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[hg] galaxy 3249: redo panel template change
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/85d032d94db1 changeset: 3249:85d032d94db1 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 19 13:41:53 2010 -0500 description: redo panel template change diffstat: static/june_2007_style/panel_layout.css.tmpl | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (27 lines): diff -r 08e1f40f2b93 -r 85d032d94db1 static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:29:19 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Tue Jan 19 13:41:53 2010 -0500 @@ -139,12 +139,13 @@ display: inline-block; cursor: pointer; margin: -1px; padding: 1px; + margin-top: -0.2em; + border: solid #999 1px; padding-right: 0.5em; padding-left: 0.5em; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; - background: #bbb; } .panel-header-button.popup { @@ -154,7 +155,7 @@ .panel-header-button:hover { color: black; - background-color: #aaaaaa; + background-color: #ccc; } .panel-header-button:active {

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[hg] galaxy 3248: Use Lucida Grande for better unicode support, ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/08e1f40f2b93 changeset: 3248:08e1f40f2b93 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Jan 15 17:29:19 2010 -0500 description: Use Lucida Grande for better unicode support, clean up some css diffstat: static/june_2007_style/base.css.tmpl | 4 ++-- static/june_2007_style/blue/base.css | 4 ++-- static/june_2007_style/blue/history.css | 2 +- static/june_2007_style/blue/panel_layout.css | 9 ++------- static/june_2007_style/history.css.tmpl | 1 + static/june_2007_style/panel_layout.css.tmpl | 13 ++++--------- templates/root/history_common.mako | 2 +- 7 files changed, 13 insertions(+), 22 deletions(-) diffs (134 lines): diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -1,5 +1,5 @@ -## Font settings from YUI + verdana -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} +## Lucida Grande for proper mac unicode characters, verdana/arial stack for others +body{font:13px/1.231 "Lucida Grande",verdana,arial,helvetica,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% "Lucida Grande",verdana,arial,helvetica,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} body{font-size:75%;} ## Mixins diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/base.css Fri Jan 15 17:29:19 2010 -0500 @@ -1,5 +1,5 @@ -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;} -select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;} +body{font:13px/1.231 "Lucida Grande",verdana,arial,helvetica,sans-serif;*font-size:small;*font:x-small;} +select,input,button,textarea,button{font:99% "Lucida Grande",verdana,arial,helvetica,sans-serif;} table{font-size:inherit;font:100%;} pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} body{font-size:75%;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/history.css Fri Jan 15 17:29:19 2010 -0500 @@ -3,7 +3,7 @@ div.historyLinks{padding:5px;margin:5px 0 5px 0;} div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;background:#EEEEEE;} div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} -div.historyItem .historyItemTitle{line-height:16px;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} div.historyItem div.historyItem{margin-right:-11px;} div.historyItem-ok{border-color:#66AA66;background:#CCFFCC;} div.historyItem-ok .state-icon{display:none;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/panel_layout.css Fri Jan 15 17:29:19 2010 -0500 @@ -1,10 +1,5 @@ -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;} -select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;} -table{font-size:inherit;font:100%;} -pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -body{font-size:75%;} body,html{overflow:hidden;margin:0;padding:0;width:100%;height:100%;} -body{font:75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;background:#eee;} +body{font:75% "Lucida Grande",verdana,arial,helvetica,sans-serif;background:#eee;} .unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} #background{position:absolute;background:#eee;z-index:-1;top:0;left:0;margin:0;padding:0;width:100%;height:100%;} #messagebox{position:absolute;top:33px;left:0;width:100%;height:24px !important;overflow:hidden;border-bottom:solid #999 1px;font-size:90%;} @@ -37,7 +32,7 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;} .panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;} .panel-info-message{background-image:url(info_small.png);background-color:#CCCCFF;} -#masthead{position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2C3143;color:#fff;border-bottom:solid #444 1px;z-index:15000;padding:0;} +#masthead{font-family: verdana;arial;sans-serif;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2C3143;color:#fff;border-bottom:solid #444 1px;z-index:15000;padding:0;} #masthead a{color:#eeeeee;text-decoration:none;} #masthead .title{padding:3px 10px;font-size:175%;font-weight:bold;} #masthead a:hover{text-decoration:underline;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/history.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -36,6 +36,7 @@ background-repeat: no-repeat; } .historyItemTitle { + font-weight: bold; line-height: 16px; } } diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -1,8 +1,3 @@ -## Font settings from YUI + verdana -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -body{font-size:75%;} - - body, html { overflow: hidden; margin: 0; @@ -12,7 +7,7 @@ } body { - font: 75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif; + font: 75% "Lucida Grande",verdana,arial,helvetica,sans-serif; background: ${layout_bg}; } @@ -144,13 +139,12 @@ display: inline-block; cursor: pointer; margin: -1px; padding: 1px; - margin-top: -0.2em; - border: solid #999 1px; padding-right: 0.5em; padding-left: 0.5em; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; + background: #bbb; } .panel-header-button.popup { @@ -160,7 +154,7 @@ .panel-header-button:hover { color: black; - background-color: #ccc; + background-color: #aaaaaa; } .panel-header-button:active { @@ -235,6 +229,7 @@ ## Masthead #masthead { + font-family: verdana;arial;sans-serif; position:absolute; top:0; left:0; diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 templates/root/history_common.mako --- a/templates/root/history_common.mako Fri Jan 15 17:12:50 2010 -0500 +++ b/templates/root/history_common.mako Fri Jan 15 17:29:19 2010 -0500 @@ -43,7 +43,7 @@ %endif </div> <span class="state-icon"></span> - <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span> + <span class="historyItemTitle">${hid}: ${data.display_name()}</span> </div> ## Body for history items, extra info and actions, data "peek"

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[hg] galaxy 3247: Updated csFasta sniff method to handle sequenc...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e7c1fe8fab8 changeset: 3247:4e7c1fe8fab8 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jan 15 17:12:50 2010 -0500 description: Updated csFasta sniff method to handle sequences with dots in them (T123..32.020......23) instead of being just numbers with a leading capital letter diffstat: lib/galaxy/datatypes/sequence.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r 9cc57a489be0 -r 4e7c1fe8fab8 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Fri Jan 15 12:51:45 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Fri Jan 15 17:12:50 2010 -0500 @@ -66,7 +66,7 @@ A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. - All lines should be shorter than 80 charcters + All lines should be shorter than 80 characters For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml @@ -139,7 +139,7 @@ break elif line[0] not in string.ascii_uppercase: return False - elif len( line ) > 1 and not re.search( '^\d+$', line[1:] ): + elif len( line ) > 1 and not re.search( '^[\d.]+$', line[1:] ): return False return True else:

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[hg] galaxy 3246: Corrected counting of sequences in fastq set_meta
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9cc57a489be0 changeset: 3246:9cc57a489be0 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jan 15 12:51:45 2010 -0500 description: Corrected counting of sequences in fastq set_meta diffstat: lib/galaxy/datatypes/sequence.py | 18 +++++++++++++++--- 1 files changed, 15 insertions(+), 3 deletions(-) diffs (35 lines): diff -r fa318a093bf2 -r 9cc57a489be0 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Jan 14 17:49:20 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Fri Jan 15 12:51:45 2010 -0500 @@ -160,16 +160,28 @@ """ data_lines = 0 sequences = 0 + seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() if line and line.startswith( '#' ): # We don't count comment lines for sequence data types continue - if line and line.startswith( '@' ): - sequences += 1 - data_lines +=1 + if line and line.startswith( '@' ): + if seq_counter >= 4: + # count previous block + # blocks should be 4 lines long + sequences += 1 + seq_counter = 1 + else: + # in case quality line starts with @ + seq_counter += 1 + data_lines += 1 else: data_lines += 1 + seq_counter += 1 + if seq_counter >= 4: + # count final block + sequences += 1 dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences def sniff ( self, filename ):

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[hg] galaxy 3245: trackster: fix thick region display bug, stack...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/fa318a093bf2 changeset: 3245:fa318a093bf2 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 14 17:49:20 2010 -0500 description: trackster: fix thick region display bug, stacking bugs, enable right-panel diffstat: lib/galaxy/web/controllers/tracks.py | 1 - lib/galaxy/web/controllers/visualization.py | 15 +-- static/scripts/packed/galaxy.panels.js | 2 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 110 ++++++++++++++++----------- static/trackster.css | 6 +- templates/base_panels.mako | 2 +- templates/panels.mako | 2 +- templates/tracks/browser.mako | 35 ++++++-- 9 files changed, 105 insertions(+), 70 deletions(-) diffs (447 lines): diff -r 44526498cd00 -r fa318a093bf2 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Jan 14 15:22:10 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Jan 14 17:49:20 2010 -0500 @@ -221,7 +221,6 @@ converted dataset (possibly new) is returned, if it cannot be converted, None is returned. """ - log.debug("Inside dataset as type") # Already of correct type if dataset.extension == type: return dataset diff -r 44526498cd00 -r fa318a093bf2 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Thu Jan 14 15:22:10 2010 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Thu Jan 14 17:49:20 2010 -0500 @@ -25,17 +25,16 @@ return query.filter_by( user=trans.user ) class VisualizationController( BaseController ): - + list_grid = VisualizationListGrid() @web.expose @web.require_login() - def index( self, trans ): - return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) ) + def index( self, trans, *args, **kwargs ): + return trans.fill_template( "panels.mako", grid=self.list_grid( trans, *args, **kwargs ), active_view='visualization', main_url=url_for( action='list' ) ) - list_grid = VisualizationListGrid() - @web.expose - @web.require_login() - def list( self, trans, *args, **kwargs ): - return self.list_grid( trans, *args, **kwargs ) + # @web.expose + # @web.require_login() + # def list( self, trans, *args, **kwargs ): + # return self.list_grid( trans, *args, **kwargs ) #(a)web.expose #(a)web.require_admin diff -r 44526498cd00 -r fa318a093bf2 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var 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crolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file diff -r 44526498cd00 -r fa318a093bf2 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/packed/trackster.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("line -track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_ px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);retu rn c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addCla ss("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc _slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_sl ots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.st rand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureT rack.prototype,{draw_tile:function(w,A,n,o){if(!this.values){return}var B=A*DENSITY*w,f=(A+1)*DENSITY*w,r=DENSITY*w;var E,q,k;k=this.height_px;q=this.zo_slots;E=this.values;var u=Math.ceil(r*o),s=$("<canvas class='tile'></canvas>");var b=$("<canvas></canvas>").get(0).getContext("2d");s.css({position:"absolute",top:0,left:(B-this.view.low)*o-this.left_offset});s.get(0).width=u+this.left_offset;s.get(0).height=k;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font=this.default_font;v.textAlign="right";var t=v.measureText("A").width;var x=0;for(var y=0,z=E.length;y<z;y++){var m=E[y];if(m.start<=f&&m.end>=B){var h=Math.floor(Math.max(0,(m.start-B)*o)),l=Math.ceil(Math.min(u,(m.end-B)*o)),g=q[m.uid]*this.vertical_gap;var a,F,e=null,p=null;if(o>t){for(var C=0,d=m.name.length;C<d;C++){var D=Math.floor(Math.max(0,(m.start+C-B)*o));v.fillText(m.name[C],D+this.left_offset,g+8)}}else{v.fillRect(h+this.left_offset,g+4,l-h,3)}}}n.append(s);return s}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;retu rn}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b =(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.con tainer_div.addClass("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"25px"});b.prependTo(a.container_div);d.css({position :"relative",top:a.height_px+55+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n. stroke();m.append(c);return c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nod ata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px ")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c =(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*(this.showin g_details?this.vertical_detail_px:this.vertical_nodetail_px);var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_details){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b!==undefined&&(o<=s||H>=b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=L EFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.base_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor (Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 44526498cd00 -r fa318a093bf2 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/trackster.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,5 +1,5 @@ /* Trackster - 2009, James Taylor, Kanwei Li + 2010, James Taylor, Kanwei Li */ var DEBUG = false; @@ -19,22 +19,22 @@ right_img.src = "../images/visualization/strand_right.png"; right_img.onload = function() { RIGHT_STRAND = CONTEXT.createPattern(right_img, "repeat"); -} +}; var left_img = new Image(); left_img.src = "../images/visualization/strand_left.png"; left_img.onload = function() { LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); -} +}; var right_img_inv = new Image(); right_img_inv.src = "../images/visualization/strand_right_inv.png"; right_img_inv.onload = function() { RIGHT_STRAND_INV = CONTEXT.createPattern(right_img_inv, "repeat"); -} +}; var left_img_inv = new Image(); left_img_inv.src = "../images/visualization/strand_left_inv.png"; left_img_inv.onload = function() { LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); -} +}; function commatize( number ) { number += ''; // Convert to string @@ -49,7 +49,7 @@ this.num_elements = num_elements; this.obj_cache = {}; this.key_ary = []; -} +}; $.extend( Cache.prototype, { get: function( key ) { var index = this.key_ary.indexOf(key); @@ -109,7 +109,7 @@ // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); - this.zoom_res = Math.max(1,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); + this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview $("#overview-box").css( { @@ -282,10 +282,10 @@ var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); - max_label.css({ position: "relative", top: "35px" }); - max_label.prependTo(track.container_div) + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); - min_label.css({ position: "relative", top: track.height_px + 32 + "px" }); + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); min_label.prependTo(track.container_div); track.draw(); @@ -371,13 +371,15 @@ this.dataset_id = dataset_id; this.zo_slots = {}; this.show_labels_scale = 0.001; - this.showing_labels = false; - this.vertical_gap = 10; + this.showing_details = false; + this.vertical_detail_px = 10; + this.vertical_nodetail_px = 3; this.base_color = "#2C3143"; this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; this.inc_slots = {}; this.data_queue = {}; + this.s_e_by_tile = {}; this.data_cache = new Cache(20); }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { @@ -425,10 +427,8 @@ } }, calc_slots: function() { - // console.log("num vals: " + this.values.length); var end_ary = [], scale = this.content_div.width() / (this.view.high - this.view.low), - max_high = this.view.max_high, max_low = this.view.max_low; // console.log(scale, this.view.high, this.view.low); for (var i = 0, len = this.values.length; i < len; i++) { @@ -447,43 +447,62 @@ j++; } } - this.height_px = end_ary.length * this.vertical_gap + 15; + this.height_px = end_ary.length * this.vertical_nodetail_px + 15; this.content_div.css( "height", this.height_px + "px" ); }, incremental_slots: function( level, features ) { if (!this.inc_slots[level]) { this.inc_slots[level] = {}; - this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1); + this.inc_slots[level].w_scale = 1 / level; + this.s_e_by_tile[level] = {}; } - var slots = this.inc_slots[level]; - // console.log(level, slots.w_scale, slots); - var end_ary = [], + // TODO: Should calculate zoom tile index, which will improve performance + // by only having to look at a smaller subset + // if (this.s_e_by_tile[0] === undefined) { this.s_e_by_tile[0] = []; } + var w_scale = this.inc_slots[level].w_scale, undone = [], highest_slot = 0, // To measure how big to draw canvas dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"), max_low = this.view.max_low; + var f_start, f_end, slotted = []; + + // If feature already exists in slots (from previously seen tiles), use the same slot, + // otherwise if not seen, add to "undone" list for slot calculation for (var i = 0, len = features.length; i < len; i++) { var feature = features[i]; - // console.log(feature.name, feature.uid, slots[feature.uid]); - if (slots[feature.uid]) { - highest_slot = Math.max(highest_slot, slots[feature.uid]); - end_ary[ slots[feature.uid] ] = Math.ceil( (feature.end - max_low) * slots.w_scale ); + if (this.inc_slots[level][feature.uid] !== undefined) { + highest_slot = Math.max(highest_slot, this.inc_slots[level][feature.uid]); + slotted.push(this.inc_slots[level][feature.uid]); } else { - undone.push(feature); - } + undone.push(i); + } } + + // console.log("Slotted: ", features.length - undone.length, "/", features.length, slotted); for (var i = 0, len = undone.length; i < len; i++) { - var feature = undone[i]; - f_start = Math.floor( (feature.start - max_low) * slots.w_scale ); + var feature = features[undone[i]]; + f_start = Math.floor( (feature.start - max_low) * w_scale ); f_start -= dummy_canvas.measureText(feature.name).width; - f_end = Math.ceil( (feature.end - max_low) * slots.w_scale ); - // console.log(f_start, f_end, feature.name); + f_end = Math.ceil( (feature.end - max_low) * w_scale ); + var j = 0; + // Try to fit the feature to the first slot that doesn't overlap any other features in that slot while (true) { - if (end_ary[j] === undefined || end_ary[j] < f_start) { - end_ary[j] = f_end; - slots[feature.uid] = j; + var found = true; + if (this.s_e_by_tile[level][j] !== undefined) { + for (var k = 0, k_len = this.s_e_by_tile[level][j].length; k < k_len; k++) { + var s_e = this.s_e_by_tile[level][j][k]; + if (f_end > s_e[0] && f_start < s_e[1]) { + found = false; + break; + } + } + } + if (found) { + if (this.s_e_by_tile[level][j] === undefined) { this.s_e_by_tile[level][j] = []; } + this.s_e_by_tile[level][j].push([f_start, f_end]); + this.inc_slots[level][feature.uid] = j; highest_slot = Math.max(highest_slot, j); break; } @@ -504,8 +523,8 @@ // Once we zoom in enough, show name labels var data, slots, required_height; if (w_scale > this.show_labels_scale) { - if (!this.showing_labels) { - this.showing_labels = true; + if (!this.showing_details) { + this.showing_details = true; } for (var k in this.data_cache.obj_cache) { var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; @@ -519,12 +538,13 @@ this.get_data(tile_low, tile_high); return; } - required_height = this.incremental_slots( this.view.zoom_res, data ) * this.vertical_gap + 15; + // Calculate new slots incrementally for this new chunk of data and update height if necessary + required_height = this.incremental_slots( this.view.zoom_res, data ) * this.vertical_detail_px + 15; // console.log(required_height); slots = this.inc_slots[this.view.zoom_res]; } else { - if (this.showing_labels) { - this.showing_labels = false; + if (this.showing_details) { + this.showing_details = false; } required_height = this.height_px; slots = this.zo_slots; @@ -554,14 +574,14 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = slots[feature.uid] * this.vertical_gap; + y_center = slots[feature.uid] * (this.showing_details ? this.vertical_detail_px : this.vertical_nodetail_px); var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); } - if (!this.showing_labels) { + if (!this.showing_details) { // Non-detail levels ctx.fillRect(f_start + this.left_offset, y_center + 5, f_end - f_start, 1); } else { @@ -569,6 +589,7 @@ if (ctx.fillText && feature.start > tile_low) { ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); // ctx.fillText(commatize(feature.start), f_start - 1 + this.left_offset, y_center + 8); + // ctx.fillText(slots[feature.uid], f_start - 1 + this.left_offset, y_center + 8); } var blocks = feature.blocks; if (blocks) { @@ -592,13 +613,12 @@ thickness = 5; y_start = 3; ctx.fillRect(block_start + this.left_offset, y_center + y_start, block_end - block_start, thickness); - - if (thick_start && (block_start < thick_end || block_end > thick_start) ) { + + if (thick_start !== undefined && (block_start <= thick_end || block_end >= thick_start) ) { thickness = 9; y_start = 1; var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start + this.left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); } @@ -654,9 +674,7 @@ // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), new_canvas = $("<canvas class='tile'></canvas>"); - - var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); - + new_canvas.css({ position: "absolute", top: 0, @@ -677,7 +695,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = slots[feature.uid] * this.vertical_gap; + y_center = slots[feature.uid] * this.vertical_detail_px; var thickness, y_start, thick_start = null, thick_end = null; if (w_scale > px_per_char) { diff -r 44526498cd00 -r fa318a093bf2 static/trackster.css --- a/static/trackster.css Thu Jan 14 15:22:10 2010 -0500 +++ b/static/trackster.css Thu Jan 14 17:49:20 2010 -0500 @@ -22,7 +22,6 @@ #nav-container { position: fixed; bottom: 0; - width: 100%; } input { @@ -60,7 +59,8 @@ width: 100%; margin: 0px; color: white; - margin-top: 10px; + margin-top: -6px; + margin-bottom: -3px; } #overview-viewport { @@ -82,7 +82,7 @@ } #viewport { - overflow-x: hidden; +/* overflow-x: hidden;*/ background-color: #fff; /* overflow: scroll;*/ /* border-bottom: 2px solid black;*/ diff -r 44526498cd00 -r fa318a093bf2 templates/base_panels.mako --- a/templates/base_panels.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/base_panels.mako Thu Jan 14 17:49:20 2010 -0500 @@ -318,8 +318,8 @@ <head> <title>${self.title()}</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + ${self.stylesheets()} ${self.javascripts()} - ${self.stylesheets()} </head> <body scroll="no" class="${self.body_class}"> diff -r 44526498cd00 -r fa318a093bf2 templates/panels.mako --- a/templates/panels.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/panels.mako Thu Jan 14 17:49:20 2010 -0500 @@ -11,6 +11,6 @@ <%def name="center_panel()"> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${main_url}"> </iframe> + ${grid} </%def> diff -r 44526498cd00 -r fa318a093bf2 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/tracks/browser.mako Thu Jan 14 17:49:20 2010 -0500 @@ -1,4 +1,13 @@ -<%inherit file="/base.mako"/> +<%inherit file="/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=True + self.active_view="visualization" + self.message_box_visible=False +%> +</%def> <%def name="stylesheets()"> ${parent.stylesheets()} @@ -53,13 +62,16 @@ }); // To adjust the size of the viewport to fit the fixed-height footer - $(window).resize( function( e ) { - $("#content").height( $(window).height() - $("#nav-container").height() ); + var refresh = function( e ) { + $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); + $("#nav-container").width( $("#center").width() ); view.redraw(); - }); - - $(window).resize(); + }; + $(window).bind( "resize", function(e) { refresh(e); } ); + $("#right-border").bind( "click", function(e) { refresh(e); } ); + $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $(window).trigger( "resize" ); $("#viewport").bind( "dragstart", function( e ) { this.original_low = view.low; @@ -103,15 +115,16 @@ </script> </%def> +<%def name="center_panel()"> <div id="content"> <div id="top-labeltrack"></div> <div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"> <div id="viewport"></div> </div> - <div id="nav-labeltrack"></div> + </div> <div id="nav-container"> - ## <div style="height: 5px; border-top: solid #ccc 1px"></div> + <div id="nav-labeltrack"></div> <div id="nav"> <div id="overview"> <div id="overview-viewport"> @@ -133,3 +146,9 @@ </div> </div> </div> +</%def> + +<%def name="right_panel()"> + <div>Configs</div> + +</%def> \ No newline at end of file

