,18,14,36,229,2,135,95,141,881, 0,1316,5365,8933,9065,9720,9760,9902,16169,16185,21851,26421,58026, -chr16 357566 360222 NM_024227 0 - 357683 360219 0 6 15,100,84,134,153,291, 0,117,762,936,1502,2365, -chr16 357687 360222 NM_001045996 0 - 357687 360219 0 5 96,84,136,153,291, 0,641,813,1381,2244, -chr16 357717 359125 NM_001031359 0 - 357717 359125 0 5 66,87,4,131,57, 0,611,737,788,1351, -chr16 358328 360221 NM_001024399 0 - 358328 360219 0 3 75,135,290, 0,173,1603, -chr16 358328 360219 NM_001016451 0 - 358328 360219 0 4 87,135,153,288, 0,173,740,1603, -chr16 358328 360219 NM_001094081 0 - 358328 360219 0 3 87,153,288, 0,740,1603, -chr16 360792 371762 NM_021793 0 - 361987 371762 0 19 36,30,10,21,293,4,120,144,177,138,124,91,316,255,131,102,63,142,61, 0,54,143,1149,1195,1710,1819,3216,3429,3962,4341,4553,5357,5762,6244,6595,6730,6915,10909, -chr16 360798 373390 NM_001106991 0 - 361987 373390 0 17 30,21,293,4,120,144,177,139,125,17,99,268,128,208,138,40,11, 0,1143,1189,1704,1813,3210,3423,3956,4337,5369,5449,5747,6239,6580,6914,10922,12581, -chr16 361985 371761 NM_001098907 0 - 361987 371761 0 17 296,120,147,179,133,4,124,73,151,102,189,74,92,78,175,6,60, 0,623,2020,2236,2771,3058,3148,3360,4166,4344,4560,5096,5391,5519,5683,9375,9716, -chr16 387218 390579 NM_001109478 0 + 387223 390343 0 6 45,135,102,113,124,108, 0,1771,2161,2409,3001,3253, -chr16 388989 390579 NM_019731 0 + 388989 390343 0 5 135,102,113,127,108, 0,390,638,1230,1482, -chr16 388989 390416 NM_001077906 0 + 388989 390416 0 5 135,102,87,128,42, 0,390,638,1227,1385, -chr16 389010 390304 NM_001045774 0 + 389010 390304 0 4 114,102,113,85, 0,369,617,1209, -chr16 389010 390304 NM_001095218 0 + 389010 390304 0 4 110,106,113,85, 0,365,617,1209, -chr16 391951 401555 NM_001078122 0 + 391964 401382 0 8 88,74,46,136,125,94,105,194, 0,3000,4395,5474,8292,8740,9021,9410, -chr16 391963 653132 NM_011933 0 + 391964 401579 0 9 75,73,54,136,125,94,104,168,31, 0,2987,4381,5462,8280,8728,9009,9448,261138, -chr16 391964 401531 NM_171996 0 + 391964 401531 0 8 74,73,48,136,125,94,103,172, 0,2986,4380,5461,8279,8727,9008,9395, -chr16 631979 638450 NM_026633 0 + 631992 638191 0 7 65,124,4,130,100,83,181, 0,141,381,5436,5804,6141,6290, -chr16 631979 638450 NM_001109475 0 + 631992 638191 0 7 69,120,4,130,100,83,180, 0,145,381,5436,5804,6141,6291, -chr16 639765 656718 NM_001097176 0 + 639765 656718 0 26 78,171,84,165,60,117,105,60,24,120,69,21,115,134,108,123,111,126,63,138,180,99,27,132,102,27, 0,226,489,779,1268,3570,3760,3979,5331,5540,5812,5920,6010,6537,6964,8005,9125,11282,11577,12159,12909,15938,16185,16230,16720,16926, -chr16 658185 663607 NM_181823 0 + 658200 663607 0 19 52,59,82,62,53,109,98,103,107,121,5,82,143,80,135,42,123,203,127, 0,168,303,1360,1938,2064,2271,2486,2707,2896,3253,3515,3675,3899,4065,4340,4518,4743,5295, -chr16 658185 663607 NM_145999 0 + 658200 663607 0 20 52,59,83,16,54,53,109,98,103,107,122,4,82,143,79,136,42,123,197,127, 0,168,303,499,1368,1938,2064,2271,2486,2707,2896,3145,3515,3675,3899,4064,4340,4518,4749,5295, -chr16 658185 663608 NM_214325 0 + 658200 663607 0 18 52,59,83,54,53,109,102,104,102,121,82,143,83,137,76,123,203,128, 0,168,303,1368,1938,2064,2271,2490,2712,2896,3515,3675,3899,4063,4306,4518,4743,5295, -chr16 658194 663538 NM_001080866 0 + 658200 663538 0 15 43,59,87,54,111,102,99,109,119,72,75,140,48,138,57, 0,159,294,1359,2053,2262,2481,2698,2889,3513,3895,4053,4325,4737,5287, -chr16 658196 663556 NM_001006724 0 + 658200 663556 0 16 41,59,84,54,111,98,103,109,119,40,74,123,36,81,69,75, 0,157,292,1357,2051,2260,2475,2696,2887,3769,3890,4054,4335,4549,4810,5285, -chr16 658200 663066 NM_001037679 0 + 658200 663066 0 16 36,51,84,54,36,105,102,112,119,66,27,66,126,81,3,135, 