[hg] galaxy 3792: More tweaks to some snp/wga composite output t... - galaxy-commits

25 May 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/2d49a94c8d28
changeset: 3792:2d49a94c8d28
user:      fubar: ross Lazarus at gmail period com
date:      Thu May 20 12:38:35 2010 -0400
description:
More tweaks to some snp/wga composite output test comparisons - all png/pdf should be sim_size rather than lines_diff
Updated test outputs for snp/wga tools
Testing a new hgignore so welcome.html should not be overwritten
diffstat:
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py       |   119 +
 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml      |    18 +
 lib/galaxy/datatypes/genetics.py                                  |    51 +-
 static/welcome.html                                               |     6 +-
 test-data/rgtestouts/rgEigPCA/Rplots.pdf                          |    46 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R                     |     2 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html                  |    31 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf           |    50 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf |     0 
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps  |     2 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls              |     2 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt               |     6 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls               |    80 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par           |     6 +-
 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt                     |    18 +-
 test-data/rgtestouts/rgGRR/rgGRRtest1.html                        |    37 +-
 test-data/rgtestouts/rgGRR/rgGRRtest1.svg                         |   529 ++-
 test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls                   |  1562 +++++-----
 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf           |     0 
 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png           |     0 
 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf              |     0 
 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png              |     0 
 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG           |     0 
 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt         |    16 +-
 test-data/rgtestouts/rgHaploView/alljoin.pdf                      |     0 
 test-data/rgtestouts/rgHaploView/allnup.pdf                       |     0 
 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html            |    16 +-
 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG      |     0 
 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS        |    18 +-
 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS       |    14 +-
 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg             |     0 
 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf             |   182 +-
 test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls     |    36 +-
 test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls            |    72 +-
 test-data/rgtestouts/rgQC/ldp_tinywga.bed                         |     2 +-
 test-data/rgtestouts/rgQC/ldp_tinywga.bim                         |    10 +-
 test-data/rgtestouts/rgQC/ldp_tinywga.log                         |    18 +-
 test-data/rgtestouts/rgQC/rgQCtest1.html                          |   208 +-
 test-data/rgtestouts/rgQC/tinywga.het                             |    80 +-
 test-data/rgtestouts/rgQC/tinywga.log                             |     6 +-
 test-data/rgtestouts/rgQC/tinywga.prune.in                        |    10 +-
 test-data/rgtestouts/rgQC/tinywga.prune.out                       |    10 +-
 test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf                     |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg                 |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg                 |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg                 |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg                 |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg                 |     0 
 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf                   |     0 
 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg                    |     0 
 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf                    |    50 +-
 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg                |     0 
 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf                |    52 +-
 test-data/rgtestouts/rgQC/tinywga_s_het.jpg                       |     0 
 test-data/rgtestouts/rgQC/tinywga_s_het.pdf                       |   343 +-
 test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg                   |     0 
 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf                   |   182 +-
 test/functional/test_toolbox.py                                   |     2 +-
 tools/rgenetics/rgEigPCA.xml                                      |     2 +-
 tools/rgenetics/rgGRR.xml                                         |     2 +-
 tools/rgenetics/rgLDIndep.xml                                     |     4 +-
 tools/rgenetics/rgQC.xml                                          |    10 +-
 tools/rgenetics/rgutils.py                                        |    81 -
 63 files changed, 2104 insertions(+), 1887 deletions(-)
diffs (truncated from 5382 to 3000 lines):
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py	Thu May 20 12:38:35 2010 -0400
@@ -0,0 +1,119 @@
+# converter for ldreduced rgenetics datatype
+# used for grr and eigenstrat - shellfish if we get around to it
+#
+
+import os,sys,tempfile,subprocess,time
+
+from galaxy import eggs
+
+prog="pbed_ldreduced_converter.py"
+
+galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
+<!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="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+