1 0

[hg] galaxy 3244: Fix typo in last commit.
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/44526498cd00 changeset: 3244:44526498cd00 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 14 15:22:10 2010 -0500 description: Fix typo in last commit. diffstat: templates/tool_form.mako | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 54a31dda709b -r 44526498cd00 templates/tool_form.mako --- a/templates/tool_form.mako Thu Jan 14 15:13:01 2010 -0500 +++ b/templates/tool_form.mako Thu Jan 14 15:22:10 2010 -0500 @@ -166,7 +166,7 @@ # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. field_html = field.get_html( prefix ) - if field_html is not unicode: + if type( field_html ) is not unicode: field_html = unicode( field_html, 'utf-8' ) %> <div class="form-row-input">${field_html}</div>

1 0

[hg] galaxy 3243: Fix unicode bug when displaying dataset names ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/54a31dda709b changeset: 3243:54a31dda709b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 14 15:13:01 2010 -0500 description: Fix unicode bug when displaying dataset names in HTML select boxes in tool forms. diffstat: templates/tool_form.mako | 11 ++++++++--- 1 files changed, 8 insertions(+), 3 deletions(-) diffs (22 lines): diff -r 5d5e5da2fcda -r 54a31dda709b templates/tool_form.mako --- a/templates/tool_form.mako Thu Jan 14 14:20:01 2010 -0500 +++ b/templates/tool_form.mako Thu Jan 14 15:13:01 2010 -0500 @@ -161,10 +161,15 @@ </label> %endif <% - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if field_html is not unicode: + field_html = unicode( field_html, 'utf-8' ) %> - <div class="form-row-input">${field.get_html( prefix )}</div> + <div class="form-row-input">${field_html}</div> %if parent_errors.has_key( param.name ): <div class="form-row-error-message"> <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>

1 0

[hg] galaxy 3242: Small edit for the help section
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5d5e5da2fcda changeset: 3242:5d5e5da2fcda user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 14 14:20:01 2010 -0500 description: Small edit for the help section diffstat: tools/samtools/pileup_parser.xml | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (16 lines): diff -r ec77ae7f9b4f -r 5d5e5da2fcda tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Jan 14 14:13:42 2010 -0500 +++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:20:01 2010 -0500 @@ -272,9 +272,9 @@ will report everything from the original file:: - chrM 412 A 2 ., II 0 0 0 0 2 - chrM 413 G 4 ..t, III2 0 0 0 1 3 - chrM 414 C 4 ...a III2 0 0 0 0 3 + chrM 412 A 2 ., II 2 0 0 0 2 + chrM 413 G 4 ..t, III2 0 0 2 1 3 + chrM 414 C 4 ...a III2 3 0 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).

1 0

[hg] galaxy 3241: restoring welcome.html
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ec77ae7f9b4f changeset: 3241:ec77ae7f9b4f user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 14 14:13:42 2010 -0500 description: restoring welcome.html diffstat: static/welcome.html | 158 ++++----------------------------------------------- 1 files changed, 13 insertions(+), 145 deletions(-) diffs (169 lines): diff -r be8f54671d56 -r ec77ae7f9b4f static/welcome.html --- a/static/welcome.html Thu Jan 14 14:07:05 2010 -0500 +++ b/static/welcome.html Thu Jan 14 14:13:42 2010 -0500 @@ -2,152 +2,20 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> -<link rel="stylesheet" href="style/base.css" type="text/css" /> -<style type="text/css"> - - .quickie { - text-align: center; - background: black; - margin: 10px; - } - - .current-quickie { - width: 300px; - background: white; - margin: auto; - } - - .current-quickie img { - padding: 15px; - border: 1px solid #ccc; - margin: auto; - background-color: white; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - - .previous { - width: 100%; - overflow: auto; - border: solid #ccc 1px; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - .previous .quickie { - padding-top: 10px; - min-height: 90px; - min-width: 150px; - } - #screencasts { - max-width: 50em; - margin-left: auto; - margin-right: auto; - } - -</style> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> -<script type="text/javascript"> - -$(document).ready(function() { - $('.current-quickie').cycle({ - fx: 'fade', - pause: 1, - speed: 100 - }); -}); -</script> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <link rel="stylesheet" href="style/base.css" type="text/css" /> </head> <body> -<div class="document"> -<h3 align="center">Galaxy in 2010...</h3> -<div align="center" class="current-quickie"> - <a target="_blank" href="http://galaxy.psu.edu/dev2010/"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"/></a> - <a target="_blank" href="http://www.iscb.org/ismb2010"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /></a> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> - <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> -</div> -<br> -<hr> - -<h3 align="center">Galaxy Quickies</h3> - -<div class="previous" id="previous"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie1_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie2_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie3_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie4_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie5_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie6_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie7_small.png" border="0"> - </div> - </a> - </td> - </tr> - </table> -</div> - -<script type="text/javascript"> - // Scroll to last quickie in box - document.getElementById("previous").scrollLeft = 100000000; -</script> - -<br/> -<br/> -<br/> -<hr/> - -<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> - -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. -<p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> -</div> -</div> + <div class="document"> + <div class="warningmessagelarge"> + <strong>Hello world! It's running...</strong> + <hr> + To customize this page edit <code>static/welcome.html</code> + </div> + <br/> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <hr/> + This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + </div> </body> </html>