0,158,285,1353,1923,2053,2256,2689,2883,3513,3779,3894,4050,4545,4637,4731, -chr16 658200 663617 NM_178316 0 + 658200 663607 0 20 37,59,83,54,47,115,102,99,107,121,5,82,143,79,138,48,123,3,200,137, 0,153,288,1353,1923,2043,2256,2475,2692,2881,3238,3500,3660,3884,4048,4319,4503,4637,4731,5280, -chr16 665791 668053 NM_001092742 0 + 665791 668053 0 8 39,159,225,150,112,101,60,270, 0,548,881,1180,1486,1668,1848,1992, -chr16 670383 672524 NM_019719 0 + 670526 672490 0 8 54,192,199,166,88,57,117,160, 0,110,769,1055,1410,1637,1782,1981, -chr16 670395 672524 NM_001025625 0 + 670526 672490 0 8 18,192,199,166,88,57,117,160, 0,98,757,1043,1398,1625,1770,1969, -chr16 670413 672719 NM_001075166 0 + 670526 672490 0 9 51,208,199,166,88,57,117,158,30, 0,64,739,1025,1380,1607,1752,1951,2276, -chr16 670549 672490 NM_001031406 0 + 670549 672490 0 7 136,197,167,48,57,111,132, 0,605,889,1284,1471,1616,1809, -chr16 670574 672490 NM_001078879 0 + 670574 672490 0 7 110,200,166,28,57,111,132, 0,577,864,1219,1446,1591,1784, - -chr16 1762351 1763112 NM_001007376 0 - 1762351 1763112 0 2 165,309, 0,452, -chr16 1766771 1771856 NM_001106988 0 - 1767098 1771726 0 10 33,75,247,126,103,189,177,134,82,42, 0,324,427,977,1176,1364,1666,4588,4873,5043, -chr16 1767095 1771726 NM_027141 0 - 1767098 1771726 0 8 51,284,126,103,189,177,136,80, 0,66,653,852,1040,1342,4264,4551, -chr16 1767098 1771494 NM_001034506 0 - 1767098 1771485 0 7 42,243,126,103,188,178,135, 0,104,650,849,1037,1338,4261, -chr16 1767209 1771485 NM_001095367 0 - 1767209 1771485 0 9 236,128,101,186,15,15,93,24,87, 0,539,740,926,1231,1273,1312,4150,4189, -chr16 1767209 1771485 NM_001017350 0 - 1767209 1771485 0 8 236,128,101,186,57,93,24,75, 0,539,740,926,1231,1312,4150,4201, -chr16 1776526 1778680 NM_011956 0 + 1776526 1778680 0 7 131,194,5,149,115,70,110, 0,232,543,1152,1410,1613,2044, -chr16 1776537 1778704 NM_001011891 0 + 1776537 1778704 0 7 120,194,5,149,115,72,132, 0,221,532,1141,1399,1602,2035, -chr16 1776537 1778722 NM_001034505 0 + 1776537 1778716 0 6 120,199,155,107,74,152, 0,221,1141,1405,1598,2033, -chr16 1776543 1778050 NM_001037114 0 + 1776543 1778050 0 4 114,102,152,114, 0,215,1132,1393, -chr16 1776543 1777833 NM_001103064 0 + 1776543 1777833 0 3 114,199,155, 0,215,1135, -chr16 1776543 1778053 NM_001093143 0 + 1776543 1778053 0 4 114,199,149,117, 0,215,1135,1393, -chr16 1776546 1778692 NM_001007833 0 + 1776546 1778692 0 6 111,199,149,113,74,122, 0,212,1132,1390,1589,2024, -chr16 1776564 1778211 NM_209444 0 + 1776564 1778211 0 4 96,63,158,72, 0,326,1111,1575, -chr16 1776570 1778053 NM_140986 0 + 1776570 1778053 0 3 90,84,117, 0,1113,1366, -chr16 1780596 1782405 NM_001048186 0 - 1780601 1782405 0 1 1809, 0, -chr16 1780598 1782406 NM_008340 0 - 1780601 1782406 0 1 1808, 0, -chr16 1780601 1783695 NM_053329 0 - 1780601 1782406 0 2 1805,33, 0,3061, -chr16 1780604 1782257 NM_001099896 0 - 1780604 1782257 0 3 84,960,36, 0,621,1617, -chr16 1780604 1782420 NM_001075963 0 - 1780604 1782420 0 1 1816, 0, diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/2.pep --- a/test-data/2.pep +++ /dev/null @@ -1,19 +0,0 @@ ->HSFAU1_3 -PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV -LLAG-PLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKVAKQEKKK -KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS ->HSFAU2_3 -PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV -LLAGAPLEDALWASAGWRP ->HSFAU3_3 -PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV -LLAGAPLEDEATLGQCGVEALTTLEVAGRMLG-GKVHGSLARAGKVRGQTPKGAKQEKKK -KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS ->HSFAU4_3 -PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHEIASLEGIAPEDQVV -LLAGAPLEDEATLGQCGVEALTTLEVAGRMLARGKVHGSLARAGKVRGQTPKVAKQEKKK -KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS ->HSFAU5_3 -PLSRLHLRGSWDRRSVANMQLFVRAQELHTFEVTGQETVAQIKAHVAS-LEGIAPEDQVV -LLAGAPLEDEATLGQCGVEALTTLEVGRMLFG-GKVHGSLARAGKVRGQTPKVAKQEKKK -KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS \ No newline at end of file diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/454Length.txt --- a/test-data/454Length.txt +++ /dev/null @@ -1,18 +0,0 @@ -1 54 -2 222 -3 95 -4 115 -5 116 -6 78 -7 47 -8 115 -9 187 -10 54 -11 57 -12 54 -13 60 -14 83 -15 83 -16 64 -17 82 -18 69 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/8.tabular --- a/test-data/8.tabular +++ /dev/null @@ -1,29 +0,0 @@ -AF099740 ENST00000296869 -AF377960 ENST00000160373 -AK131266 ENST00000350908 -BC005078 ENST00000319432 -BC007833 ENST00000349792 -NM_000054 ENST00000337474 -NM_000127 ENST00000333324 -NM_000425 ENST00000361699 -NM_000492 ENST00000003084 -NM_000588 ENST00000296870 -NM_001167 ENST00000245836 -NM_001666 ENST00000350060 -NM_001927 ENST00000273074 -NM_002651 ENST00000271657 -NM_002796 ENST00000290541 -NM_003269 ENST00000230083 -NM_003391 ENST00000265441 -NM_003687 ENST00000253754 -NM_004199 ENST00000166534 -NM_005997 ENST00000295315 -NM_006773 ENST00000263239 -NM_007214 ENST00000027474 -NM_014908 ENST00000308871 -NM_015354 ENST00000259310 -NM_020145 ENST00000291931 -NM_024536 ENST00000243776 -NM_145315 ENST00000258002 -NM_152827 ENST00000230085 -NM_174933 ENST00000308941 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/aggregate_binned_scores_in_intervals.bed --- a/test-data/aggregate_binned_scores_in_intervals.bed +++ /dev/null @@ -1,1 +0,0 @@ -chr7 60000002 60000010 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/assembly_stats.tabular --- a/test-data/assembly_stats.tabular +++ /dev/null @@ -1,1 +0,0 @@ -5 2589 524 517 518 5 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/bowtie_out10.sam --- a/test-data/bowtie_out10.sam +++ /dev/null @@ -1,36 +0,0 @@ -Dummy:1:1:1570:620 141 * 0 0 * * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1570:620 77 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1572:270 131 phiX174 3577 255 50M = 3518 -109 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:270 67 phiX174 3518 255 50M = 3577 109 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:324 141 * 0 0 * * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1572:324 77 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 -Dummy:1:1:1578:331 131 phiX174 268 255 50M = 209 -109 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1578:331 67 phiX174 209 255 50M = 268 109 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1582:633 141 * 0 0 * * 0 0 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1582:633 77 * 0 0 * * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1598:534 131 phiX174 1772 255 50M = 1717 -105 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1598:534 67 phiX174 1717 255 50M = 1772 105 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 131 phiX174 868 255 50M = 803 -115 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 67 phiX174 803 255 50M = 868 115 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 131 phiX174 2773 255 50M = 2718 -105 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 67 phiX174 2718 255 50M = 2773 105 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 131 phiX174 2355 255 50M = 2301 -104 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 67 phiX174 2301 255 50M = 2355 104 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 131 phiX174 4473 255 50M = 4418 -105 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 67 phiX174 4418 255 50M = 4473 105 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 131 phiX174 451 255 50M = 401 -100 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 