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commit/galaxy-central: greg: Handle issues with invalid dicts received when from the tool shed api.
by commits-noreply@bitbucket.org 09 Jan '14
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/
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commit/galaxy-central: carlfeberhard: Functional browser tests: update history options tests
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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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 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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commit/galaxy-central: carlfeberhard: Functional browser tests: update hda state tests
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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commit/galaxy-central: greg: Fix the single broken tool shed functional test.
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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commit/galaxy-central: carlfeberhard: Functional browser tests: update history panel tests
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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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 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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commit/galaxy-central: carlfeberhard: Functional browser tests: update anon history tests
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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0

commit/galaxy-central: inithello: Allow specifying the functional tests' install_database_connection with an environment variable.
by commits-noreply@bitbucket.org 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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/
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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 09 Jan '14
by commits-noreply@bitbucket.org 09 Jan '14
09 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
-chrX 152868998 152869602 EarlyRepSeg
-chrX 152869727 152870175 EarlyRepSeg
-chrX 152876992 152877431 EarlyRepSeg
-chrX 152877498 152878262 EarlyRepSeg
-chrX 152901180 152901356 EarlyRepSeg
-chrX 152901520 152901723 EarlyRepSeg
-chrX 152903274 152903322 EarlyRepSeg
-chrX 152904885 152907019 EarlyRepSeg
-chrX 153090357 153101014 EarlyRepSeg
-chrX 153101371 153104136 EarlyRepSeg
-chrX 153104196 153106352 EarlyRepSeg
-chrX 153297819 153305186 EarlyRepSeg
-chrX 153367214 153398065 EarlyRepSeg
-chrX 153409564 153409652 EarlyRepSeg
-chrX 153409708 153452751 EarlyRepSeg
-chrX 153825634 153825902 EarlyRepSeg
-chrX 153825944 153832126 EarlyRepSeg
-chrX 153833045 153834044 EarlyRepSeg
-chr13 29689066 29689271 EarlyRepSeg
-chr13 29689993 29691138 EarlyRepSeg
-chr13 29691184 29691786 EarlyRepSeg
-chr13 29699635 29723447 EarlyRepSeg
-chr13 29724097 29724150 EarlyRepSeg
-chr13 29724437 29729278 EarlyRepSeg
-chr13 29729324 29729541 EarlyRepSeg
-chr13 29748182 29749259 EarlyRepSeg
-chr13 29749301 29749322 EarlyRepSeg
-chr13 29750436 29778548 EarlyRepSeg
-chr13 29779059 29779318 EarlyRepSeg
-chr13 29779377 29782224 EarlyRepSeg
-chr13 29782457 29782521 EarlyRepSeg