1 0

[hg] galaxy 3240: Modification of pileup filter behavior, bases ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/be8f54671d56 changeset: 3240:be8f54671d56 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 14 14:07:05 2010 -0500 description: Modification of pileup filter behavior, bases not different from the references are included in the report as well. Also changed the image for closing screencast panels. A new icon is urgently needed. diffstat: static/scripts/galaxy.panels.js | 2 +- static/welcome.html | 158 ++- test-data/pileup_parser.10col.20-3-yes-yes.pileup.out | 162 +- test-data/pileup_parser.6col.20-3-no-no.pileup.out | 1174 ++++++++-------- test-data/pileup_parser.6col.20-3-yes-no.pileup.out | 2 +- test-data/pileup_parser.6col.20-3-yes-yes.pileup.out | 2 +- tools/samtools/pileup_parser.pl | 4 +- tools/samtools/pileup_parser.xml | 6 +- 8 files changed, 822 insertions(+), 688 deletions(-) diffs (1586 lines): diff -r 517bd810a6b2 -r be8f54671d56 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Thu Jan 14 11:26:08 2010 -0500 +++ b/static/scripts/galaxy.panels.js Thu Jan 14 14:07:05 2010 -0500 @@ -210,7 +210,7 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:3px;top:3px;' src='../images/icon_error_sml.gif'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-12px;top:-12px;' src='../images/delete_icon.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); $("#close_button").bind( "click", function() { hide_modal() } ); } diff -r 517bd810a6b2 -r be8f54671d56 static/welcome.html --- a/static/welcome.html Thu Jan 14 11:26:08 2010 -0500 +++ b/static/welcome.html Thu Jan 14 14:07:05 2010 -0500 @@ -2,20 +2,152 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link rel="stylesheet" href="style/base.css" type="text/css" /> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> +<link rel="stylesheet" href="style/base.css" type="text/css" /> +<style type="text/css"> + + .quickie { + text-align: center; + background: black; + margin: 10px; + } + + .current-quickie { + width: 300px; + background: white; + margin: auto; + } + + .current-quickie img { + padding: 15px; + border: 1px solid #ccc; + margin: auto; + background-color: white; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + + .previous { + width: 100%; + overflow: auto; + border: solid #ccc 1px; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + .previous .quickie { + padding-top: 10px; + min-height: 90px; + min-width: 150px; + } + #screencasts { + max-width: 50em; + margin-left: auto; + margin-right: auto; + } + +</style> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> +<script type="text/javascript"> + +$(document).ready(function() { + $('.current-quickie').cycle({ + fx: 'fade', + pause: 1, + speed: 100 + }); +}); +</script> </head> <body> - <div class="document"> - <div class="warningmessagelarge"> - <strong>Hello world! It's running...</strong> - <hr> - To customize this page edit <code>static/welcome.html</code> - </div> - <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> - <hr/> - This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. - </div> +<div class="document"> +<h3 align="center">Galaxy in 2010...</h3> +<div align="center" class="current-quickie"> + <a target="_blank" href="http://galaxy.psu.edu/dev2010/"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"/></a> + <a target="_blank" href="http://www.iscb.org/ismb2010"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /></a> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> + <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> +</div> +<br> +<hr> + +<h3 align="center">Galaxy Quickies</h3> + +<div class="previous" id="previous"> + <table border="0" cellpadding="0" cellspacing="0" width="100%"> + <tr> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie1_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie2_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie3_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie4_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie5_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie6_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie7_small.png" border="0"> + </div> + </a> + </td> + </tr> + </table> +</div> + +<script type="text/javascript"> + // Scroll to last quickie in box + document.getElementById("previous").scrollLeft = 100000000; +</script> + +<br/> +<br/> +<br/> +<hr/> + +<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> + +This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. +<p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> +</div> +</div> </body> </html> diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out --- a/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,86 +1,86 @@ -chrM 13 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII 0 0 1 0 17 -chrM 18 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A 0 0 1 0 19 -chrM 35 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII 0 0 1 0 28 -chrM 58 59 A A 50 0 24 16 ...............C IB20III:<DIII#II 0 1 0 0 13 -chrM 59 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI 1 0 0 0 16 +chrM 13 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII 16 0 1 0 17 +chrM 18 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A 0 0 1 18 19 +chrM 35 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII 27 0 1 0 28 +chrM 58 59 A A 50 0 24 16 ...............C IB20III:<DIII#II 12 1 0 0 13 +chrM 59 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI 1 15 0 0 16 chrM 157 158 A G 117 117 19 62 GGGGGGGGGGGGGGGGGGGNNNGGGGGG.GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGg^:g II6IIII<4I+IIIIIIII"""IIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII> 0 0 56 0 56 -chrM 170 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 0 0 1 0 46 -chrM 172 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII 0 1 0 0 37 -chrM 173 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII 0 1 0 0 39 -chrM 187 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII 0 0 1 0 12 -chrM 195 196 T T 17 0 19 5 G.... <IIII 0 0 1 0 5 -chrM 284 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII 0 0 0 1 11 -chrM 285 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II 1 0 0 0 8 -chrM 303 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* 1 0 0 0 12 -chrM 310 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* 0 1 0 0 12 -chrM 347 348 T T 4 0 20 3 ,$.$A IIA 1 0 0 0 3 -chrM 354 355 A C 14 36 25 4 .ccc IIII 0 3 0 0 4 +chrM 170 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 0 0 1 45 46 +chrM 172 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII 36 1 0 0 37 +chrM 173 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII 38 1 0 0 39 +chrM 187 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII 11 0 1 0 12 +chrM 195 196 T T 17 0 19 5 G.... <IIII 0 0 1 4 5 +chrM 284 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII 0 0 10 1 11 +chrM 285 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II 1 0 0 7 8 +chrM 303 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* 1 0 11 0 12 +chrM 310 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* 0 1 0 11 12 +chrM 347 348 T T 4 0 20 3 ,$.$A IIA 1 0 0 2 3 +chrM 354 355 A C 14 36 25 4 .ccc IIII 1 3 0 0 4 chrM 355 356 T C 39 39 25 4 Cccc IIII 0 4 0 0 4 chrM 380 381 C T 77 108 25 28 tttttttTttttgttttttttttt^:t^:t^:t^:t IIIIIIIIIIII&I7CI>BCA296+IA1 0 0 0 24 24 -chrM 383 384 A A 76 0 25 30 ,,,,,,,.,c,,g,,,,,,,g,,,,,,g,. IIIIIIIIIIII$IIIIIII$IIIIF,4II 0 1 0 0 26 +chrM 383 384 A A 76 0 25 30 ,,,,,,,.,c,,g,,,,,,,g,,,,,,g,. IIIIIIIIIIII$IIIIIII$IIIIF,4II 25 1 0 0 26 chrM 385 386 A G 88 120 25 32 gggggggGggnggggggggggggggggggGgg III>IIIIII"I&IIIIIIIIIIII?IIDI94 0 0 29 0 29 chrM 414 415 C T 75 75 25 16 t$t$tttttTttttTTTT IIIIIII>II93IIII 0 0 0 15 15 -chrM 464 465 C C 169 0 25 65 ,.............,,.....A.,......,..............,,,..........,a...,^:A IIIIBI>H1IIIIB$)IIIII$IIIIIIIIII0IIIII6IIIIIIHIIIIIIIIIIIII&IIICI 1 0 0 0 59 -chrM 468 469 T T 207 0 25 66 .$.$.$.........,,.......,......,..............,n,..........,,...,G... III>I44EIIICI@IIEDC$IBIIII(IIIIDIIII@IIIIII1"0IIII%IIIIII1III7IIII 0 0 1 0 57 -chrM 471 472 C C 187 0 25 72 .$.$.....,t.......,....A.,..............,a,..........,a...,A.......,,^:.^:.^:.^:.^:. I@IIIIII&IIIFG6IIIIII$IIIIIIIII$IIFIIII:IIIIIIIIIIII%IIII,IIIIII/I-IIIII 1 0 0 0 65 -chrM 490 491 C C 212 0 23 79 ..n,,....A.....,,...,........t,.....,....,..........,....,.,,...,.....,,..,.,., II"IIIIII&II:IIIIIIII(II@HIII;IIIIIIIIIIIIIIIIII?IIIIIIIIIIFIIIIIIIIIII+IIII3II 0 0 0 1 74 -chrM 506 507 A A 150 0 21 76 .$.$.$.$C$,....,..........c....,.,,...,.....,,..,.,.,,,,...,,,..,,....,,.,....^:.^:,^:, /I:3&I33.;I,./<G=I?IIIAIIIIIIIDI*IIIIIIIIIIIHDIIIIIIII=DIIIICIIII@IIIIII(I@6 0 1 0 0 65 -chrM 510 511 C C 213 0 21 72 .$.$.