67 phiX174 401 255 50M = 451 100 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1652:270 141 * 0 0 * * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1652:270 77 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 -Dummy:1:1:1673:514 131 phiX174 4072 255 50M = 4018 -104 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1673:514 67 phiX174 4018 255 50M = 4072 104 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1746:351 141 * 0 0 * * 0 0 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII XM:i:0 -Dummy:1:1:1746:351 77 * 0 0 * * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1749:466 131 phiX174 2251 255 50M = 2201 -100 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1749:466 67 phiX174 2201 255 50M = 2251 100 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 131 phiX174 69 255 50M = 5 -114 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 67 phiX174 5 255 50M = 69 114 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 131 phiX174 2566 255 50M = 2501 -115 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 67 phiX174 2501 255 50M = 2566 115 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 131 phiX174 3173 255 50M = 3118 -105 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 67 phiX174 3118 255 50M = 3173 105 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/bowtie_out9.sam --- a/test-data/bowtie_out9.sam +++ /dev/null @@ -1,26 +0,0 @@ -HWI-EAS91_1_30788AAXX:1:1:1090:409/1 16 chrM 15014 255 36M * 0 0 TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 16 chrM 14023 255 36M * 0 0 AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC III/:&GII3III;IIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1218:141/1 4 * 0 0 * * 0 0 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1269:520/1 16 chrM 11036 255 36M * 0 0 CGACAAACCGATCTAAAATCACTTATTCCATACTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27G8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 16 chrM 14866 255 36M * 0 0 AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1310:991/1 16 chrM 10002 255 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTACCACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 16 chrM 11616 255 36M * 0 0 GATCTAGAAACAGAAACTTAATATTTCCCATTTACC II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1398:854/1 16 chrM 3921 255 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII XA:i:2 MD:Z:27T0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 16 chrM 9331 255 36M * 0 0 CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA &,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII XA:i:1 MD:Z:28G7 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1454:975/1 16 chrM 8929 255 36M * 0 0 TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1461:255/1 0 chrM 12988 255 36M * 0 0 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I XA:i:2 MD:Z:7A0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1491:637/1 16 chrM 10864 255 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCCCAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 16 chrM 2334 255 36M * 0 0 AAATATATAATCACTTATTGATCCAAACCATTGATC IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1601:805/1 0 chrM 12584 255 36M * 0 0 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III XA:i:2 MD:Z:7A0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1630:59/1 16 chrM 12387 255 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1634:211/1 0 chrM 9350 255 36M * 0 0 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1663:724/1 0 chrM 15012 255 36M * 0 0 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 XA:i:2 MD:Z:7T0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1698:516/1 16 chrM 2735 255 