-chr13 29782985 29783026 EarlyRepSeg
-chr13 29783068 29783105 EarlyRepSeg
-chr13 29783187 29794875 EarlyRepSeg
-chr13 29795145 29795419 EarlyRepSeg
-chr13 29795506 29795568 EarlyRepSeg
-chr13 29795610 29795657 EarlyRepSeg
-chr13 29797042 29797089 EarlyRepSeg
-chr13 29797248 29805175 EarlyRepSeg
-chr13 29807253 29807274 EarlyRepSeg
-chr13 29807727 29812203 EarlyRepSeg
-chr13 29812642 29820660 EarlyRepSeg
-chr13 29842265 29842438 EarlyRepSeg
-chr13 29854299 29854461 EarlyRepSeg
-chr13 29855916 29863126 EarlyRepSeg
-chr13 29865139 29866737 EarlyRepSeg
-chr13 29867798 29867842 EarlyRepSeg
-chr13 29867923 29868153 EarlyRepSeg
-chr13 29870372 29870486 EarlyRepSeg
-chr13 29870595 29871893 EarlyRepSeg
-chr13 29875493 29875515 EarlyRepSeg
-chr13 29875906 29876049 EarlyRepSeg
-chr13 29876280 29876544 EarlyRepSeg
-chr13 29877549 29877594 EarlyRepSeg
-chr13 29877640 29877755 EarlyRepSeg
-chr13 29888848 29889116 EarlyRepSeg
-chr13 29913298 29915450 EarlyRepSeg
-chr13 29916692 29916808 EarlyRepSeg
-chr13 29916871 29916912 EarlyRepSeg
-chr12 38857192 38857838 EarlyRepSeg
-chr12 38858064 38859517 EarlyRepSeg
-chr11 64242393 64242795 EarlyRepSeg
-chr11 64244176 64244321 EarlyRepSeg
-chr11 64297901 64321446 EarlyRepSeg
-chr11 116114836 116128702 EarlyRepSeg
-chr11 116134467 116135228 EarlyRepSeg
-chr11 116256326 116256395 EarlyRepSeg
-chr11 116256453 116256519 EarlyRepSeg
-chr11 116257093 116257138 EarlyRepSeg
-chr11 116257203 116257403 EarlyRepSeg
-chr11 116259428 116260093 EarlyRepSeg
-chr11 116280588 116294899 EarlyRepSeg
-chr11 116294934 116295981 EarlyRepSeg
-chr11 116296783 116298100 EarlyRepSeg
-chr11 116298577 116298670 EarlyRepSeg
-chr11 116298713 116299250 EarlyRepSeg
-chr11 116320712 116321239 EarlyRepSeg
-chr11 116326943 116398307 EarlyRepSeg
-chr11 116398468 116398525 EarlyRepSeg
-chr11 116398574 116398772 EarlyRepSeg
-chr11 116398840 116399053 EarlyRepSeg
-chr11 116400410 116401850 EarlyRepSeg
-chr11 116401898 116402342 EarlyRepSeg
-chr11 116402425 116403775 EarlyRepSeg
-chr11 116406023 116415188 EarlyRepSeg
-chr11 116415423 116417404 EarlyRepSeg
-chr11 116417596 116441864 EarlyRepSeg
-chr11 116443999 116444201 EarlyRepSeg
-chr11 116444843 116445008 EarlyRepSeg
-chr11 116445046 116448354 EarlyRepSeg
-chr11 116448391 116448434 EarlyRepSeg
-chr11 116448672 116448715 EarlyRepSeg
-chr11 116461947 116462084 EarlyRepSeg
-chr22 30129315 30200724 EarlyRepSeg
-chr22 30200767 30200791 EarlyRepSeg
-chr22 30200897 30205649 EarlyRepSeg
-chr22 30230684 30231848 EarlyRepSeg
-chr22 30239701 30239723 EarlyRepSeg
-chr22 30240912 30240933 EarlyRepSeg
-chr22 30241666 30241903 EarlyRepSeg
-chr22 30243634 30243709 EarlyRepSeg
-chr22 30243791 30244495 EarlyRepSeg
-chr22 30247809 30247829 EarlyRepSeg
-chr22 30247864 30248161 EarlyRepSeg
-chr22 30314600 30316228 EarlyRepSeg
-chr22 30316287 30317023 EarlyRepSeg
-chr22 30317489 30321462 EarlyRepSeg
-chr22 30352638 30354524 EarlyRepSeg
-chr22 30358006 30369571 EarlyRepSeg
-chr22 30373001 30373025 EarlyRepSeg
-chr22 30373688 30374213 EarlyRepSeg
-chr22 30375809 30390770 EarlyRepSeg
-chr22 30391746 30391889 EarlyRepSeg
-chr22 30394782 30394870 EarlyRepSeg
-chr22 30395266 30398830 EarlyRepSeg
-chr22 30400519 30400864 EarlyRepSeg
-chr22 30404073 30424199 EarlyRepSeg
-chr22 30424283 30424687 EarlyRepSeg