$....,....,.,,...,.....,,..,.,.,,,,...,,,..,,....,,.,...A.,,..,,,,,,,^:, III@/IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHIIIIIICIIEII6II/562I 1 0 0 0 69 -chrM 526 527 A A 164 0 22 58 ,,,...,,,..,,....,,.,.....,,..,,,,,,,,,..,,,..C,,,,,.,,,,, III3I=III;/II7I24II3I'II9IIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 1 0 0 52 -chrM 527 528 A A 164 0 22 58 g$,$,...,,,..,,....,,.,.....,,..,,,,,,,,,..,,,...,,,,,.,,,,, IIIF$9IIIIIII0A6(II4I+FI%:II4=IIIII'IIIIIIIIIIIIIIII3IIIII 0 0 1 0 49 -chrM 536 537 A A 138 0 23 49 .c,.,.....,,..,,,,,,,,,..,,,...,,,,,.,,,,,.,,,,,, 7II+I$0I8III/@IIIIIIIIIIIIIIIIIIIIIIIIIIIIII4I46I 0 1 0 0 43 -chrM 557 558 T T 83 0 23 27 ,$,$,$.,,,,,.,,,,,,.,.,....G.^:. III+IIIIIII>IHDIG4I4IIIIIII 0 0 1 0 24 -chrM 606 607 G G 105 0 24 43 ..............,....T..T..................^:.^!, BI-&*1&6IIIGIIII%;9I.;>IIIIIIIIIIIIIIIIIII3 0 0 0 2 35 -chrM 618 619 T T 117 0 24 48 ,.........C..C..............,...........N..,...^:. I2&-+)(4I+>CI$&I15@IIIIIIIII,IIIIIIIIIII"II5IIII 0 1 0 0 35 -chrM 627 628 G G 108 0 22 57 .$...........A........,..............,................A^!.^!.^:. 5GI<=4;>G=I<%IIIIII.IIII'IIIIIIII$IIIIIIIIIIIIIIIIIIIIIII 1 0 0 0 52 -chrM 659 660 C C 166 0 19 58 .$.$.............,...n,.,,......,......................a,... /CII>9@II277IIII9II"IIIIIIFIIIIIIBIIIIIIIIIIIIIIII$II7IIII 1 0 0 0 54 -chrM 668 669 C C 135 0 19 42 .$,$,$......,.....................Ga,......,^:. IIIIIII@IIFI@IIIIIIIII;IIIIHIII56IIIIIIIAI 1 0 1 0 42 -chrM 713 714 A A 127 0 23 96 ...,..C.....................,......................,............................C...........^:.^:.^:.^:. 67'II>(IIIAFI<IIIII?I$EI>GAGII4III8IIDIIIDIIIFIIIIG$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 1 0 0 91 -chrM 719 720 T T 130 0 24 96 .....C...........,...C.....G............,............G....................A...................^:.^:. D?76/$I'@'<,I7;I<I5GI'H+B.3%;=<3II1CGIIB@FII8@II0II4II$IIIII537IIIIIIIIIII#IIIIIIIII=III$IIIIIII 0 0 1 0 78 -chrM 736 737 A A 98 0 24 98 .$.$.$..............................C................T.......................C..................^:.^:.^:.^:.^:. AI709I4I>IDII.7IIC+938AEC5?IDIC5I*IIII7I21?5B1AIII#IIIIIIIIIIAIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 1 0 0 88 -chrM 747 748 A A 97 0 25 86 .$.$C$.$.$.$.$.$.$.........................................................................^:.^:.^:.^:. ?DIIIII<I8I@>B2IIFB%IIIIIIHIII;4III3IIIEEIIIIIIIIIIIIIIIIIIIIIIIIII$IIIIIIIIIIII@IIIII 0 1 0 0 81 -chrM 749 750 A A 93 0 25 77 .$.$............................C......C......................................^:. I2GII,II%@IAIIIII9IIIIIIIIIDII>I>II=IIIIIIIIIIIIIIIIIIIIIIIII8IIIII.IIIIIIIII 0 2 0 0 73 -chrM 759 760 T T 106 0 25 86 A$.....A..............G........................A........G........................^:.^:.^:.^:.^:.^:. #6<EF9$330.II4*;EII7+$I;II:3IICB4073I6;IEIIII5+II@IIIII:I+IIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0 1 0 70 -chrM 762 763 A A 99 0 25 83 N........................................................................C......... "IC:6,1III=CIIIIB6GIII7G<DI>IIIIII8IIII$IHIII=I&IIIIIIIIIIIIIIIIIIIIIIII39IIIIIIIII 0 1 0 0 77 -chrM 763 764 G G 107 0 25 86 .$.$.$.$.$.$.$.$T$.....NN......................................AN...........................^:.^:.^:. 9I9I@8I4-I7IC&""=&=I+II=>I>IIIIIIIIIIIII@IIII+IIIIIIIII"II%IIIII@IIIIIIIIIIIIIIIIIIIII 1 0 0 0 76 -chrM 764 765 G G 88 0 25 77 .$.$.$.$.$.T..T.T............................................N.................... :,I;&I7D.%I'III<HD7IIIII*CIIIIIIIIII%IIIIIIIIIIIIIIIHIII"IIIIIIIIIIIIIIIIIIII 0 0 0 1 69 -chrM 767 768 T T 102 0 25 71 .$.$................................A.................................... &IBGII@5ICF>0?BII2IIIIII@+II;IEIII7I,III8IIIIIIIIIIIE@IIIIIIII8IIIIIIII 1 0 0 0 66 -chrM 777 778 G G 108 0 25 63 .$.$...T.....C......T...................T.......................^:. AG(II$IIIII&6BIII:'IIIII9IIIII=IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0 0 1 59 -chrM 784 785 A A 99 0 25 63 .$.........................................................C...^:. 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IHEF8II?+GI:I@I7%IIIIAIIII+IIA'II>II@IIIIIII3IIIII/III7IIIII5IIIIIIIIIIIIII+IIIIIIIIIIIIIIIAI6IIIIII;I8IIIIIIIIIIFIIIIIIIIIIIIIIIIIIIII""IIIAIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0 1 0 160 -chrM 816 817 A A 254 0 22 171 .$.C.......T..Nn..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,n,N,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,.^:.^!. 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IIIIIIIIIIII:IIIII%II5IIIIIIIIII?0B1I<IIGI)II1IDII*IIIIIIII)&III&I4>%5*II4(I 1 0 0 0 62 -chrM 951 952 A A 223 0 24 81 c.,,,,,,,,,,,,,,,c,,.,,,.,,,,,,,,,,,,,,,.,..,.,..,........,,,.,,.,,,,,..,,.^:.^:.^:.^:,^:,^:, IBIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIII8IIIIIIIIIIIIIIIIIIIIICIIII4IGIIIIIIIIIIIIII? 0 2 0 0 80 -chrM 952 953 C C 179 0 24 86 ,.,,,,,,,,,,,,,,,,,,.n,,.,,a,,,,,,a,,,,,.,..,.,..,........a,,.,,.,,,,,..,a....,,a^:.^!.^!.^:a^:a IIIIIIIIIIIIIIIIIIIII"IIIII)III6I1)I4II(I7II?I9II(IIIIIIII+1III0I+214%II79IIIIBB0III%I 2 0 0 0 69 -chrM 956 957 T T 237 0 23 110 ,.,,,,,,,,,,,,,,,,,,N,,,N,,,,,,,,,,,,,,,G,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,NN,^:.^:,^:,^:,^:.^:.^:. 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III+IIIIIII>IHDIG4I4IIIIIII 0 0 1 23 24 +chrM 606 607 G G 105 0 24 43 ..............,....T..T..................^:.^!, BI-&*1&6IIIGIIII%;9I.;>IIIIIIIIIIIIIIIIIII3 0 0 33 2 35 +chrM 618 619 T T 117 0 24 48 ,.........C..C..............,...........N..,...^:. I2&-+)(4I+>CI$&I15@IIIIIIIII,IIIIIIIIIII"II5IIII 0 1 0 34 35 +chrM 627 628 G G 108 0 22 57 .$...........A........,..............,................A^!.^!.^:. 5GI<=4;>G=I<%IIIIII.IIII'IIIIIIII$IIIIIIIIIIIIIIIIIIIIIII 1 0 51 0 52 +chrM 659 660 C C 166 0 19 58 .$.$.............,...n,.,,......,......................a,... /CII>9@II277IIII9II"IIIIIIFIIIIIIBIIIIIIIIIIIIIIII$II7IIII 1 53 0 0 54 +chrM 668 669 C C 135 0 19 42 .$,$,$......,.....................Ga,......,^:. IIIIIII@IIFI@IIIIIIIII;IIIIHIII56IIIIIIIAI 1 40 1 0 42 +chrM 713 714 A A 127 0 23 96 ...,..C.....................,......................,............................C...........^:.^:.^:.^:. 67'II>(IIIAFI<IIIII?I$EI>GAGII4III8IIDIIIDIIIFIIIIG$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 90 1 0 0 91 +chrM 719 720 T T 130 0 24 96 .....C...........,...C.....G............,............G....................A...................^:.^:. D?76/$I'@'<,I7;I<I5GI'H+B.3%;=<3II1CGIIB@FII8@II0II4II$IIIII537IIIIIIIIIII#IIIIIIIII=III$IIIIIII 0 0 1 77 78 +chrM 736 737 A A 98 0 24 98 .$.$.$..............................C................T.......................C..................^:.^:.^:.^:.^:. 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IIII 0 0 0 0 4 -chrM 249 T 4 ,,,. II)I 0 0 0 0 3 -chrM 250 G 4 ,,,. II2I 0 0 0 0 3 -chrM 251 A 4 ,,,. II(I 0 0 0 0 3 -chrM 252 T 4 ,,,. II*I 0 0 0 0 3 -chrM 253 A 4 ,,,. II7I 0 0 0 0 4 -chrM 254 A 4 ,,,. II1I 0 0 0 0 3 -chrM 255 A 4 ,,,. II?I 0 0 0 0 4 -chrM 256 A 4 ,,,. II9I 0 0 0 0 4 -chrM 257 A 4 ,,,. II?I 0 0 0 0 4 -chrM 258 T 4 ,,,. II$I 0 0 0 0 3 -chrM 259 T 5 ,,,.^:. II&II 0 0 0 0 4 -chrM 260 A 5 ,,,.. II,II 0 0 0 0 4 -chrM 261 A 5 ,,,.. II/II 0 0 0 0 4 -chrM 262 G 5 ,,,.. II5II 0 0 0 0 5 -chrM 263 C 5 ,,a.. II%II 0 0 0 0 4 -chrM 264 T 5 ,$,$,.. II%II 0 0 0 0 4 -chrM 265 A 3 ,.. )II 0 0 0 0 2 -chrM 266 T 3 ,.. +II 0 0 0 0 2 -chrM 267 G 4 ,..^:. *III 0 0 0 0 3 -chrM 268 A 4 ,... EIII 0 0 0 0 4 -chrM 269 A 4 ,... =III 0 0 0 0 4 -chrM 270 C 4 a... ;III 1 0 0 0 4 -chrM 271 G 4 ,... ;III 0 0 0 0 4 -chrM 272 A 4 ,... 8@II 0 0 0 0 4 -chrM 273 A 4 ,... 1III 0 0 0 0 3 -chrM 274 A 4 ,... ICII 0 0 0 0 4 -chrM 275 G 4 ,... IIII 0 0 0 0 4 -chrM 276 T 4 ,... IIII 0 0 0 0 4 -chrM 277 T 4 ,... 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III 0 0 0 0 3 -chrM 317 C 3 ,.. III 0 0 0 0 3 -chrM 318 C 3 ,.. III 0 0 0 0 3 -chrM 319 A 3 ,$.. III 0 0 0 0 3 -chrM 390 A 3 ..^:. III 0 0 0 0 3 -chrM 391 A 3 ... >II 0 0 0 0 3 -chrM 392 A 3 ... III 0 0 0 0 3 -chrM 393 T 3 ... III 0 0 0 0 3 -chrM 394 A 3 ... III 0 0 0 0 3 -chrM 395 A 3 .$.. III 0 0 0 0 3 -chrM 400 A 3 ..^:. III 0 0 0 0 3 -chrM 401 A 3 ... III 0 0 0 0 3 -chrM 402 A 3 ... III 0 0 0 0 3 -chrM 403 A 3 ... III 0 0 0 0 3 -chrM 404 C 3 ... III 0 0 0 0 3 -chrM 405 C 3 ... III 0 0 0 0 3 -chrM 406 C 3 ... EII 0 0 0 0 3 -chrM 407 A 3 ... III 0 0 0 0 3 -chrM 408 G 3 ... III 0 0 0 0 3 -chrM 409 T 3 ... 0II 0 0 0 0 2 -chrM 410 T 3 ... III 0 0 0 0 3 -chrM 411 A 4 ...^:, IIII 0 0 0 0 4 -chrM 412 A 4 ..., FIII 0 0 0 0 4 -chrM 413 G 4 ..., IIIH 0 0 0 0 4 -chrM 414 C 4 ...a III2 0 0 0 0 3 +chrM 45 A 3 ..^:. III 3 0 0 0 3 +chrM 46 G 4 ...^:. IIII 0 0 4 0 4 +chrM 47 A 5 ....^:, IIIII 5 0 0 0 5 +chrM 48 T 5 ...., IIIII 0 0 0 5 5 +chrM 49 G 5 ...., IIIII 0 0 5 0 5 +chrM 50 A 5 ...., IIIII 5 0 0 0 5 +chrM 51 G 5 ...., IIIII 0 0 5 0 5 +chrM 52 T 5 ...., IIIII 0 0 0 5 5 +chrM 53 A 5 ...., IIIII 5 0 0 0 5 +chrM 54 T 5 ...., IIIII 0 0 0 5 5 +chrM 55 T 5 ...., IIIII 0 0 0 5 5 +chrM 56 C 5 ...., IIIII 0 5 0 0 5 +chrM 57 T 5 ...., IIIII 0 0 0 5 5 +chrM 58 T 5 ...., IIIII 0 0 0 5 5 +chrM 59 A 5 ...., IIIII 5 0 0 0 5 +chrM 60 C 5 ...., IIIII 0 5 0 0 5 +chrM 61 T 5 ...., IIIII 0 0 0 5 5 +chrM 62 C 5 ...., IIIII 0 5 0 0 5 +chrM 63 C 5 ...., IIIII 0 5 0 0 5 +chrM 64 A 5 ...., IIIII 5 0 0 0 5 +chrM 65 T 5 ...., IIIII 0 0 0 5 5 +chrM 66 A 5 ...., IIIII 5 0 0 0 5 +chrM 67 A 5 ...., IIIII 5 0 0 0 5 +chrM 68 A 5 ...., IIICI 5 0 0 0 5 +chrM 69 C 5 ...., IIIII 0 5 0 0 5 +chrM 70 A 5 ...., IIIII 5 0 0 0 5 +chrM 71 C 5 ...., IIIII 0 5 0 0 5 +chrM 72 A 5 ...., IAIII 5 0 0 0 5 +chrM 73 T 5 ...., IIIII 0 0 0 5 5 +chrM 74 A 5 ...., IIIII 5 0 0 0 5 +chrM 75 G 5 ...., %IIII 0 0 4 0 4 +chrM 76 G 5 T..., *IIII 0 0 4 0 4 +chrM 77 C 5 .