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1711:249/1 16 chrM 10617 255 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1716:413/1 0 chrM 6040 255 36M * 0 0 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 16 chrM 15787 255 36M * 0 0 ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1775:764/1 0 chrM 16613 255 36M * 0 0 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC IIIIIII""III@IIII+IIIIII8H8IIIIIIICI XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:795:325/1 16 chrM 4249 255 36M * 0 0 AAACTTGGACTCACACCATTCCACTTCCCAGTACCC IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:850:117/1 16 chrM 5540 255 36M * 0 0 CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC ?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:873:453/1 16 chrM 3188 255 36M * 0 0 ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/branchlength_fasta_in.dat --- a/test-data/branchlength_fasta_in.dat +++ /dev/null @@ -1,44 +0,0 @@ ->hg17.chr7(+):26907301-26907310|hg17_0 -GTGGGAGGT ->panTro1.chr6(+):28037319-28037328|panTro1_0 -GTGGGAGGT ->mm5.chr6(+):52104022-52104031|mm5_0 -GTGGGAGGT ->rn3.chr4(+):80734395-80734404|rn3_0 -GTGGGAGGT ->canFam1.chr14(+):42826409-42826418|canFam1_0 -GTGGGAGGT - ->hg17.chr7(+):26907310-26907326|hg17_1 -AGTCAGAGTGTCTGAG ->panTro1.chr6(+):28037328-28037344|panTro1_1 -AGTCAGAGTGTCTGAG ->mm5.chr6(+):52104031-52104047|mm5_1 -AGTCAGAGTGTCTGAG ->rn3.chr4(+):80734404-80734420|rn3_1 -AGTCAGAGTATCTGAG ->canFam1.chr14(+):42826418-42826434|canFam1_1 -AGTCAGAGTGTCTGAG - ->hg17.chr7(+):26907326-26907338|hg17_2 -GTAGAAGACCCC ->panTro1.chr6(+):28037344-28037356|panTro1_2 -GTAGAAGACCCC ->mm5.chr6(+):52104047-52104059|mm5_2 -GTAGACGATGCC ->rn3.chr4(+):80734420-80734432|rn3_2 -GTAGATGATGCG ->canFam1.chr14(+):42826434-42826446|canFam1_2 -GTAGAAGACCCC - ->hg17.chr7(+):26907338-26907654|hg17_3 -GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC ->panTro1.chr6(+):28037356-28037672|panTro1_3 -GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC ->mm5.chr6(+):52104059-52104375|mm5_3 -GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC ->rn3.chr4(+):80734432-80734748|rn3_3 -GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC ->canFam1.chr14(+):42826446-42826762|canFam1_3 -GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC - diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/branchlength_out.dat --- a/test-data/branchlength_out.dat +++ /dev/null @@ -1,33 +0,0 @@ -Block Branch Length LowerBound UpperBound -1 hg17.chr7(+):26907301-26907310|hg17_0 4.93827e-31 0 0.23542 -1 panTro1.chr6(+):28037319-28037328|panTro1_0 4.93827e-31 0 0.23542 -1 Node1 4.93827e-31 0 0.23542 -1 mm5.chr6(+):52104022-52104031|mm5_0 4.93827e-31 0 0.23542 -1 rn3.chr4(+):80734395-80734404|rn3_0 4.93827e-31 0 0.23542 -1 Node4 4.93827e-31 0 0.23542 -1 canFam1.chr14(+):42826409-42826418|canFam1_0 4.93827e-31 0 0.23542 -1 Total Tree 3.45679e-30 2.60643e-34 2.54701e-20 -2 hg17.chr7(+):26907310-26907326|hg17_1 1.90313e-31 0 0.13592 -2 panTro1.chr6(+):28037328-28037344|panTro1_1 1.90313e-31 0 0.13592 -2 Node1 4.10285e-19 0 0.13592 -2 mm5.chr6(+):52104031-52104047|mm5_1 2.02063e-19 0 0.13592 -2 rn3.chr4(+):80734404-80734420|rn3_1 0.069102 0.00372954 0.421893 -2 Node4 1.90313e-31 0 0.13592 -2 canFam1.chr14(+):42826418-42826434|canFam1_1 1.13513e-19 0 0.13592 -2 Total Tree 0.069102 0.00372954 0.421893 -3 hg17.chr7(+):26907326-26907338|hg17_2 8.84162e-30 0 0.167446 -3 panTro1.chr6(+):28037344-28037356|panTro1_2 8.84162e-30 0 0.167446 -3 Node1 0 0 0.167446 -3 mm5.chr6(+):52104047-52104059|mm5_2 0 0 0.24858 -3 rn3.chr4(+):80734420-80734432|rn3_2 0.201494 0.0309976 0.7364 -3 Node4 0.31691 0.0691821 1.08477 -3 canFam1.chr14(+):42826434-42826446|canFam1_2 0 0 0.167446 -3 Total Tree 