-chr22 30424727 30424952 EarlyRepSeg
-chr22 30433357 30433997 EarlyRepSeg
-chr22 30435197 30437931 EarlyRepSeg
-chr22 30440803 30450151 EarlyRepSeg
-chr22 30458187 30462627 EarlyRepSeg
-chr22 30462670 30462856 EarlyRepSeg
-chr22 30502987 30513365 EarlyRepSeg
-chr22 30513992 30515580 EarlyRepSeg
-chr22 30520887 30530176 EarlyRepSeg
-chr22 30530212 30530945 EarlyRepSeg
-chr22 30531203 30535572 EarlyRepSeg
-chr22 30540983 30541043 EarlyRepSeg
-chr22 30541107 30541527 EarlyRepSeg
-chr22 30556465 30556478 EarlyRepSeg
-chr22 30556865 30604008 EarlyRepSeg
-chr22 30606868 30606911 EarlyRepSeg
-chr22 30606958 30616014 EarlyRepSeg
-chr22 30626838 30632058 EarlyRepSeg
-chr22 30632517 30633323 EarlyRepSeg
-chr22 30634821 30634842 EarlyRepSeg
-chr22 30678345 30691941 EarlyRepSeg
-chr22 30691979 30696363 EarlyRepSeg
-chr22 30711525 30731359 EarlyRepSeg
-chr22 30735405 30753182 EarlyRepSeg
-chr22 31296060 31296144 EarlyRepSeg
-chr22 31296268 31296857 EarlyRepSeg
-chr22 31298098 31300256 EarlyRepSeg
-chr22 31300336 31302162 EarlyRepSeg
-chr22 31303418 31306260 EarlyRepSeg
-chr22 31306323 31307916 EarlyRepSeg
-chr22 31307969 31308066 EarlyRepSeg
-chr22 31308112 31308264 EarlyRepSeg
-chr22 31313549 31313659 EarlyRepSeg
-chr22 31313726 31313930 EarlyRepSeg
-chr22 31316904 31316969 EarlyRepSeg
-chr16 100314 100528 EarlyRepSeg
-chr16 100577 143948 EarlyRepSeg
-chr16 196729 255742 EarlyRepSeg
-chr16 327386 345225 EarlyRepSeg
-chr16 420528 499964 EarlyRepSeg
-chr16 25780441 25782479 EarlyRepSeg
-chr15 41520416 41610592 EarlyRepSeg
-chr15 41617282 41617384 EarlyRepSeg
-chr15 41617425 41622100 EarlyRepSeg
-chr15 41625197 41872249 EarlyRepSeg
-chr15 41872351 41872407 EarlyRepSeg
-chr15 41915847 41915868 EarlyRepSeg
-chr15 41915967 41916752 EarlyRepSeg
-chr15 41916818 41916836 EarlyRepSeg
-chr15 41930084 41935449 EarlyRepSeg
-chr21 32669080 32677736 EarlyRepSeg
-chr21 32679799 32679870 EarlyRepSeg
-chr21 32679914 32680795 EarlyRepSeg
-chr21 32681127 32681942 EarlyRepSeg
-chr21 32682560 32708225 EarlyRepSeg
-chr21 32708295 32708358 EarlyRepSeg
-chr21 32708395 32708786 EarlyRepSeg
-chr21 32708933 32709007 EarlyRepSeg
-chr21 32755446 32777739 EarlyRepSeg
-chr21 32777860 32781095 EarlyRepSeg
-chr21 32784633 32784877 EarlyRepSeg
-chr21 32785037 32787843 EarlyRepSeg
-chr21 32789267 32789327 EarlyRepSeg
-chr21 32790767 32793305 EarlyRepSeg
-chr21 32793700 32794302 EarlyRepSeg
-chr21 32795603 32795626 EarlyRepSeg
-chr21 32823257 32834186 EarlyRepSeg
-chr21 32835989 32836025 EarlyRepSeg
-chr21 32838501 32838523 EarlyRepSeg
-chr21 32838557 32838598 EarlyRepSeg
-chr21 32838643 32838756 EarlyRepSeg
-chr21 32838799 32838988 EarlyRepSeg
-chr21 32839538 32877989 EarlyRepSeg
-chr21 32878079 32878098 EarlyRepSeg
-chr21 32878144 32878203 EarlyRepSeg
-chr21 32878246 32878267 EarlyRepSeg
-chr21 32879333 32879475 EarlyRepSeg
-chr21 32879966 32879983 EarlyRepSeg
-chr21 32912504 32915865 EarlyRepSeg
-chr21 32932980 32967601 EarlyRepSeg
-chr21 32967643 33018889 EarlyRepSeg
-chr21 33024974 33025376 EarlyRepSeg
-chr21 33026349 33028938 EarlyRepSeg
-chr21 33031749 33032829 EarlyRepSeg
-chr21 33524233 33524260 EarlyRepSeg
-chr21 33524376 33524397 EarlyRepSeg
-chr21 33524744 33524770 EarlyRepSeg
-chr21 33550677 33553459 EarlyRepSeg