$..., GIIII 0 5 0 0 5 +chrM 78 T 4 .$.., IIII 0 0 0 4 4 +chrM 79 T 3 .., III 0 0 0 3 3 +chrM 80 G 3 .$., I1I 0 0 2 0 2 +chrM 181 A 3 ,,^:, III 3 0 0 0 3 +chrM 182 G 3 ,,, III 0 0 3 0 3 +chrM 183 G 3 ,,, III 0 0 3 0 3 +chrM 184 T 3 ,,, III 0 0 0 3 3 +chrM 185 A 3 ,,, III 3 0 0 0 3 +chrM 186 T 3 ,,, III 0 0 0 3 3 +chrM 187 C 3 ,,, III 0 3 0 0 3 +chrM 188 A 3 ,,, III 3 0 0 0 3 +chrM 189 A 3 ,,, III 3 0 0 0 3 +chrM 190 G 3 ,,, III 0 0 3 0 3 +chrM 191 C 3 ,$,, III 0 3 0 0 3 +chrM 229 A 3 .^:,^:, %II 2 0 0 0 2 +chrM 230 C 3 .,, 8II 0 3 0 0 3 +chrM 231 C 3 .,, 9II 0 3 0 0 3 +chrM 232 C 3 .,, III 0 3 0 0 3 +chrM 233 C 3 .,, AI' 0 2 0 0 2 +chrM 234 C 3 .,, DI+ 0 2 0 0 2 +chrM 235 A 3 .,, &I@ 2 0 0 0 2 +chrM 236 C 3 .$,a +I$ 0 1 0 0 1 +chrM 244 A 3 ,,^:, II; 3 0 0 0 3 +chrM 245 G 3 ,,, II* 0 0 2 0 2 +chrM 246 C 3 ,,n II" 0 2 0 0 2 +chrM 247 A 3 ,,, III 3 0 0 0 3 +chrM 248 G 4 ,,,^:. IIII 0 0 4 0 4 +chrM 249 T 4 ,,,. II)I 0 0 0 3 3 +chrM 250 G 4 ,,,. II2I 0 0 3 0 3 +chrM 251 A 4 ,,,. II(I 3 0 0 0 3 +chrM 252 T 4 ,,,. II*I 0 0 0 3 3 +chrM 253 A 4 ,,,. II7I 4 0 0 0 4 +chrM 254 A 4 ,,,. II1I 3 0 0 0 3 +chrM 255 A 4 ,,,. II?I 4 0 0 0 4 +chrM 256 A 4 ,,,. II9I 4 0 0 0 4 +chrM 257 A 4 ,,,. II?I 4 0 0 0 4 +chrM 258 T 4 ,,,. II$I 0 0 0 3 3 +chrM 259 T 5 ,,,.^:. II&II 0 0 0 4 4 +chrM 260 A 5 ,,,.. II,II 4 0 0 0 4 +chrM 261 A 5 ,,,.. II/II 4 0 0 0 4 +chrM 262 G 5 ,,,.. II5II 0 0 5 0 5 +chrM 263 C 5 ,,a.. II%II 0 4 0 0 4 +chrM 264 T 5 ,$,$,.. II%II 0 0 0 4 4 +chrM 265 A 3 ,.. )II 2 0 0 0 2 +chrM 266 T 3 ,.. +II 0 0 0 2 2 +chrM 267 G 4 ,..^:. *III 0 0 3 0 3 +chrM 268 A 4 ,... EIII 4 0 0 0 4 +chrM 269 A 4 ,... =III 4 0 0 0 4 +chrM 270 C 4 a... ;III 1 3 0 0 4 +chrM 271 G 4 ,... ;III 0 0 4 0 4 +chrM 272 A 4 ,... 8@II 4 0 0 0 4 +chrM 273 A 4 ,... 1III 3 0 0 0 3 +chrM 274 A 4 ,... ICII 4 0 0 0 4 +chrM 275 G 4 ,... IIII 0 0 4 0 4 +chrM 276 T 4 ,... IIII 0 0 0 4 4 +chrM 277 T 4 ,... IIII 0 0 0 4 4 +chrM 278 C 4 ,... IIII 0 4 0 0 4 +chrM 279 G 4 ,$... IIII 0 0 4 0 4 +chrM 280 A 3 ... III 3 0 0 0 3 +chrM 281 C 3 ... GII 0 3 0 0 3 +chrM 282 T 3 ... III 0 0 0 3 3 +chrM 283 A 3 .$.. IFI 3 0 0 0 3 +chrM 284 A 3 ..^:, IAI 3 0 0 0 3 +chrM 285 G 3 .., ;II 0 0 3 0 3 +chrM 286 T 4 ..,^:. IIII 0 0 0 4 4 +chrM 287 C 4 ..,. II4I 0 3 0 0 3 +chrM 288 A 4 ..,. @III 4 0 0 0 4 +chrM 289 T 4 ..,. IIII 0 0 0 4 4 +chrM 290 A 4 ..,. @:II 4 0 0 0 4 +chrM 291 T 4 ..,. IIAI 0 0 0 4 4 +chrM 292 T 4 ..,. IIII 0 0 0 4 4 +chrM 293 A 4 ..,. 8;II 4 0 0 0 4 +chrM 294 A 4 .$.,. I<II 4 0 0 0 4 +chrM 295 A 3 .,. 4II 2 0 0 0 2 +chrM 296 T 3 .,. III 0 0 0 3 3 +chrM 297 A 3 .,. BII 3 0 0 0 3 +chrM 298 A 3 .,. CII 3 0 0 0 3 +chrM 299 G 3 .,. III 0 0 3 0 3 +chrM 300 G 3 .,. ;II 0 0 3 0 3 +chrM 301 G 3 .,. III 0 0 3 0 3 +chrM 302 T 3 .$,. III 0 0 0 3 3 +chrM 312 T 3 ,.^:. III 0 0 0 3 3 +chrM 313 C 3 ,.. III 0 3 0 0 3 +chrM 314 G 3 ,.. III 0 0 3 0 3 +chrM 315 T 3 ,.. III 0 0 0 3 3 +chrM 316 G 3 ,.. III 0 0 3 0 3 +chrM 317 C 3 ,.. III 0 3 0 0 3 +chrM 318 C 3 ,.. III 0 3 0 0 3 +chrM 319 A 3 ,$.. III 3 0 0 0 3 +chrM 390 A 3 ..^:. III 3 0 0 0 3 +chrM 391 A 3 ... >II 3 0 0 0 3 +chrM 392 A 3 ... III 3 0 0 0 3 +chrM 393 T 3 ... III 0 0 0 3 3 +chrM 394 A 3 ... III 3 0 0 0 3 +chrM 395 A 3 .$.. III 3 0 0 0 3 +chrM 400 A 3 ..^:. III 3 0 0 0 3 +chrM 401 A 3 ... III 3 0 0 0 3 +chrM 402 A 3 ... III 3 0 0 0 3 +chrM 403 A 3 ... III 3 0 0 0 3 +chrM 404 C 3 ... III 0 3 0 0 3 +chrM 405 C 3 ... III 0 3 0 0 3 +chrM 406 C 3 ... EII 0 3 0 0 3 +chrM 407 A 3 ... III 3 0 0 0 3 +chrM 408 G 3 ... III 0 0 3 0 3 +chrM 409 T 3 ... 0II 0 0 0 2 2 +chrM 410 T 3 ... III 0 0 0 3 3 +chrM 411 A 4 ...^:, IIII 4 0 0 0 4 +chrM 412 A 4 ..., FIII 4 0 0 0 4 +chrM 413 G 4 ..., IIIH 0 0 4 0 4 +chrM 414 C 4 ...a III2 0 3 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 -chrM 416 G 5 ...,^:, II?7: 0 0 0 0 5 -chrM 417 T 5 ...,, ;IIE@ 0 0 0 0 5 -chrM 418 A 5 ...,, IIIII 0 0 0 0 5 -chrM 419 A 5 ...,, IIIII 0 0 0 0 5 -chrM 420 A 5 ...,, FIIII 0 0 0 0 5 -chrM 421 A 5 ...,, IIIII 0 0 0 0 5 -chrM 422 A 5 ...,, >IIII 0 0 0 0 5 -chrM 423 G 6 ...,,^:, HII/I, 0 0 0 0 4 -chrM 424 C 6 .$..a,, ;II-I: 0 0 0 0 5 -chrM 425 T 5 .$.,,, IIIIF 0 0 0 0 5 -chrM 426 A 5 .,,,^:, III@I 0 0 0 0 5 -chrM 427 C 5 .,,,, III$I 0 0 0 0 4 -chrM 428 A 5 .,,,, IIIII 0 0 0 0 5 -chrM 429 A 5 .,,,, IIII. 0 0 0 0 4 -chrM 430 C 5 .,,,a I%I5' 0 0 0 0 3 -chrM 431 C 5 .,,,, I(I5< 0 0 0 0 4 -chrM 432 A 5 .,,,, IIIII 0 0 0 0 5 -chrM 433 A 5 .,,,, 0IIII 0 0 0 0 4 -chrM 434 A 5 .,,,, =IIII 0 0 0 0 5 -chrM 435 G 5 .$,,,, EIIII 0 0 0 0 5 -chrM 436 T 4 ,,,, III5 0 0 0 0 4 -chrM 437 A 4 ,,,, IIII 0 0 0 0 4 -chrM 438 A 4 ,,,, IIII 0 0 0 0 4 -chrM 439 A 4 ,,,, IIII 0 0 0 0 4 -chrM 440 A 4 ,,,, IIIF 0 0 0 0 4 -chrM 441 T 6 ,,,,^:.^:. III;II 0 0 0 0 6 -chrM 442 A 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 443 G 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 444 A 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 445 C 6 ,,,,.. IIIIII 0 0 0 0 6 -chrM 446 T 6 ,$,,,.. IIIIII 0 0 0 0 6 -chrM 447 A 5 ,,,.. IIIII 0 0 0 0 5 -chrM 448 C 5 ,,,.. IIIII 0 0 0 0 5 -chrM 449 G 6 ,,,..^:, IIIII6 0 0 0 0 6 -chrM 450 A 6 ,,,.., IIIIII 0 0 0 0 6 -chrM 451 A 6 ,$,,.., IIIIII 0 0 0 0 6 -chrM 452 A 5 ,,.., IIIII 0 0 0 0 5 -chrM 453 G 5 ,,.., IIIII 0 0 0 0 5 -chrM 454 T 6 ,,..,^:, IIIIII 0 0 0 0 6 -chrM 455 G 6 ,,..,, IIIIII 0 0 0 0 6 -chrM 456 A 6 ,,..,, IIIIII 0 0 0 0 6 -chrM 457 C 6 ,,..,, IIIII= 0 0 0 0 6 -chrM 458 T 6 ,$,..,, IIIIII 0 0 0 0 6 -chrM 459 T 5 ,..,, IIIII 0 0 0 0 5 -chrM 460 T 5 ,..,, IIIII 0 0 0 0 5 -chrM 461 A 5 ,$..,, IIIII 0 0 0 0 5 -chrM 462 A 4 ..,, IIII 0 0 0 0 4 -chrM 463 T 4 ..,, IIIC 0 0 0 0 4 -chrM 464 A 4 ..,, IIII 0 0 0 0 4 -chrM 465 C 4 ..,, IIII 0 0 0 0 4 -chrM 466 C 4 ..,, IIII 0 0 0 0 4 -chrM 467 T 4 ..,, II>? 0 0 0 0 4 -chrM 468 C 4 ..,, IIII 0 0 0 0 4 -chrM 469 T 4 ..,, IIIG 0 0 0 0 4 -chrM 470 G 4 ..,, %III 0 0 0 0 3 -chrM 471 A 4 ..,, 4;II 0 0 0 0 3 -chrM 472 C 4 ..,, II3I 0 0 0 0 3 -chrM 473 T 4 ..,, IIII 0 0 0 0 4 -chrM 474 A 4 ..,, ;III 0 0 0 0 4 -chrM 475 C 4 ..,, IIII 0 0 0 0 4 -chrM 476 A 4 .$.$,, 32II 0 0 0 0 2 -chrM 480 T 3 ,,^:. III 0 0 0 0 3 -chrM 481 A 3 ,,. III 0 0 0 0 3 -chrM 482 G 3 ,,. III 0 0 0 0 3 -chrM 483 C 4 ,,.^:, IIIE 0 0 0 0 4 -chrM 484 T 4 ,$,., III9 0 0 0 0 4 -chrM 485 A 3 ,., III 0 0 0 0 3 -chrM 486 A 3 ,., III 0 0 0 0 3 -chrM 487 G 3 ,., III 0 0 0 0 3 -chrM 488 A 3 ,., III 0 0 0 0 3 -chrM 489 C 3 ,$., III 0 0 0 0 3 -chrM 510 C 3 .,^:. III 0 0 0 0 3 -chrM 511 C 3 .,. III 0 0 0 0 3 -chrM 512 A 3 .,. 6II 0 0 0 0 3 -chrM 513 C 3 .,. III 0 0 0 0 3 -chrM 514 T 3 .,. III 0 0 0 0 3 -chrM 515 A 3 .$,. III 0 0 0 0 3 -chrM 518 C 3 ,$.^:. III 0 0 0 0 3 -chrM 520 T 3 ..^:, III 0 0 0 0 3 -chrM 521 A 3 .., III 0 0 0 0 3 -chrM 522 G 3 .., II, 0 0 0 0 2 -chrM 523 C 3 .., III 0 0 0 0 3 -chrM 524 C 3 .., II7 0 0 0 0 3 -chrM 525 C 3 .., III 0 0 0 0 3 -chrM 526 T 3 .., II? 0 0 0 0 3 -chrM 527 A 3 .., III 0 0 0 0 3 -chrM 528 A 3 .., III 0 0 0 0 3 -chrM 529 A 3 .., FII 0 0 0 0 3 -chrM 530 C 3 .., II+ 0 0 0 0 2 -chrM 531 T 3 .., III 0 0 0 0 3 -chrM 532 A 3 .., :II 0 0 0 0 3 -chrM 533 A 3 .., DGI 0 0 0 0 3 -chrM 534 A 3 .., III 0 0 0 0 3 -chrM 535 A 3 .., ?CI 0 0 0 0 3 -chrM 536 T 3 .., III 0 0 0 0 3 -chrM 537 A 3 .., 9II 0 0 0 0 3 -chrM 538 G 3 .., III 0 0 0 0 3 -chrM 539 C 3 .., III 0 0 0 0 3 -chrM 540 T 3 .., III 0 0 0 0 3 -chrM 541 T 3 .., III 0 0 0 0 3 -chrM 542 A 4 ..,^:. IIII 0 0 0 0 4 -chrM 543 C 4 ..,. IIII 0 0 0 0 4 -chrM 544 C 4 ..,. IIII 0 0 0 0 4 -chrM 545 A 4 N$.,. "III 0 0 0 0 3 -chrM 546 C 3 .,. III 0 0 0 0 3 -chrM 547 A 3 .,. DII 0 0 0 0 3 -chrM 548 A 3 .,. EII 0 0 0 0 3 -chrM 549 C 3 .,. III 0 0 0 0 3 -chrM 550 A 3 .,. III 0 0 0 0 3 -chrM 551 A 3 .,. 6II 0 0 0 0 3 -chrM 552 A 3 .,. GII 0 0 0 0 3 -chrM 553 G 3 .$,. ?II 0 0 0 0 3 -chrM 577 A 3 .$.^:. III 0 0 0 0 3 -chrM 580 A 3 ..^:, III 0 0 0 0 3 -chrM 581 G 3 .., III 0 0 0 0 3 -chrM 582 C 3 .., II? 0 0 0 0 3 -chrM 583 C 3 ..a II- 0 0 0 0 2 -chrM 584 T 3 .., IIH 0 0 0 0 3 -chrM 585 A 3 .., III 0 0 0 0 3 -chrM 586 A 3 .., III 0 0 0 0 3 -chrM 587 A 4 ..,^:, IIII 0 0 0 0 4 -chrM 588 A 4 ..,, IIII 0 0 0 0 4 -chrM 589 C 4 ..,, IIII 0 0 0 0 4 -chrM 590 T 4 ..,, II.5 0 0 0 0 3 -chrM 591 C 4 .$.,, II<I 0 0 0 0 4 -chrM 592 A 3 .,, III 0 0 0 0 3 -chrM 593 A 3 .,, III 0 0 0 0 3 -chrM 594 A 3 .,, III 0 0 0 0 3 -chrM 595 G 3 .,, III 0 0 0 0 3 -chrM 596 G 3 .,, III 0 0 0 0 3 -chrM 597 A 3 .,, :EI 0 0 0 0 3 -chrM 598 C 3 .,, III 0 0 0 0 3 -chrM 599 T 4 .,,^:. II@I 0 0 0 0 4 -chrM 600 T 4 .,,. IIII 0 0 0 0 4 -chrM 601 G 4 .,,. IIII 0 0 0 0 4 -chrM 602 G 4 .,,. IIII 0 0 0 0 4 -chrM 603 C 4 .,,. IIII 0 0 0 0 4 -chrM 604 G 4 .,,. IIII 0 0 0 0 4 -chrM 605 G 4 .,,. IIII 0 0 0 0 4 -chrM 606 T 4 .,,. 5III 0 0 0 0 4 -chrM 607 G 4 .,,. IIII 0 0 0 0 4 -chrM 608 C 4 .,,. *III 0 0 0 0 3 -chrM 609 T 5 .,,.