+plinke = 'plink' 
+
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+def pruneLD(plinktasks=[],cd='./',vclbase = []):
+    """
+    """
+    fplog,plog = tempfile.mkstemp()
+    alog = []
+    alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
+    for task in plinktasks: # each is a list
+        vcl = vclbase + task
+        sto = file(plog,'w')
+        x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
+        retval = x.wait()
+        sto.close()
+        try:
+            lplog = file(plog,'r').readlines()
+            lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
+            alog += lplog
+            alog.append('\n')
+            os.unlink(plog) # no longer needed
+        except:
+            alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
+    return alog
+ 
+
+def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False,
+        winsize="60", winmove="40", r2thresh="0.1" ):
+    """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
+    """
+    ldr = basename # we store ld reduced and thinned data
+    ldreduced = os.path.join(outfpath,ldr) # note where this is going
+    outbase = os.path.join(outfpath,basename)
+    inbase = os.path.join(infpath)
+    loglines = []
+    ldbedname = '%s.bed' % ldreduced
+    bedname = '%s.bed' % basename
+    ldbedfn = os.path.join(infpath,ldbedname)
+    bedfn = os.path.join(infpath,bedname)
+    bmap = os.path.join(infpath,'%s.bim' % basename)
+    plinktasks = []
+    vclbase = [plinke,'--noweb']
+    plinktasks += [['--bfile',inbase,'--indep-pairwise %s %s %s' % (winsize,winmove,r2thresh),'--out %s' % outbase],
+            ['--bfile',inbase,'--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
+    vclbase = [plinke,'--noweb']
+    loglines = pruneLD(plinktasks=plinktasks,cd=outfpath,vclbase = vclbase)
+
+def main():
+    """
+    need to work with rgenetics composite datatypes
+    so in and out are html files with data in extrafiles path
+  <command interpreter="python">
+   pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' 
+   '$output1' '$output1.files_path' 'plink'    
+  </command>
+    """
+    nparm = 7
+    if len(sys.argv) < nparm:
+        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
+        sys.exit(1)
+    inpedfilepath = sys.argv[1]
+    base_name = os.path.split(inpedfilepath)[-1]
+    winsize = sys.argv[2]
+    winmove = sys.argv[3]
+    r2thresh = sys.argv[4]
+    outhtmlname = sys.argv[5]
+    outfilepath = sys.argv[6]
+    try:
+        os.makedirs(outfilepath)
+    except:
+        pass
+    plink = sys.argv[7]
+    makeLDreduced(base_name,infpath=inpedfilepath,outfpath=outfilepath,plinke=plink,forcerebuild=False,returnFname=False,
+        winsize=winsize,winmove=winmove,r2thresh=r2thresh)
+    f = file(outhtmlname,'w')
+    f.write(galhtmlprefix % prog)
+    flist = os.listdir(outfilepath)
+    s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+    s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name,winsize,winmove,r2thresh)
+    print '%s %s' % (s1,s2)
+    f.write('<div>%s\n%s\n<ol>' % (s1,s2))
+    for i, data in enumerate( flist ):
+        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+    f.write("</div></body></html>")
+    f.close()
+  
+
+if __name__ == "__main__":
+   main()
+
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml	Thu May 20 12:38:35 2010 -0400
@@ -0,0 +1,18 @@
+<tool id="pbed2ldindepconvert" name="Convert plink pbed to ld reduced format" version="0.01">
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- Used on the metadata edit page. -->
+  <command interpreter="python">
+   pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '60' '55' '0.1' '$output1' '$output1.files_path' 'plink'
+  </command>
+  <inputs>
+   <page>
+     <param format="pbed" name="input1" type="data" label="Choose a compressed Plink binary format genotype file"/>
+   </page>
+  </inputs>
+  <outputs>
+    <data format="ldindep" name="output1" metadata_source="input1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
+ 
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py	Wed May 19 10:28:41 2010 -0400
+++ b/lib/galaxy/datatypes/genetics.py	Thu May 20 12:38:35 2010 -0400
@@ -349,18 +349,6 @@
         return True
-class ldIndep(Rgenetics):
-    """
-    LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno
-    """
-    file_ext="ldreduced"
-
-    def __init__( self, **kwd ):
-        Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s_INDEP.bim', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s_INDEP.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s_INDEP.fam', substitute_name_with_metadata = 'base_name', is_binary = True )
-
class SNPMatrix(Rgenetics):
     """
@@ -396,8 +384,8 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False )
+        self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )
class Pphe(Rgenetics):
@@ -408,7 +396,7 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = False )
@@ -432,7 +420,8 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' )
+        self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name',
+             is_binary = False )
@@ -445,7 +434,8 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' )
+        self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name',
+              is_binary = False )
class Pbed(Rgenetics):
@@ -456,9 +446,24 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
         self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )
+
+class ldIndep(Rgenetics):
+    """
+    LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno
+    This is really a plink binary, but some tools work better with less redundancy so are constrained to
+    these files
+    """
+    file_ext="ldreduced"
+
+    def __init__( self, **kwd ):
+        Rgenetics.__init__(self, **kwd)
+        self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
+        self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )
+
class Eigenstratgeno(Rgenetics):
     """
@@ -470,9 +475,9 @@