-chr21 33553902 33558482 EarlyRepSeg
-chr21 33580367 33580388 EarlyRepSeg
-chr21 33580473 33581913 EarlyRepSeg
-chr21 33581954 33582007 EarlyRepSeg
-chr21 33583555 33583569 EarlyRepSeg
-chr21 33588909 33696499 EarlyRepSeg
-chr21 33701210 33702335 EarlyRepSeg
-chr21 33703711 33846043 EarlyRepSeg
-chr21 33849912 33850091 EarlyRepSeg
-chr21 33850300 33850348 EarlyRepSeg
-chr21 33850908 33853290 EarlyRepSeg
-chr21 33853477 33853863 EarlyRepSeg
-chr21 33854415 33854525 EarlyRepSeg
-chr21 33860617 33861553 EarlyRepSeg
-chr21 33866117 33867043 EarlyRepSeg
-chr21 33867103 33867476 EarlyRepSeg
-chr21 33867667 33867813 EarlyRepSeg
-chr21 33867890 33867925 EarlyRepSeg
-chr21 33868277 33868602 EarlyRepSeg
-chr21 34062073 34062141 EarlyRepSeg
-chr21 34065246 34066028 EarlyRepSeg
-chr21 34083525 34084396 EarlyRepSeg
-chr21 34084507 34084731 EarlyRepSeg
-chr21 34084771 34084899 EarlyRepSeg
-chr21 34084941 34085007 EarlyRepSeg
-chr21 34085853 34086015 EarlyRepSeg
-chr21 34086163 34086256 EarlyRepSeg
-chr21 34086596 34147021 EarlyRepSeg
-chr21 34147160 34147200 EarlyRepSeg
-chr21 34147243 34166659 EarlyRepSeg
-chr21 34187295 34187336 EarlyRepSeg
-chr21 34187430 34187454 EarlyRepSeg
-chr21 34187857 34188159 EarlyRepSeg
-chr21 34188471 34227545 EarlyRepSeg
-chr21 34229001 34229045 EarlyRepSeg
-chr21 34229089 34233826 EarlyRepSeg
-chr21 34233903 34234848 EarlyRepSeg
-chr21 34235342 34235364 EarlyRepSeg
-chr21 34242364 34243816 EarlyRepSeg
-chr21 34244824 34245017 EarlyRepSeg
-chr21 34245242 34246040 EarlyRepSeg
-chr21 34250064 34254276 EarlyRepSeg
-chr21 34262783 34263806 EarlyRepSeg
-chr21 39244471 39407125 EarlyRepSeg
-chr21 39407872 39408136 EarlyRepSeg
-chr21 39408196 39408258 EarlyRepSeg
-chr21 39408975 39409067 EarlyRepSeg
-chr21 39409165 39446186 EarlyRepSeg
-chr21 39446250 39446293 EarlyRepSeg
-chr21 39446335 39449236 EarlyRepSeg
-chr21 39449276 39449691 EarlyRepSeg
-chr21 39449734 39449769 EarlyRepSeg
-chr21 39449840 39500135 EarlyRepSeg
-chr21 39500212 39500230 EarlyRepSeg
-chr21 39500273 39500291 EarlyRepSeg
-chr21 39500380 39504958 EarlyRepSeg
-chr21 39505923 39505963 EarlyRepSeg
-chr21 39506003 39506049 EarlyRepSeg
-chr21 39506091 39506345 EarlyRepSeg
-chr21 39506424 39506484 EarlyRepSeg
-chr21 39506703 39507084 EarlyRepSeg
-chr21 39507119 39630459 EarlyRepSeg
-chr21 39630770 39631537 EarlyRepSeg
-chr21 39631609 39632660 EarlyRepSeg
-chr21 39634408 39634612 EarlyRepSeg
-chr21 39634672 39637021 EarlyRepSeg
-chr21 39637718 39637740 EarlyRepSeg
-chr21 39638104 39639318 EarlyRepSeg
-chr21 39639514 39639764 EarlyRepSeg
-chr21 39639832 39640101 EarlyRepSeg
-chr21 39640247 39640471 EarlyRepSeg
-chr21 39642473 39642490 EarlyRepSeg
-chr21 39642699 39643256 EarlyRepSeg
-chr21 39643292 39643361 EarlyRepSeg
-chr20 33304928 33309185 EarlyRepSeg
-chr20 33331535 33662613 EarlyRepSeg
-chr20 33663823 33784967 EarlyRepSeg
-chr8 119109535 119109779 EarlyRepSeg
-chr8 119133176 119314664 EarlyRepSeg
-chr8 119314783 119314804 EarlyRepSeg
-chr8 119315080 119315854 EarlyRepSeg
-chr8 119316284 119317841 EarlyRepSeg
-chr8 119317881 119319990 EarlyRepSeg
-chr8 119321302 119322430 EarlyRepSeg
-chr8 119322628 119322752 EarlyRepSeg
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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