^:, ?IIII 0 0 0 0 5 -chrM 610 T 5 .,,., IIII8 0 0 0 0 5 -chrM 611 T 5 .,,., IIIII 0 0 0 0 5 -chrM 612 A 5 T$,,., 3IIII 0 0 0 0 4 -chrM 613 C 4 ,,., III) 0 0 0 0 3 -chrM 614 A 4 ,,., IIII 0 0 0 0 4 -chrM 615 T 4 ,$,., IIII 0 0 0 0 4 -chrM 616 C 3 ,., III 0 0 0 0 3 -chrM 617 C 3 ,., III 0 0 0 0 3 -chrM 618 C 3 ,., III 0 0 0 0 3 -chrM 619 T 3 ,., IF9 0 0 0 0 3 -chrM 620 C 3 ,., II7 0 0 0 0 3 -chrM 621 T 3 ,., III 0 0 0 0 3 -chrM 622 A 3 ,$., I7I 0 0 0 0 3 -chrM 652 C 3 .,^:, II) 0 0 0 0 2 -chrM 653 G 3 .,, II2 0 0 0 0 2 -chrM 654 A 3 .,, III 0 0 0 0 3 -chrM 655 T 4 .,,^:. II*I 0 0 0 0 3 -chrM 656 A 4 .,,. IIII 0 0 0 0 4 -chrM 657 A 4 .,,. IIII 0 0 0 0 4 -chrM 658 A 4 .,,. IIII 0 0 0 0 4 -chrM 659 C 4 .,,. IIII 0 0 0 0 4 -chrM 660 C 4 .,,. IIII 0 0 0 0 4 -chrM 661 C 4 .,,. IIII 0 0 0 0 4 -chrM 662 C 4 .,,. IIFI 0 0 0 0 4 -chrM 663 A 4 .,,. =IDI 0 0 0 0 4 -chrM 664 C 4 .,,. II6I 0 0 0 0 4 -chrM 665 C 5 .,,.^:, IIIII 0 0 0 0 5 -chrM 666 A 5 .,,., BIIII 0 0 0 0 5 -chrM 667 T 5 .,,., II5I+ 0 0 0 0 4 -chrM 668 C 5 .,,., IIIII 0 0 0 0 5 -chrM 669 C 5 .,,., IIIII 0 0 0 0 5 -chrM 670 C 5 .,a., II.II 0 0 0 0 4 -chrM 671 T 5 .,,., IIIIA 0 0 0 0 5 -chrM 672 T 6 .,,.,^:. FI9I.I 0 0 0 0 5 -chrM 673 G 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 674 C 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 675 T 6 .,,.,. IIIIII 0 0 0 0 6 -chrM 676 A 6 .,,.,. ,IIEII 0 0 0 0 5 -chrM 677 A 7 .,,.,.^:. 3II;III 0 0 0 0 6 -chrM 678 T 7 .,,.,.. IIIIDII 0 0 0 0 7 -chrM 679 T 7 .,,.,.. CIIIIII 0 0 0 0 7 -chrM 680 C 7 .,,.,.. IIIIIII 0 0 0 0 7 -chrM 681 A 7 .$,,.,.. 9IIIIII 0 0 0 0 7 -chrM 682 G 6 ,,.,.. II$III 0 0 0 0 5 -chrM 683 C 6 ,,.,.. IIIIII 0 0 0 0 6 -chrM 684 C 6 ,$,.,.. IIIIII 0 0 0 0 6 -chrM 685 T 5 ,.,.. IIIII 0 0 0 0 5 -chrM 686 A 5 ,.,.. IIIII 0 0 0 0 5 -chrM 687 T 5 ,$.,.. IIIII 0 0 0 0 5 -chrM 688 A 4 .,.. IIII 0 0 0 0 4 -chrM 689 T 4 .,.. IIII 0 0 0 0 4 -chrM 690 A 4 .$,.. IIII 0 0 0 0 4 -chrM 691 C 3 ,.. III 0 0 0 0 3 -chrM 692 C 3 ,.. III 0 0 0 0 3 -chrM 693 G 4 ,..^:, IIII 0 0 0 0 4 -chrM 694 C 4 ,.., IIII 0 0 0 0 4 -chrM 695 C 4 ,.., IIII 0 0 0 0 4 -chrM 696 A 4 ,.., IIII 0 0 0 0 4 -chrM 697 T 4 ,.., IIII 0 0 0 0 4 -chrM 698 C 4 ,.., IIII 0 0 0 0 4 -chrM 699 T 4 ,.., IIII 0 0 0 0 4 -chrM 700 T 4 ,$.., IIII 0 0 0 0 4 -chrM 701 C 3 .., III 0 0 0 0 3 -chrM 702 A 3 .., III 0 0 0 0 3 -chrM 703 G 3 .., 2II 0 0 0 0 2 -chrM 704 C 3 .., III 0 0 0 0 3 -chrM 705 A 3 N., "II 0 0 0 0 2 -chrM 706 A 3 .., I5I 0 0 0 0 3 -chrM 707 A 3 .$., GII 0 0 0 0 3 -chrM 726 A 3 ,,^:. III 0 0 0 0 3 -chrM 727 G 3 ,,. III 0 0 0 0 3 -chrM 728 T 3 ,$,. III 0 0 0 0 3 -chrM 732 C 3 a.^:. $II 0 0 0 0 2 -chrM 733 A 3 ,.. III 0 0 0 0 3 -chrM 734 C 3 ,.. %II 0 0 0 0 2 -chrM 735 A 3 ,.. III 0 0 0 0 3 -chrM 736 A 3 ,.. *II 0 0 0 0 2 -chrM 737 A 3 ,.. III 0 0 0 0 3 -chrM 738 T 3 ,.. III 0 0 0 0 3 -chrM 739 A 3 ,.. III 0 0 0 0 3 -chrM 740 T 3 ,.. III 0 0 0 0 3 -chrM 741 C 3 ,.. III 0 0 0 0 3 -chrM 742 C 3 ,.. III 0 0 0 0 3 -chrM 743 A 3 ,.. III 0 0 0 0 3 -chrM 744 A 3 ,.. III 0 0 0 0 3 -chrM 745 C 3 ,.. III 0 0 0 0 3 -chrM 746 A 3 ,.. IIE 0 0 0 0 3 -chrM 747 T 3 ,.. III 0 0 0 0 3 -chrM 748 A 3 ,.. III 0 0 0 0 3 -chrM 749 A 3 ,.. III 0 0 0 0 3 -chrM 750 A 3 ,.. III 0 0 0 0 3 -chrM 751 A 3 ,.. IAI 0 0 0 0 3 -chrM 752 A 3 ,.. III 0 0 0 0 3 -chrM 753 C 3 ,.. III 0 0 0 0 3 -chrM 754 G 3 ,$.. III 0 0 0 0 3 -chrM 756 T 3 ..^:, III 0 0 0 0 3 -chrM 757 A 3 .., III 0 0 0 0 3 -chrM 758 G 3 .., III 0 0 0 0 3 -chrM 759 G 3 .., III 0 0 0 0 3 -chrM 760 T 3 .., =II 0 0 0 0 3 -chrM 761 C 3 .$., IID 0 0 0 0 3 -chrM 767 G 3 .$,^:, III 0 0 0 0 3 -chrM 769 A 3 ,,^:, III 0 0 0 0 3 -chrM 770 G 3 ,,, III 0 0 0 0 3 -chrM 771 C 3 ,,, IHI 0 0 0 0 3 -chrM 772 C 3 ,a, I)/ 0 0 0 0 1 -chrM 773 C 3 ,,, I7I 0 0 0 0 3 -chrM 774 A 4 ,,,^:. II:I 0 0 0 0 4 -chrM 775 T 4 ,,,. IH.I 0 0 0 0 3 -chrM 776 G 4 ,,,. IIII 0 0 0 0 4 -chrM 777 G 4 ,,,. IIII 0 0 0 0 4 -chrM 778 G 4 ,,,. IIII 0 0 0 0 4 -chrM 779 A 4 ,,,. IIAI 0 0 0 0 4 -chrM 780 T 4 ,,,. IIGI 0 0 0 0 4 -chrM 781 G 4 ,,,. IIII 0 0 0 0 4 -chrM 782 G 4 ,,,. IIII 0 0 0 0 4 -chrM 783 A 4 ,,,. IIII 0 0 0 0 4 -chrM 784 G 4 ,,,. IIII 0 0 0 0 4 -chrM 785 A 4 ,,,. IIII 0 0 0 0 4 -chrM 786 G 4 ,,,. IIII 0 0 0 0 4 -chrM 787 A 4 ,,,. IIII 0 0 0 0 4 -chrM 788 A 4 ,,,. IIII 0 0 0 0 4 -chrM 789 A 4 ,,,. IIII 0 0 0 0 4 -chrM 790 T 5 ,,,.^:. IIIII 0 0 0 0 5 -chrM 791 G 5 ,$,,.. IIIII 0 0 0 0 5 -chrM 792 G 4 ,,.. IIII 0 0 0 0 4 -chrM 793 G 4 ,,.. IIII 0 0 0 0 4 -chrM 794 C 4 ,,.. IIII 0 0 0 0 4 -chrM 795 T 4 ,,.. IIII 0 0 0 0 4 -chrM 796 A 4 ,,.. IIII 0 0 0 0 4 -chrM 797 C 4 ,,.. IIII 0 0 0 0 4 -chrM 798 A 4 ,,.. IIII 0 0 0 0 4 -chrM 799 T 4 ,,.. IIII 0 0 0 0 4 -chrM 800 T 4 ,,.. IIII 0 0 0 0 4 -chrM 801 T 4 ,,.. IIII 0 0 0 0 4 -chrM 802 T 4 ,$,.. IIII 0 0 0 0 4 -chrM 803 C 3 ,.. III 0 0 0 0 3 -chrM 804 T 3 ,$.. III 0 0 0 0 3 -chrM 806 C 3 ..^:. III 0 0 0 0 3 -chrM 807 C 3 ... III 0 0 0 0 3 -chrM 808 C 3 ... III 0 0 0 0 3 -chrM 809 T 3 .$.. III 0 0 0 0 3 -chrM 810 A 3 ..^:, III 0 0 0 0 3 -chrM 811 A 3 .., III 0 0 0 0 3 -chrM 812 G 3 .., II7 0 0 0 0 3 -chrM 813 A 3 .., III 0 0 0 0 3 -chrM 814 A 3 .., III 0 0 0 0 3 -chrM 815 C 3 .., III 0 0 0 0 3 -chrM 816 A 3 .., III 0 0 0 0 3 -chrM 817 A 3 .., III 0 0 0 0 3 -chrM 818 G 3 .., III 0 0 0 0 3 -chrM 819 A 3 .., III 0 0 0 0 3 -chrM 820 A 3 .., &II 0 0 0 0 2 -chrM 821 C 3 .., III 0 0 0 0 3 -chrM 822 T 3 .., III 0 0 0 0 3 -chrM 823 T 3 ..n II" 0 0 0 0 2 -chrM 824 T 3 .., III 0 0 0 0 3 -chrM 825 A 3 .$., III 0 0 0 0 3 -chrM 826 A 3 .,^:. III 0 0 0 0 3 -chrM 827 C 3 .,. III 0 0 0 0 3 -chrM 828 C 3 .,. III 0 0 0 0 3 -chrM 829 C 4 .,.^:, IIII 0 0 0 0 4 -chrM 830 G 4 .,., IIII 0 0 0 0 4 -chrM 831 G 4 .,., IIII 0 0 0 0 4 -chrM 832 A 4 .,., IIII 0 0 0 0 4 -chrM 833 C 4 .,., IIII 0 0 0 0 4 -chrM 834 G 4 .,., IIII 0 0 0 0 4 -chrM 835 A 4 .,., IIII 0 0 0 0 4 -chrM 836 A 4 .,., 8III 0 0 0 0 4 -chrM 837 A 4 .,., IIII 0 0 0 0 4 -chrM 838 G 4 .,., IIII 0 0 0 0 4 -chrM 839 T 5 .,.,^:, 4:IIG 0 0 0 0 4 -chrM 840 C 5 .,.,, IIIII 0 0 0 0 5 -chrM 841 T 5 .$,.,, IIIII 0 0 0 0 5 -chrM 842 C 4 ,.,, IIII 0 0 0 0 4 -chrM 843 C 4 ,.,, IIII 0 0 0 0 4 -chrM 844 A 4 ,.,, IIII 0 0 0 0 4 -chrM 845 T 4 ,$.,, IIII 0 0 0 0 4 -chrM 846 G 3 .,, @II 0 0 0 0 3 -chrM 847 A 3 .,, III 0 0 0 0 3 -chrM 848 A 3 .,, III 0 0 0 0 3 -chrM 849 A 3 .,, III 0 0 0 0 3 -chrM 850 C 3 .,, III 0 0 0 0 3 -chrM 851 T 3 .,, III 0 0 0 0 3 -chrM 852 G 3 .,, III 0 0 0 0 3 -chrM 853 G 3 .,, III 0 0 0 0 3 -chrM 854 A 3 .,, EII 0 0 0 0 3 -chrM 855 G 3 .,, DII 0 0 0 0 3 -chrM 856 A 3 .,, III 0 0 0 0 3 -chrM 857 C 3 .,, III 0 0 0 0 3 -chrM 858 T 4 .,,^:, IIIA 0 0 0 0 4 -chrM 859 A 4 .,,, @III 0 0 0 0 4 -chrM 860 A 4 .,,, IIII 0 0 0 0 4 -chrM 861 A 4 .$,,, EIII 0 0 0 0 4 -chrM 862 G 3 ,,, III 0 0 0 0 3 -chrM 863 G 3 ,,, III 0 0 0 0 3 -chrM 864 A 3 ,$,, III 0 0 0 0 3 -chrM 905 C 3 ,.^:, III 0 0 0 0 3 -chrM 906 A 3 ,., III 0 0 0 0 3 -chrM 907 G 3 ,., III 0 0 0 0 3 -chrM 908 G 3 ,., III 0 0 0 0 3 -chrM 909 C 3 ,., III 0 0 0 0 3 -chrM 910 C 3 ,., III 0 0 0 0 3 -chrM 911 A 4 ,.,^:, IIII 0 0 0 0 4 -chrM 912 T 4 ,.,, IIEG 0 0 0 0 4 -chrM 913 G 4 ,.,, III: 0 0 0 0 4 -chrM 914 A 4 ,.,, IIII 0 0 0 0 4 -chrM 915 A 4 ,.,, IIII 0 0 0 0 4 -chrM 916 G 4 ,.,, III5 0 0 0 0 4 -chrM 917 C 4 ,.,, III5 0 0 0 0 4 -chrM 918 G 4 ,.,, IIII 0 0 0 0 4 -chrM 919 C 4 ,.,, III< 0 0 0 0 4 -chrM 920 G 4 ,.,, IIII 0 0 0 0 4 -chrM 921 C 4 ,.,, IIII 0 0 0 0 4 -chrM 922 A 4 ,.,, IIII 0 0 0 0 4 -chrM 923 C 4 ,.,, III8 0 0 0 0 4 -chrM 924 A 4 ,.,, IFII 0 0 0 0 4 -chrM 925 C 4 ,.,, IIII 0 0 0 0 4 -chrM 926 A 4 ,.,, IIII 0 0 0 0 4 -chrM 927 C 4 ,.,, IIII 0 0 0 0 4 -chrM 928 C 5 ,.,,^:, IIII: 0 0 0 0 5 -chrM 929 G 5 ,.,,, IIIE: 0 0 0 0 5 -chrM 930 C 5 ,.,,, IIIII 0 0 0 0 5 -chrM 931 C 5 ,.,,, IIIIF 0 0 0 0 5 -chrM 932 C 5 ,.,,, IIIIC 0 0 0 0 5 -chrM 933 G 5 ,$.,,, I?II: 0 0 0 0 5 -chrM 934 T 4 .$,,, 4II> 0 0 0 0 3 -chrM 935 C 3 ,,, III 0 0 0 0 3 -chrM 936 A 3 ,,, III 0 0 0 0 3 -chrM 937 C 3 ,,, II1 0 0 0 0 2 -chrM 938 C 3 ,,, III 0 0 0 0 3 -chrM 939 C 3 ,,, III 0 0 0 0 3 -chrM 940 T 3 ,$,, III 0 0 0 0 3 -chrM 958 C 3 ,.^:. III 0 0 0 0 3 -chrM 959 A 3 ,.. III 0 0 0 0 3 -chrM 960 T 3 ,.. III 0 0 0 0 3 -chrM 961 A 3 ,.. III 0 0 0 0 3 -chrM 962 A 3 ,.. III 0 0 0 0 3 -chrM 963 C 4 ,$..^:. IIII 0 0 0 0 4 -chrM 964 A 3 ... I(; 0 0 0 0 2 -chrM 965 T 3 ... III 0 0 0 0 3 -chrM 966 A 4 ...^:. IIII 0 0 0 0 4 -chrM 967 A 4 .... IIII 0 0 0 0 4 -chrM 968 C 4 .... IEII 0 0 0 0 4 -chrM 969 A 4 .... IIII 0 0 0 0 4 -chrM 970 T 4 .... IIII 0 0 0 0 4 -chrM 971 A 4 .... IIII 0 0 0 0 4 -chrM 972 A 4 .... IIII 0 0 0 0 4 -chrM 973 A 4 .... II0I 0 0 0 0 3 -chrM 974 A 5 ....^:. IIIII 0 0 0 0 5 -chrM 975 C 5 ..... IIIII 0 0 0 0 5 -chrM 976 C 5 ..... IIIII 0 0 0 0 5 -chrM 977 G 5 ..... IIIII 0 0 0 0 5 -chrM 978 T 5 ..... IIIII 0 0 0 0 5 -chrM 979 G 5 ..... I0III 0 0 0 0 4 -chrM 980 A 5 ..... IIII4 0 0 0 0 4 -chrM 981 C 5 ..... IIIII 0 0 0 0 5 -chrM 982 C 5 ..... IIIII 0 0 0 0 5 -chrM 983 C 5 ..... IIIII 0 0 0 0 5 -chrM 984 A 5 ..... -IGII 0 0 0 0 4 -chrM 985 A 5 ..... 4GIII 0 0 0 0 4 -chrM 986 A 5 ..... BDGII 0 0 0 0 5 -chrM 987 C 5 ..... IDIII 0 0 0 0 5 -chrM 988 A 5 ..... @<III 0 0 0 0 5 -chrM 989 T 5 ..... IIIII 0 0 0 0 5 -chrM 990 A 5 .