[hg] galaxy 3240: Modification of pileup filter behavior, bases ... - galaxy-dev

23 Jan 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/be8f54671d56
changeset: 3240:be8f54671d56
user:      Anton Nekrutenko anton@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/>
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-    </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>
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+
+<div class="previous" id="previous">
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+	                   <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">
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+                <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>
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+	                   <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$</b></small></p>
+</div>
+</div>
 </body>
 </html>
diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out
--- a/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out	Thu Jan 14 11:26:08 2010 -0500
+++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out	Thu Jan 14 14:07:05 2010 -0500
@@ -1,86 +1,86 @@
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diff -r 517bd810a6b2 -r be8f54671d56 test-data/pileup_parser.6col.20-3-no-no.pileup.out
--- a/test-data/pileup_parser.6col.20-3-no-no.pileup.out	Thu Jan 14 11:26:08 2010 -0500
+++ b/test-data/pileup_parser.6col.20-3-no-no.pileup.out	Thu Jan 14 14:07:05 2010 -0500
@@ -1,588 +1,588 @@
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+chrM	683	C	6	,,.,..	IIIIII	0	6	0	0	6
+chrM	684	C	6	,$,.,..	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::

    