0.518404 0.168855 1.26753 -4 hg17.chr7(+):26907338-26907654|hg17_3 1.11429e-19 0 0.0061265 -4 panTro1.chr6(+):28037356-28037672|panTro1_3 1.11866e-19 0 0.0061265 -4 Node1 0.0583134 0.0318643 0.0951333 -4 mm5.chr6(+):52104059-52104375|mm5_3 0.0357704 0.0167845 0.0644066 -4 rn3.chr4(+):80734432-80734748|rn3_3 0.0320354 0.0141331 0.0594834 -4 Node4 0.0770295 0.0463471 0.11848 -4 canFam1.chr14(+):42826446-42826762|canFam1_3 0.0575307 0.0316345 0.0936592 -4 Total Tree 0.260679 0.205255 0.325684 diff -r 6c269fbd11a43236a0dd4c7df388125fdaf8962d -r 16495aaa26ea3d8feabcd25ee395608568156b6f test-data/cc.EarlyRepSeg.20051216.bed --- a/test-data/cc.EarlyRepSeg.20051216.bed +++ /dev/null @@ -1,568 +0,0 @@ -chr7 26853157 26854215 EarlyRepSeg -chr7 26865558 26956110 EarlyRepSeg -chr7 26956330 26958851 EarlyRepSeg -chr7 26958893 26959464 EarlyRepSeg -chr7 26959504 26959533 EarlyRepSeg -chr7 26960356 26960376 EarlyRepSeg -chr7 26960632 26960801 EarlyRepSeg -chr7 89741530 89743766 EarlyRepSeg -chr7 89743824 89744003 EarlyRepSeg -chr7 89744088 89744106 EarlyRepSeg -chr7 89745480 89968351 EarlyRepSeg -chr7 90542632 90542691 EarlyRepSeg -chr7 113919823 113919871 EarlyRepSeg -chr7 113919935 113920029 EarlyRepSeg -chr7 113920113 113920978 EarlyRepSeg -chr7 113922569 113924554 EarlyRepSeg -chr7 113924746 113924793 EarlyRepSeg -chr7 113924833 113927725 EarlyRepSeg -chr7 113927893 113928509 EarlyRepSeg -chr7 113929396 113929453 EarlyRepSeg -chr7 113933276 114108846 EarlyRepSeg -chr7 114108947 114119346 EarlyRepSeg -chr7 114119404 114119556 EarlyRepSeg -chr7 114119621 114123541 EarlyRepSeg -chr7 114124457 114124490 EarlyRepSeg -chr7 114124634 114136954 EarlyRepSeg -chr7 114142730 114142885 EarlyRepSeg -chr7 114143714 114143737 EarlyRepSeg -chr7 114143779 114144176 EarlyRepSeg -chr7 114144305 114144327 EarlyRepSeg -chr7 114360998 114361020 EarlyRepSeg -chr7 114362526 114363858 EarlyRepSeg -chr7 115404471 116251468 EarlyRepSeg -chr7 116251612 116251638 EarlyRepSeg -chr7 116251693 116251827 EarlyRepSeg -chr7 116251956 116252352 EarlyRepSeg -chr7 116252418 116253165 EarlyRepSeg -chr7 116463012 116463121 EarlyRepSeg -chr7 116474219 116474393 EarlyRepSeg -chr7 116474517 116474771 EarlyRepSeg -chr7 116484623 116561352 EarlyRepSeg -chr7 116561778 116562791 EarlyRepSeg -chr7 116563539 116571400 EarlyRepSeg -chr7 116572311 116572335 EarlyRepSeg -chr7 116572377 116572548 EarlyRepSeg -chr7 116576381 116576667 EarlyRepSeg -chr7 116597894 116597915 EarlyRepSeg -chr7 116598129 116598237 EarlyRepSeg -chr7 116598300 116608071 EarlyRepSeg -chr7 116608165 116608209 EarlyRepSeg -chr7 116608255 116608278 EarlyRepSeg -chr7 116608335 116608527 EarlyRepSeg -chr7 116609208 116609273 EarlyRepSeg -chr7 116630981 116631297 EarlyRepSeg -chr7 116633902 116634213 EarlyRepSeg -chr7 116634270 116641382 EarlyRepSeg -chr7 116694148 116698403 EarlyRepSeg -chr7 116698511 116698606 EarlyRepSeg -chr7 116698648 116698807 EarlyRepSeg -chr7 116699036 116699669 EarlyRepSeg -chr7 116735241 116737872 EarlyRepSeg -chr7 116738045 116738948 EarlyRepSeg -chr7 116739086 116739461 EarlyRepSeg -chr7 116739526 116742149 EarlyRepSeg -chr7 116742220 116744605 EarlyRepSeg -chr7 116746201 116746659 EarlyRepSeg -chr7 116746728 116746820 EarlyRepSeg -chr7 116747018 116758597 EarlyRepSeg -chr7 116763552 116928910 EarlyRepSeg -chr7 116929761 116930077 EarlyRepSeg -chr7 116931422 116931446 EarlyRepSeg -chr6 41867303 41867713 EarlyRepSeg -chr6 41868622 41868636 EarlyRepSeg -chr6 41871084 41871127 EarlyRepSeg -chr6 41871277 41871508 EarlyRepSeg -chr6 41881436 41904567 EarlyRepSeg -chr6 74114855 74115081 EarlyRepSeg -chr6 74115174 74289952 EarlyRepSeg -chr6 108641673 108641689 EarlyRepSeg -chr6 108641837 108645076 EarlyRepSeg -chr6 108645288 108645828 