$.... I@III 0 0 0 0 5 -chrM 991 T 4 .... IICI 0 0 0 0 4 -chrM 992 G 4 T... )III 0 0 0 0 3 -chrM 993 A 4 .$... ?ICI 0 0 0 0 4 -chrM 994 A 3 ... III 0 0 0 0 3 -chrM 995 A 3 ... III 0 0 0 0 3 -chrM 996 G 3 ... III 0 0 0 0 3 -chrM 997 G 3 ... III 0 0 0 0 3 -chrM 998 A 3 .$.. 4II 0 0 0 0 2 -chrM 999 G 3 ..^:. III 0 0 0 0 3 -chrM 1000 A 3 ... III 0 0 0 0 3 -chrM 1001 C 3 .$.. III 0 0 0 0 3 -chrM 1043 A 3 ..^:, III 0 0 0 0 3 -chrM 1044 A 3 .., III 0 0 0 0 3 -chrM 1045 C 3 .., II7 0 0 0 0 3 -chrM 1046 C 3 .., II- 0 0 0 0 2 -chrM 1047 A 3 .., III 0 0 0 0 3 -chrM 1048 A 3 .., III 0 0 0 0 3 -chrM 1049 A 3 .., III 0 0 0 0 3 -chrM 1050 G 3 .., III 0 0 0 0 3 -chrM 1051 T 3 .., III 0 0 0 0 3 -chrM 1052 G 3 .., III 0 0 0 0 3 -chrM 1053 T 3 .., GII 0 0 0 0 3 -chrM 1054 A 3 .., III 0 0 0 0 3 -chrM 1055 G 3 .., :II 0 0 0 0 3 -chrM 1056 C 3 ..a HI% 0 0 0 0 2 -chrM 1057 T 3 .., III 0 0 0 0 3 -chrM 1058 T 3 .., III 0 0 0 0 3 -chrM 1059 A 3 .., BII 0 0 0 0 3 -chrM 1060 A 3 .., GII 0 0 0 0 3 -chrM 1061 A 3 .., HII 0 0 0 0 3 -chrM 1062 C 3 .., III 0 0 0 0 3 -chrM 1063 A 3 .., DII 0 0 0 0 3 -chrM 1064 A 3 .., BII 0 0 0 0 3 -chrM 1065 A 3 .., 1II 0 0 0 0 2 -chrM 1066 G 3 .$., &II 0 0 0 0 2 +chrM 416 G 5 ...,^:, II?7: 0 0 5 0 5 +chrM 417 T 5 ...,, ;IIE@ 0 0 0 5 5 +chrM 418 A 5 ...,, IIIII 5 0 0 0 5 +chrM 419 A 5 ...,, IIIII 5 0 0 0 5 +chrM 420 A 5 ...,, FIIII 5 0 0 0 5 +chrM 421 A 5 ...,, IIIII 5 0 0 0 5 +chrM 422 A 5 ...,, >IIII 5 0 0 0 5 +chrM 423 G 6 ...,,^:, HII/I, 0 0 4 0 4 +chrM 424 C 6 .$..a,, ;II-I: 0 5 0 0 5 +chrM 425 T 5 .$.,,, IIIIF 0 0 0 5 5 +chrM 426 A 5 .,,,^:, III@I 5 0 0 0 5 +chrM 427 C 5 .,,,, III$I 0 4 0 0 4 +chrM 428 A 5 .,,,, IIIII 5 0 0 0 5 +chrM 429 A 5 .,,,, IIII. 4 0 0 0 4 +chrM 430 C 5 .,,,a I%I5' 0 3 0 0 3 +chrM 431 C 5 .,,,, I(I5< 0 4 0 0 4 +chrM 432 A 5 .,,,, IIIII 5 0 0 0 5 +chrM 433 A 5 .,,,, 0IIII 4 0 0 0 4 +chrM 434 A 5 .,,,, =IIII 5 0 0 0 5 +chrM 435 G 5 .$,,,, EIIII 0 0 5 0 5 +chrM 436 T 4 ,,,, III5 0 0 0 4 4 +chrM 437 A 4 ,,,, IIII 4 0 0 0 4 +chrM 438 A 4 ,,,, IIII 4 0 0 0 4 +chrM 439 A 4 ,,,, IIII 4 0 0 0 4 +chrM 440 A 4 ,,,, IIIF 4 0 0 0 4 +chrM 441 T 6 ,,,,^:.^:. III;II 0 0 0 6 6 +chrM 442 A 6 ,,,,.. IIIIII 6 0 0 0 6 +chrM 443 G 6 ,,,,.. IIIIII 0 0 6 0 6 +chrM 444 A 6 ,,,,.. IIIIII 6 0 0 0 6 +chrM 445 C 6 ,,,,.. IIIIII 0 6 0 0 6 +chrM 446 T 6 ,$,,,.. IIIIII 0 0 0 6 6 +chrM 447 A 5 ,,,.. IIIII 5 0 0 0 5 +chrM 448 C 5 ,,,.. IIIII 0 5 0 0 5 +chrM 449 G 6 ,,,..^:, IIIII6 0 0 6 0 6 +chrM 450 A 6 ,,,.., IIIIII 6 0 0 0 6 +chrM 451 A 6 ,$,,.., IIIIII 6 0 0 0 6 +chrM 452 A 5 ,,.., IIIII 5 0 0 0 5 +chrM 453 G 5 ,,.., IIIII 0 0 5 0 5 +chrM 454 T 6 ,,..,^:, IIIIII 0 0 0 6 6 +chrM 455 G 6 ,,..,, IIIIII 0 0 6 0 6 +chrM 456 A 6 ,,..,, IIIIII 6 0 0 0 6 +chrM 457 C 6 ,,..,, IIIII= 0 6 0 0 6 +chrM 458 T 6 ,$,..,, IIIIII 0 0 0 6 6 +chrM 459 T 5 ,..,, IIIII 0 0 0 5 5 +chrM 460 T 5 ,..,, IIIII 0 0 0 5 5 +chrM 461 A 5 ,$..,, IIIII 5 0 0 0 5 +chrM 462 A 4 ..,, IIII 4 0 0 0 4 +chrM 463 T 4 ..,, IIIC 0 0 0 4 4 +chrM 464 A 4 ..,, IIII 4 0 0 0 4 +chrM 465 C 4 ..,, IIII 0 4 0 0 4 +chrM 466 C 4 ..,, IIII 0 4 0 0 4 +chrM 467 T 4 ..,, II>? 0 0 0 4 4 +chrM 468 C 4 ..,, IIII 0 4 0 0 4 +chrM 469 T 4 ..,, IIIG 0 0 0 4 4 +chrM 470 G 4 ..,, %III 0 0 3 0 3 +chrM 471 A 4 ..,, 4;II 3 0 0 0 3 +chrM 472 C 4 ..,, II3I 0 3 0 0 3 +chrM 473 T 4 ..,, IIII 0 0 0 4 4 +chrM 474 A 4 ..,, ;III 4 0 0 0 4 +chrM 475 C 4 ..,, IIII 0 4 0 0 4 +chrM 476 A 4 .$.$,, 32II 2 0 0 0 2 +chrM 480 T 3 ,,^:. III 0 0 0 3 3 +chrM 481 A 3 ,,. III 3 0 0 0 3 +chrM 482 G 3 ,,. III 0 0 3 0 3 +chrM 483 C 4 ,,.^:, IIIE 0 4 0 0 4 +chrM 484 T 4 ,$,., III9 0 0 0 4 4 +chrM 485 A 3 ,., III 3 0 0 0 3 +chrM 486 A 3 ,., III 3 0 0 0 3 +chrM 487 G 3 ,., III 0 0 3 0 3 +chrM 488 A 3 ,., III 3 0 0 0 3 +chrM 489 C 3 ,$., III 0 3 0 0 3 +chrM 510 C 3 .,^:. III 0 3 0 0 3 +chrM 511 C 3 .,. III 0 3 0 0 3 +chrM 512 A 3 .,. 6II 3 0 0 0 3 +chrM 513 C 3 .,. III 0 3 0 0 3 +chrM 514 T 3 .,. III 0 0 0 3 3 +chrM 515 A 3 .$,. III 3 0 0 0 3 +chrM 518 C 3 ,$.^:. III 0 3 0 0 3 +chrM 520 T 3 ..^:, III 0 0 0 3 3 +chrM 521 A 3 .., III 3 0 0 0 3 +chrM 522 G 3 .., II, 0 0 2 0 2 +chrM 523 C 3 .., III 0 3 0 0 3 +chrM 524 C 3 .., II7 0 3 0 0 3 +chrM 525 C 3 .., III 0 3 0 0 3 +chrM 526 T 3 .., II? 0 0 0 3 3 +chrM 527 A 3 .., III 3 0 0 0 3 +chrM 528 A 3 .., III 3 0 0 0 3 +chrM 529 A 3 .., FII 3 0 0 0 3 +chrM 530 C 3 .., II+ 0 2 0 0 2 +chrM 531 T 3 .., III 0 0 0 3 3 +chrM 532 A 3 .., :II 3 0 0 0 3 +chrM 533 A 3 .., DGI 3 0 0 0 3 +chrM 534 A 3 .., III 3 0 0 0 3 +chrM 535 A 3 .., ?CI 3 0 0 0 3 +chrM 536 T 3 .., III 0 0 0 3 3 +chrM 537 A 3 .., 9II 3 0 0 0 3 +chrM 538 G 3 .., III 0 0 3 0 3 +chrM 539 C 3 .., III 0 3 0 0 3 +chrM 540 T 3 .., III 0 0 0 3 3 +chrM 541 T 3 .., III 0 0 0 3 3 +chrM 542 A 4 ..,^:. IIII 4 0 0 0 4 +chrM 543 C 4 ..,. IIII 0 4 0 0 4 +chrM 544 C 4 ..,. IIII 0 4 0 0 4 +chrM 545 A 4 N$.,. "III 3 0 0 0 3 +chrM 546 C 3 .,. III 0 3 0 0 3 +chrM 547 A 3 .,. DII 3 0 0 0 3 +chrM 548 A 3 .,. EII 3 0 0 0 3 +chrM 549 C 3 .,. III 0 3 0 0 3 +chrM 550 A 3 .,. III 3 0 0 0 3 +chrM 551 A 3 .,. 6II 3 0 0 0 3 +chrM 552 A 3 .,. GII 3 0 0 0 3 +chrM 553 G 3 .$,. ?II 0 0 3 0 3 +chrM 577 A 3 .$.^:. III 3 0 0 0 3 +chrM 580 A 3 ..^:, III 3 0 0 0 3 +chrM 581 G 3 .., III 0 0 3 0 3 +chrM 582 C 3 .., II? 0 3 0 0 3 +chrM 583 C 3 ..a II- 0 2 0 0 2 +chrM 584 T 3 .., IIH 0 0 0 3 3 +chrM 585 A 3 .., III 3 0 0 0 3 +chrM 586 A 3 .., III 3 0 0 0 3 +chrM 587 A 4 ..,^:, IIII 4 0 0 0 4 +chrM 588 A 4 ..,, IIII 4 0 0 0 4 +chrM 589 C 4 ..,, IIII 0 4 0 0 4 +chrM 590 T 4 ..,, II.5 0 0 0 3 3 +chrM 591 C 4 .$.,, II<I 0 4 0 0 4 +chrM 592 A 3 .,, III 3 0 0 0 3 +chrM 593 A 3 .,, III 3 0 0 0 3 +chrM 594 A 3 .,, III 3 0 0 0 3 +chrM 595 G 3 .,, III 0 0 3 0 3 +chrM 596 G 3 .,, III 0 0 3 0 3 +chrM 597 A 3 .,, :EI 3 0 0 0 3 +chrM 598 C 3 .,, III 0 3 0 0 3 +chrM 599 T 4 .,,^:. II@I 0 0 0 4 4 +chrM 600 T 4 .,,. IIII 0 0 0 4 4 +chrM 601 G 4 .,,. IIII 0 0 4 0 4 +chrM 602 G 4 .,,. IIII 0 0 4 0 4 +chrM 603 C 4 .,,. IIII 0 4 0 0 4 +chrM 604 G 4 .,,. IIII 0 0 4 0 4 +chrM 605 G 4 .,,. IIII 0 0 4 0 4 +chrM 606 T 4 .,,. 5III 0 0 0 4 4 +chrM 607 G 4 .,,. IIII 0 0 4 0 4 +chrM 608 C 4 .,,. *III 0 3 0 0 3 +chrM 609 T 5 .,,.^:, ?IIII 0 0 0 5 5 +chrM 610 T 5 .,,., IIII8 0 0 0 5 5 +chrM 611 T 5 .,,., IIIII 0 0 0 5 5 +chrM 612 A 5 T$,,., 3IIII 4 0 0 0 4 +chrM 613 C 4 ,,., III) 0 3 0 0 3 +chrM 614 A 4 ,,., IIII 4 0 0 0 4 +chrM 615 T 4 ,$,., IIII 0 0 0 4 4 +chrM 616 C 3 ,., III 0 3 0 0 3 +chrM 617 C 3 ,., III 0 3 0 0 3 +chrM 618 C 3 ,., III 0 3 0 0 3 +chrM 619 T 3 ,., IF9 0 0 0 3 3 +chrM 620 C 3 ,., II7 0 3 0 0 3 +chrM 621 T 3 ,., III 0 0 0 3 3 +chrM 622 A 3 ,$., I7I 3 0 0 0 3 +chrM 652 C 3 .,^:, II) 0 2 0 0 2 +chrM 653 G 3 .,, II2 0 0 2 0 2 +chrM 654 A 3 .,, III 3 0 0 0 3 +chrM 655 T 4 .,,^:. II*I 0 0 0 3 3 +chrM 656 A 4 .,,. IIII 4 0 0 0 4 +chrM 657 A 4 .,,. IIII 4 0 0 0 4 +chrM 658 A 4 .,,. IIII 4 0 0 0 4 +chrM 659 C 4 .,,. IIII 0 4 0 0 4 +chrM 660 C 4 .,,. IIII 0 4 0 0 4 +chrM 661 C 4 .,,. IIII 0 4 0 0 4 +chrM 662 C 4 .,,. IIFI 0 4 0 0 4 +chrM 663 A 4 .,,. =IDI 4 0 0 0 4 +chrM 664 C 4 .,,. II6I 0 4 0 0 4 +chrM 665 C 5 .,,.^:, IIIII 0 5 0 0 5 +chrM 666 A 5 .,,., BIIII 5 0 0 0 5 +chrM 667 T 5 .,,., II5I+ 0 0 0 4 4 +chrM 668 C 5 .,,., IIIII 0 5 0 0 5 +chrM 669 C 5 .,,., IIIII 0 5 0 0 5 +chrM 670 C 5 .,a., II.II 0 4 0 0 4 +chrM 671 T 5 .,,., IIIIA 0 0 0 5 5 +chrM 672 T 6 .,,.,^:. FI9I.I 0 0 0 5 5 +chrM 673 G 6 .,,.,. IIIIII 0 0 6 0 6 +chrM 674 C 6 .,,.,. IIIIII 0 6 0 0 6 +chrM 675 T 6 .,,.,. IIIIII 0 0 0 6 6 +chrM 676 A 6 .,,.,. ,IIEII 5 0 0 0 5 +chrM 677 A 7 .,,.,.^:. 3II;III 6 0 0 0 6 +chrM 678 T 7 .,,.,.. IIIIDII 0 0 0 7 7 +chrM 679 T 7 .,,.,.. CIIIIII 0 0 0 7 7 +chrM 680 C 7 .,,.,.. IIIIIII 0 7 0 0 7 +chrM 681 A 7 .$,,.,.. 9IIIIII 7 0 0 0 7 +chrM 682 G 6 ,,.,.. II$III 0 0 5 0 5 +chrM 683 C 6 ,,.,.. IIIIII 0 6 0 0 6 +chrM 684 C 6 ,$,.,.. IIIIII 0 6 0 0 6 +chrM 685 T 5 ,.,.. IIIII 0 0 0 5 5 +chrM 686 A 5 ,.,.. IIIII 5 0 0 0 5 +chrM 687 T 5 ,$.,.. IIIII 0 0 0 5 5 +chrM 688 A 4 .,.. IIII 4 0 0 0 4 +chrM 689 T 4 .,.. IIII 0 0 0 4 4 +chrM 690 A 4 .$,.. IIII 4 0 0 0 4 +chrM 691 C 3 ,.. III 0 3 0 0 3 +chrM 692 C 3 ,.. III 0 3 0 0 3 +chrM 693 G 4 ,..^:, IIII 0 0 4 0 4 +chrM 694 C 4 ,.., IIII 0 4 0 0 4 +chrM 695 C 4 ,.., IIII 0 4 0 0 4 +chrM 696 A 4 ,.., IIII 4 0 0 0 4 +chrM 697 T 4 ,.., IIII 0 0 0 4 4 +chrM 698 C 4 ,.., IIII 0 4 0 0 4 +chrM 699 T 4 ,.., IIII 0 0 0 4 4 +chrM 700 T 4 ,$.., IIII 0 0 0 4 4 +chrM 701 C 3 .., III 0 3 0 0 3 +chrM 702 A 3 .., III 3 0 0 0 3 +chrM 703 G 3 .., 2II 0 0 2 0 2 +chrM 704 C 3 .., III 0 3 0 0 3 +chrM 705 A 3 N., "II 2 0 0 0 2 +chrM 706 A 3 .., I5I 3 0 0 0 3 +chrM 707 A 3 .$., GII 3 0 0 0 3 +chrM 726 A 3 ,,^:. III 3 0 0 0 3 +chrM 727 G 3 ,,. III 0 0 3 0 3 +chrM 728 T 3 ,$,. III 0 0 0 3 3 +chrM 732 C 3 a.^:. $II 0 2 0 0 2 +chrM 733 A 3 ,.. III 3 0 0 0 3 +chrM 734 C 3 ,.. %II 0 2 0 0 2 +chrM 735 A 3 ,.. III 3 0 0 0 3 +chrM 736 A 3 ,.. *II 2 0 0 0 2 +chrM 737 A 3 ,.. III 3 0 0 0 3 +chrM 738 T 3 ,.. III 0 0 0 3 3 +chrM 739 A 3 ,.. III 3 0 0 0 3 +chrM 740 T 3 ,.. III 0 0 0 3 3 +chrM 741 C 3 ,.. III 0 3 0 0 3 +chrM 742 C 3 ,.. III 0 3 0 0 3 +chrM 743 A 3 ,.. III 3 0 0 0 3 +chrM 744 A 3 ,.. III 3 0 0 0 3 +chrM 745 C 3 ,.. III 0 3 0 0 3 +chrM 746 A 3 ,.. IIE 3 0 0 0 3 +chrM 747 T 3 ,.. III 0 0 0 3 3 +chrM 748 A 3 ,.. III 3 0 0 0 3 +chrM 749 A 3 ,.. III 3 0 0 0 3 +chrM 750 A 3 ,.. III 3 0 0 0 3 +chrM 751 A 3 ,.. IAI 3 0 0 0 3 +chrM 752 A 3 ,.. III 3 0 0 0 3 +chrM 753 C 3 ,.. III 0 3 0 0 3 +chrM 754 G 3 ,$.. III 0 0 3 0 3 +chrM 756 T 3 ..^:, III 0 0 0 3 3 +chrM 757 A 3 .., III 3 0 0 0 3 +chrM 758 G 3 .., III 0 0 3 0 3 +chrM 759 G 3 .., III 0 0 3 0 3 +chrM 760 T 3 .., =II 0 0 0 3 3 +chrM 761 C 3 .$., IID 0 3 0 0 3 +chrM 767 G 3 .$,^:, III 0 0 3 0 3 +chrM 769 A 3 ,,^:, III 3 0 0 0 3 +chrM 770 G 3 ,,, III 0 0 3 0 3 +chrM 771 C 3 ,,, IHI 0 3 0 0 3 +chrM 772 C 3 ,a, I)/ 0 1 0 0 1 +chrM 773 C 3 ,,, I7I 0 3 0 0 3 +chrM 774 A 4 ,,,^:. II:I 4 0 0 0 4 +chrM 775 T 4 ,,,. IH.I 0 0 0 3 3 +chrM 776 G 4 ,,,. IIII 0 0 4 0 4 +chrM 777 G 4 ,,,. IIII 0 0 4 0 4 +chrM 778 G 4 ,,,. IIII 0 0 4 0 4 +chrM 779 A 4 ,,,. IIAI 4 0 0 0 4 +chrM 780 T 4 ,,,. IIGI 0 0 0 4 4 +chrM 781 G 4 ,,,. IIII 0 0 4 0 4 +chrM 782 G 4 ,,,. IIII 0 0 4 0 4 +chrM 783 A 4 ,,,. IIII 4 0 0 0 4 +chrM 784 G 4 ,,,. IIII 0 0 4 0 4 +chrM 785 A 4 ,,,. IIII 4 0 0 0 4 +chrM 786 G 4 ,,,. IIII 0 0 4 0 4 +chrM 787 A 4 ,,,. IIII 4 0 0 0 4 +chrM 788 A 4 ,,,. IIII 4 0 0 0 4 +chrM 789 A 4 ,,,. IIII 4 0 0 0 4 +chrM 790 T 5 ,,,.^:. IIIII 0 0 0 5 5 +chrM 791 G 5 ,$,,.. IIIII 0 0 5 0 5 +chrM 792 G 4 ,,.. IIII 0 0 4 0 4 +chrM 793 G 4 ,,.. IIII 0 0 4 0 4 +chrM 794 C 4 ,,.. IIII 0 4 0 0 4 +chrM 795 T 4 ,,.. IIII 0 0 0 4 4 +chrM 796 A 4 ,,.. IIII 4 0 0 0 4 +chrM 797 C 4 ,,.. IIII 0 4 0 0 4 +chrM 798 A 4 ,,.. IIII 4 0 0 0 4 +chrM 799 T 4 ,,.. IIII 0 0 0 4 4 +chrM 800 T 4 ,,.. IIII 0 0 0 4 4 +chrM 801 T 4 ,,.. IIII 0 0 0 4 4 +chrM 802 T 4 ,$,.. IIII 0 0 0 4 4 +chrM 803 C 3 ,.. III 0 3 0 0 3 +chrM 804 T 3 ,$.. III 0 0 0 3 3 +chrM 806 C 3 ..^:. III 0 3 0 0 3 +chrM 807 C 3 ... III 0 3 0 0 3 +chrM 808 C 3 ... III 0 3 0 0 3 +chrM 809 T 3 .$.. III 0 0 0 3 3 +chrM 810 A 3 ..^:, III 3 0 0 0 3 +chrM 811 A 3 .., III 3 0 0 0 3 +chrM 812 G 3 .., II7 0 0 3 0 3 +chrM 813 A 3 .., III 3 0 0 0 3 +chrM 814 A 3 .., III 3 0 0 0 3 +chrM 815 C 3 .., III 0 3 0 0 3 +chrM 816 A 3 .., III 3 0 0 0 3 +chrM 817 A 3 .., III 3 0 0 0 3 +chrM 818 G 3 .., III 0 0 3 0 3 +chrM 819 A 3 .., III 3 0 0 0 3 +chrM 820 A 3 .., &II 2 0 0 0 2 +chrM 821 C 3 .., III 0 3 0 0 3 +chrM 822 T 3 .., III 0 0 0 3 3 +chrM 823 T 3 ..n II" 0 0 0 2 2 +chrM 824 T 3 .., III 0 0 0 3 3 +chrM 825 A 3 .$., III 3 0 0 0 3 +chrM 826 A 3 .,^:. III 3 0 0 0 3 +chrM 827 C 3 .,. III 0 3 0 0 3 +chrM 828 C 3 .,. III 0 3 0 0 3 +chrM 829 C 4 .,.^:, IIII 0 4 0 0 4 +chrM 830 G 4 .,., IIII 0 0 4 0 4 +chrM 831 G 4 .,., IIII 0 0 4 0 4 +chrM 832 A 4 .,., IIII 4 0 0 0 4 +chrM 833 C 4 .,., IIII 0 4 0 0 4 +chrM 834 G 4 .,., IIII 0 0 4 0 4 +chrM 835 A 4 .,., IIII 4 0 0 0 4 +chrM 836 A 4 .,., 8III 4 0 0 0 4 +chrM 837 A 4 .,., IIII 4 0 0 0 4 +chrM 838 G 4 .,., IIII 0 0 4 0 4 +chrM 839 T 5 .,.,^:, 4:IIG 0 0 0 4 4 +chrM 840 C 5 .,.,, IIIII 0 5 0 0 5 +chrM 841 T 5 .$,.,, IIIII 0 0 0 5 5 +chrM 842 C 4 ,.,, IIII 0 4 0 0 4 +chrM 843 C 4 ,.,, IIII 0 4 0 0 4 +chrM 844 A 4 ,.,, IIII 4 0 0 0 4 +chrM 845 T 4 ,$.,, IIII 0 0 0 4 4 +chrM 846 G 3 .,, @II 0 0 3 0 3 +chrM 847 A 3 .,, III 3 0 0 0 3 +chrM 848 A 3 .,, III 3 0 0 0 3 +chrM 849 A 3 .,, III 3 0 0 0 3 +chrM 850 C 3 .,, III 0 3 0 0 3 +chrM 851 T 3 .,, III 0 0 0 3 3 +chrM 852 G 3 .,, III 0 0 3 0 3 +chrM 853 G 3 .,, III 0 0 3 0 3 +chrM 854 A 3 .,, EII 3 0 0 0 3 +chrM 855 G 3 .,, DII 0 0 3 0 3 +chrM 856 A 3 .,, III 3 0 0 0 3 +chrM 857 C 3 .,, III 0 3 0 0 3 +chrM 858 T 4 .,,^:, IIIA 0 0 0 4 4 +chrM 859 A 4 .,,, @III 4 0 0 0 4 +chrM 860 A 4 .,,, IIII 4 0 0 0 4 +chrM 861 A 4 .$,,, EIII 4 0 0 0 4 +chrM 862 G 3 ,,, III 0 0 3 0 3 +chrM 863 G 3 ,,, III 0 0 3 0 3 +chrM 864 A 3 ,$,, III 3 0 0 0 3 +chrM 905 C 3 ,.^:, III 0 3 0 0 3 +chrM 906 A 3 ,., III 3 0 0 0 3 +chrM 907 G 3 ,., III 0 0 3 0 3 +chrM 908 G 3 ,., III 0 0 3 0 3 +chrM 909 C 3 ,., III 0 3 0 0 3 +chrM 910 C 3 ,., III 0 3 0 0 3 +chrM 911 A 4 ,.,^:, IIII 4 0 0 0 4 +chrM 912 T 4 ,.,, IIEG 0 0 0 4 4 +chrM 913 G 4 ,.,, III: 0 0 4 0 4 +chrM 914 A 4 ,.,, IIII 4 0 0 0 4 +chrM 915 A 4 ,.,, IIII 4 0 0 0 4 +chrM 916 G 4 ,.,, III5 0 0 4 0 4 +chrM 917 C 4 ,.,, III5 0 4 0 0 4 +chrM 918 G 4 ,.,, IIII 0 0 4 0 4 +chrM 919 C 4 ,.,, III< 0 4 0 0 4 +chrM 920 G 4 ,.,, IIII 0 0 4 0 4 +chrM 921 C 4 ,.,, IIII 0 4 0 0 4 +chrM 922 A 4 ,.,, IIII 4 0 0 0 4 +chrM 923 C 4 ,.,, III8 0 4 0 0 4 +chrM 924 A 4 ,.,, IFII 4 0 0 0 4 +chrM 925 C 4 ,.,, IIII 0 4 0 0 4 +chrM 926 A 4 ,.,, IIII 4 0 0 0 4 +chrM 927 C 4 ,.,, IIII 0 4 0 0 4 +chrM 928 C 5 ,.,,^:, IIII: 0 5 0 0 5 +chrM 929 G 5 ,.,,, IIIE: 0 0 5 0 5 +chrM 930 C 5 ,.,,, IIIII 0 5 0 0 5 +chrM 931 C 5 ,.,,, IIIIF 0 5 0 0 5 +chrM 932 C 5 ,.,,, IIIIC 0 5 0 0 5 +chrM 933 G 5 ,$.,,, I?II: 0 0 5 0 5 +chrM 934 T 4 .$,,, 4II> 0 0 0 3 3 +chrM 935 C 3 ,,, III 0 3 0 0 3 +chrM 936 A 3 ,,, III 3 0 0 0 3 +chrM 937 C 3 ,,, II1 0 2 0 0 2 +chrM 938 C 3 ,,, III 0 3 0 0 3 +chrM 939 C 3 ,,, III 0 3 0 0 3 +chrM 940 T 3 ,$,, III 0 0 0 3 3 +chrM 958 C 3 ,.^:. III 0 3 0 0 3 +chrM 959 A 3 ,.. III 3 0 0 0 3 +chrM 960 T 3 ,.. III 0 0 0 3 3 +chrM 961 A 3 ,.. III 3 0 0 0 3 +chrM 962 A 3 ,.. III 3 0 0 0 3 +chrM 963 C 4 ,$..^:. IIII 0 4 0 0 4 +chrM 964 A 3 ... I(; 2 0 0 0 2 +chrM 965 T 3 ... III 0 0 0 3 3 +chrM 966 A 4 ...^:. IIII 4 0 0 0 4 +chrM 967 A 4 .... IIII 4 0 0 0 4 +chrM 968 C 4 .... IEII 0 4 0 0 4 +chrM 969 A 4 .... IIII 4 0 0 0 4 +chrM 970 T 4 .... IIII 0 0 0 4 4 +chrM 971 A 4 .... IIII 4 0 0 0 4 +chrM 972 A 4 .... IIII 4 0 0 0 4 +chrM 973 A 4 .... II0I 3 0 0 0 3 +chrM 974 A 5 ....^:. IIIII 5 0 0 0 5 +chrM 975 C 5 ..... IIIII 0 5 0 0 5 +chrM 976 C 5 ..... IIIII 0 5 0 0 5 +chrM 977 G 5 ..... IIIII 0 0 5 0 5 +chrM 978 T 5 ..... IIIII 0 0 0 5 5 +chrM 979 G 5 ..... I0III 0 0 4 0 4 +chrM 980 A 5 ..... IIII4 4 0 0 0 4 +chrM 981 C 5 ..... IIIII 0 5 0 0 5 +chrM 982 C 5 ..... IIIII 0 5 0 0 5 +chrM 983 C 5 ..... IIIII 0 5 0 0 5 +chrM 984 A 5 ..... -IGII 4 0 0 0 4 +chrM 985 A 5 ..... 4GIII 4 0 0 0 4 +chrM 986 A 5 ..... BDGII 5 0 0 0 5 +chrM 987 C 5 ..... IDIII 0 5 0 0 5 +chrM 988 A 5 ..... @<III 5 0 0 0 5 +chrM 989 T 5 ..... IIIII 0 0 0 5 5 +chrM 990 A 5 .$.... I@III 5 0 0 0 5 +chrM 991 T 4 .... IICI 0 0 0 4 4 +chrM 992 G 4 T... )III 0 0 3 0 3 +chrM 993 A 4 .$... ?ICI 4 0 0 0 4 +chrM 994 A 3 ... III 3 0 0 0 3 +chrM 995 A 3 ... III 3 0 0 0 3 +chrM 996 G 3 ... III 0 0 3 0 3 +chrM 997 G 3 ... III 0 0 3 0 3 +chrM 998 A 3 .$.. 4II 2 0 0 0 2 +chrM 999 G 3 ..^:. III 0 0 3 0 3 +chrM 1000 A 3 ... III 3 0 0 0 3 +chrM 1001 C 3 .$.. III 0 3 0 0 3 +chrM 1043 A 3 ..^:, III 3 0 0 0 3 +chrM 1044 A 3 .., III 3 0 0 0 3 +chrM 1045 C 3 .., II7 0 3 0 0 3 +chrM 1046 C 3 .., II- 0 2 0 0 2 +chrM 1047 A 3 .., III 3 0 0 0 3 +chrM 1048 A 3 .., III 3 0 0 0 3 +chrM 1049 A 3 .., III 3 0 0 0 3 +chrM 1050 G 3 .., III 0 0 3 0 3 +chrM 1051 T 3 .., III 0 0 0 3 3 +chrM 1052 G 3 .., III 0 0 3 0 3 +chrM 1053 T 3 .., GII 0 0 0 3 3 +chrM 1054 A 3 .., III 3 0 0 0 3 +chrM 1055 G 3 .., :II 0 0 3 0 3 +chrM 1056 C 3 ..a HI% 0 2 0 0 2 +chrM 1057 T 3 .., III 0 0 0 3 3 +chrM 1058 T 3 .., III 0 0 0 3 3 +chrM 1059 A 3 .., BII 3 0 0 0 3 +chrM 1060 A 3 .., GII 3 0 0 0 3 +chrM 1061 A 3 .., HII 3 0 0 0 3 +chrM 1062 C 3 .., III 0 3 0 0 3 +chrM 1063 A 3 .., DII 3 0 0 0 3 +chrM 1064 A 3 .., BII 3 0 0 0 3 +chrM 1065 A 3 .., 1II 2 0 0 0 2 +chrM 1066 G 3 .$., &II 0 0 2 0 2 diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.6col.20-3-yes-no.pileup.out --- a/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,2 +1,2 @@ -chrM 270 C 4 a... ;III 1 0 0 0 4 +chrM 270 C 4 a... ;III 1 3 0 0 4 chrM 415 C 4 TTTt III7 0 0 0 4 4 diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.6col.20-3-yes-yes.pileup.out --- a/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Thu Jan 14 11:26:08 2010 -0500 +++ b/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Thu Jan 14 14:07:05 2010 -0500 @@ -1,2 +1,2 @@ -chrM 269 270 C 4 a... ;III 1 0 0 0 4 +chrM 269 270 C 4 a... ;III 1 3 0 0 4 chrM 414 415 C 4 TTTt III7 0 0 0 4 4 diff -r 517bd810a6b2 -r be8f54671d56 tools/samtools/pileup_parser.pl --- a/tools/samtools/pileup_parser.pl Thu Jan 14 11:26:08 2010 -0500 +++ b/tools/samtools/pileup_parser.pl Thu Jan 14 14:07:05 2010 -0500 @@ -65,7 +65,9 @@ { $SNPs_exist = 1; $SNPs{ uc( $bases[ $base ] ) } += 1; - } + } elsif ( $bases[ $base ] =~ m/[\.,]/ ) { + $SNPs{ uc( $fields[ $ref_base_column ] ) } += 1; + } } } diff -r 517bd810a6b2 -r be8f54671d56 tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Jan 14 11:26:08 2010 -0500 +++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:07:05 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="pileup_parser" name="Filter pileup"> +<tool id="pileup_parser" name="Filter pileup" version="1.0.1">> <description>on coverage and SNPs</description> <command interpreter="perl"> #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 @@ -189,7 +189,7 @@ you will get:: - chrM 413 G 4 ..t, IIIH 0 0 0 1 3 + chrM 413 G 4 ..t, IIIH 0 0 2 1 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 where:: @@ -211,7 +211,7 @@ and if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column:: - chrM 412 413 G 4 ..t, III2 0 0 0 1 3 + chrM 412 413 G 4 ..t, III2 0 0 2 1 3 chrM 414 415 C 4 TTTt III7 0 0 0 4 4 where::

1 0