EarlyRepSeg -chr6 108645850 108645872 EarlyRepSeg -chr6 108645893 108647550 EarlyRepSeg -chr6 108655265 108657582 EarlyRepSeg -chr6 108658752 108658815 EarlyRepSeg -chr6 108667835 108668566 EarlyRepSeg -chr6 108675247 108677563 EarlyRepSeg -chr6 108678755 108678800 EarlyRepSeg -chr6 108687834 108688151 EarlyRepSeg -chr6 108689330 108689377 EarlyRepSeg -chr6 108751831 108752466 EarlyRepSeg -chr6 108870546 108870611 EarlyRepSeg -chr6 132325404 132325465 EarlyRepSeg -chr6 132327970 132328191 EarlyRepSeg -chr6 132328279 132329125 EarlyRepSeg -chr6 132329408 132329455 EarlyRepSeg -chr6 132329514 132329602 EarlyRepSeg -chr6 132329683 132340765 EarlyRepSeg -chr6 132341999 132342746 EarlyRepSeg -chr6 132344613 132344841 EarlyRepSeg -chr6 132345103 132345170 EarlyRepSeg -chr6 132346006 132346044 EarlyRepSeg -chr6 132346178 132346746 EarlyRepSeg -chr6 132347078 132347478 EarlyRepSeg -chr6 132370237 132372346 EarlyRepSeg -chr6 132383528 132383567 EarlyRepSeg -chr6 132384242 132384262 EarlyRepSeg -chr6 132384405 132384422 EarlyRepSeg -chr6 132384833 132385384 EarlyRepSeg -chr6 132387114 132387150 EarlyRepSeg -chr6 132394199 132396580 EarlyRepSeg -chr5 55886021 55886041 EarlyRepSeg -chr5 55886110 55886132 EarlyRepSeg -chr5 55886176 55886195 EarlyRepSeg -chr5 55888015 55889053 EarlyRepSeg -chr5 55889099 55889140 EarlyRepSeg -chr5 55889401 55890905 EarlyRepSeg -chr5 56106962 56107249 EarlyRepSeg -chr5 56107766 56107862 EarlyRepSeg -chr5 56367460 56370292 EarlyRepSeg -chr5 56370336 56370891 EarlyRepSeg -chr5 131285263 131285306 EarlyRepSeg -chr5 131475247 131494484 EarlyRepSeg -chr5 131505619 131505861 EarlyRepSeg -chr5 131507116 131595694 EarlyRepSeg -chr5 131655935 131849308 EarlyRepSeg -chr5 131849349 131849383 EarlyRepSeg -chr5 131849499 131849515 EarlyRepSeg -chr5 131888105 132000339 EarlyRepSeg -chr5 132005729 132006017 EarlyRepSeg -chr5 132006171 132007566 EarlyRepSeg -chr5 132007757 132008189 EarlyRepSeg -chr5 132015742 132015789 EarlyRepSeg -chr5 132015951 132018096 EarlyRepSeg -chr5 132018338 132019909 EarlyRepSeg -chr5 132052942 132052981 EarlyRepSeg -chr5 132053021 132056571 EarlyRepSeg -chr5 132058138 132058229 EarlyRepSeg -chr5 132058505 132058526 EarlyRepSeg -chr5 132061788 132061810 EarlyRepSeg -chr5 132061846 132062661 EarlyRepSeg -chr5 132062832 132113831 EarlyRepSeg -chr5 132139962 132145821 EarlyRepSeg -chr5 132145885 132146737 EarlyRepSeg -chr5 132146782 132146803 EarlyRepSeg -chr5 132146845 132158072 EarlyRepSeg -chr5 132158112 132158184 EarlyRepSeg -chr5 132159741 132165336 EarlyRepSeg -chr5 132165401 132165803 EarlyRepSeg -chr5 132165876 132166736 EarlyRepSeg -chr5 132192266 132192327 EarlyRepSeg -chr5 132192395 132194449 EarlyRepSeg -chr5 132194758 132195445 EarlyRepSeg -chr5 132195811 132196282 EarlyRepSeg -chr5 132207140 132213592 EarlyRepSeg -chr5 132214738 132214752 EarlyRepSeg -chr5 132226393 132234169 EarlyRepSeg -chr5 132234504 132234598 EarlyRepSeg -chr5 132235860 132235963 EarlyRepSeg -chr5 132236046 132236459 EarlyRepSeg -chr5 132236763 132237613 EarlyRepSeg -chr5 132238255 132238299 EarlyRepSeg -chr5 132238475 132283603 EarlyRepSeg -chr5 142095059 142095166 EarlyRepSeg -chr5 142095247 142095397 EarlyRepSeg -chr5 142095465 142100861 EarlyRepSeg -chr5 142101243 142102608 EarlyRepSeg -chr5 142102655 142151401 EarlyRepSeg -chr5 142154629 142158905 EarlyRepSeg -chr5 142159158 142159198 EarlyRepSeg -chr5 142159679 142173072 EarlyRepSeg -chr18 59412370 59433985 EarlyRepSeg -chr18 59434207 59456478 EarlyRepSeg -chr18 59456699 59456831 EarlyRepSeg -chr18 59456869 59456903 EarlyRepSeg -chr18 59456922 59457354 EarlyRepSeg -chr18 59457439 59465986 EarlyRepSeg -chr18 59466027 59466067 EarlyRepSeg -chr18 59466105 59466165 EarlyRepSeg -chr18 59466225 59472274 EarlyRepSeg -chr18 59472339 59472402 EarlyRepSeg -chr18 59473339 59473490 EarlyRepSeg -chr18 59475475 59475498 EarlyRepSeg -chr18 59475900 59476000 EarlyRepSeg -chr18 59476207 59476408 EarlyRepSeg -chr18 59476471 59476911 EarlyRepSeg -chr18 59477077 59477336 EarlyRepSeg -chr18 59477401 59485966 EarlyRepSeg -chr18 59486026 59486046 EarlyRepSeg -chr18 59486215 59492264 EarlyRepSeg -chr18 59492348 59492397 EarlyRepSeg -chr18 59493339 59493451 EarlyRepSeg -chr18 59521111 59521385 EarlyRepSeg -chr18 59558120 59558177 EarlyRepSeg -chr18 59558222 59558288 EarlyRepSeg -chr2 220105509 220107457 EarlyRepSeg -chr2 234274981 234460520 EarlyRepSeg -chr1 147971142 148444534 EarlyRepSeg -chr1 148444657 148444760 EarlyRepSeg -chr1 148445123 148445166 EarlyRepSeg -chr1 148445324 148445350 EarlyRepSeg -chr1 148446462 148446660 EarlyRepSeg -chr1 148447388 148447426 EarlyRepSeg -chr1 148447762 148471133 EarlyRepSeg -chr9 128765210 128856811 EarlyRepSeg -chr9 128901865 129004365 EarlyRepSeg -chr9 129005361 129008847 EarlyRepSeg -chr9 129009370 129009735 EarlyRepSeg -chr9 129010052 129015022 EarlyRepSeg -chr9 129015082 129018165 EarlyRepSeg -chr9 129018225 129027884 EarlyRepSeg -chr9 129028821 129039792 EarlyRepSeg -chr9 129040135 129040200 EarlyRepSeg -chr9 129040288 129040309 EarlyRepSeg -chr9 129040511 129040529 EarlyRepSeg -chr9 129045169 129045941 EarlyRepSeg -chr9 129046139 129052414 EarlyRepSeg -chr9 129059485 129063706 EarlyRepSeg -chr9 129064025 129064072 EarlyRepSeg -chr9 129064243 129064284 EarlyRepSeg -chr9 129071282 129073376 EarlyRepSeg -chr9 129073850 129074365 EarlyRepSeg -chr9 129075271 129075470 EarlyRepSeg -chr9 129148128 129148471 EarlyRepSeg -chr9 129174601 129174644 EarlyRepSeg -chr9 129174683 129174867 EarlyRepSeg -chr9 129177812 129178277 EarlyRepSeg -chr9 129179593 129181321 EarlyRepSeg -chr9 129182910 129182993 EarlyRepSeg -chr9 129185792 129229546 EarlyRepSeg -chrX 122515118 122518380 EarlyRepSeg -chrX 122519180 122519262 EarlyRepSeg -chrX 122519357 122521476 EarlyRepSeg -chrX 122526240 122526737 EarlyRepSeg -chrX 122527607 122527693 EarlyRepSeg -chrX 122528249 122528336 EarlyRepSeg -chrX 122528657 122529022 EarlyRepSeg -chrX 122529666 122530817 EarlyRepSeg -chrX 122565527 122565950 EarlyRepSeg -chrX 122566173 122566198 EarlyRepSeg -chrX 122566267 122566475 EarlyRepSeg -chrX 122566527 122566817 EarlyRepSeg -chrX 122567687 122582126 EarlyRepSeg -chrX 122583489 122584103 EarlyRepSeg -chrX 122594426 122596210 EarlyRepSeg -chrX 122596274 122617296 EarlyRepSeg -chrX 122633600 122633665 EarlyRepSeg -chrX 122634493 122634584 EarlyRepSeg -chrX 122636090 122872532 EarlyRepSeg -chrX 122876952 122877037 EarlyRepSeg -chrX 122877088 122877176 EarlyRepSeg -chrX 122878185 122878198 EarlyRepSeg -chrX 122879577 122880529 EarlyRepSeg -chrX 122880573 122880754 EarlyRepSeg -chrX 122880991 122881034 EarlyRepSeg -chrX 122884162 122904171 EarlyRepSeg -chrX 122904230 122904397 EarlyRepSeg -chrX 122905605 122905631 EarlyRepSeg -chrX 122905822 122906072 EarlyRepSeg -chrX 122906141 122908153 EarlyRepSeg -chrX 122908290 122908441 EarlyRepSeg -chrX 122908471 122909074 EarlyRepSeg -chrX 122909361 122909402 EarlyRepSeg -chrX 122909482 122913104 EarlyRepSeg -chrX 122915256 122915324 EarlyRepSeg -chrX 152760672 152760721 EarlyRepSeg -chrX 152760829 152760842 EarlyRepSeg -chrX 152761258 152770914 EarlyRepSeg -chrX 152771016 152808667 EarlyRepSeg -chrX 152808758 152808842 EarlyRepSeg -chrX 152809200 152809641 EarlyRepSeg -chrX 152809809 152809850 EarlyRepSeg -chrX 152809894 152809916 EarlyRepSeg -chrX 152810266 152810965 EarlyRepSeg -chrX 152830891 152831471 EarlyRepSeg -chrX 152850880 152851459 EarlyRepSeg -chrX 152861605 152868939 EarlyRepSeg 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