def __init__( self, **kwd ):
         Rgenetics.__init__(self, **kwd)
-        self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = True )
-        self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True )
+        self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = False )
+        self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = False )
+        self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = False )
@@ -524,7 +529,7 @@
     def __init__( self, **kwd ):
         Html.__init__(self,**kwd)
         self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file', 
-          substitute_name_with_metadata = 'base_name', is_binary=True)
+          substitute_name_with_metadata = 'base_name', is_binary=False)
def generate_primary_file( self, dataset = None ):
         """ 
diff -r 7f95e51e06f7 -r 2d49a94c8d28 static/welcome.html
--- a/static/welcome.html	Wed May 19 10:28:41 2010 -0400
+++ b/static/welcome.html	Thu May 20 12:38:35 2010 -0400
@@ -8,12 +8,12 @@
 <body>
     <div class="document">
         <div class="warningmessagelarge">
-            <strong>Welcome to the <a href="http://rgenetics.org">Rgenetics</a> development site</strong>
+            <strong>Hello world! It's running...</strong>
             <hr>
-            This is a volatile and experimental resource - use the <a href="http://usegalaxy.org">main galaxy</a> for real research
+            To customize this page edit <code>static/welcome.html</code>
         </div>
         <br/>
-        <img src="images/Armitagep_manhattan.png" alt="One click manhattan plot anyone?" style="display: block; margin-left: auto; margin-right: auto;" />
+        <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>
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/Rplots.pdf
--- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf	Thu May 20 12:38:35 2010 -0400
@@ -2,8 +2,8 @@
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-/CreationDate (D:20100509212343)
-/ModDate (D:20100509212343)
+/CreationDate (D:20100519151448)
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@@ -34,42 +34,10 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R	Thu May 20 12:38:35 2010 -0400
@@ -16,4 +16,4 @@
 legend("top",legend=llist,pch=glist,col=glist,title="Sample")
 grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted")
 dev.off()
-#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:43
+#R script autogenerated by rgenetics/rgutils.py on 19/05/2010 15:14:48
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html	Thu May 20 12:38:35 2010 -0400
@@ -9,27 +9,30 @@
 </head>
 <body>
 <div class="document">
-<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/>
+<h4>Output from rgEigPCA.py run at 19/05/2010 15:14:48<br/>
 </h4>
-newfilepath=/share/shared/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td>
+newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td>
 <a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/>
-<div class="document">All Files:<ol><li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li>
-<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par  (338 B)</a></li>
+<div class="document">All Files:<ol><li><a href="Rplots.pdf">Rplots.pdf  (813 B)</a></li>
+<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R  (1.6 KB)</a></li>
+<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li>
 <li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt  (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt  (6.1 KB)</a></li>
-<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf  (10.4 KB)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf  (7.9 KB)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png  (27.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf  (2.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps  (13.6 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt  (257 B)</a></li>
 <li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls  (507 B)</a></li>
-<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls  (1.2 KB)</a></li>
-<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R  (1.6 KB)</a></li>
-<li><a href="Rplots.pdf">Rplots.pdf  (3.3 KB)</a></li>
+<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt  (6.0 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls  (1.3 KB)</a></li>
 <li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec  (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png  (27.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par  (311 B)</a></li>
 </ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par
 ### THE INPUT PARAMETERS
 ##PARAMETER NAME: VALUE
-genotypename: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
@@ -153,5 +156,5 @@
 Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193
 Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069
 </pre></div>If you need to rerun this analysis, the command line used was
-smartpca.perl -i /share/shared/galaxy/test-data/tinywga.ped -a /share/shared/galaxy/test-data/tinywga.map -b /share/shared/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2
+smartpca.perl -i /opt/galaxy/test-data/tinywga.bed -a /opt/galaxy/test-data/tinywga.bim -b /opt/galaxy/test-data/tinywga.fam -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2
 <p/></div></body></html>
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf	Thu May 20 12:38:35 2010 -0400
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf
Binary file test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps	Thu May 20 12:38:35 2010 -0400
@@ -1,6 +1,6 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls	Thu May 20 12:38:35 2010 -0400
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt	Thu May 20 12:38:35 2010 -0400
@@ -1,9 +1,9 @@
 parameter file: rgEigPCAtest1_pca.xls.par
 ### THE INPUT PARAMETERS
 ##PARAMETER NAME: VALUE
-genotypename: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls	Thu May 20 12:38:35 2010 -0400
@@ -3,43 +3,43 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par	Thu May 20 12:38:35 2010 -0400
@@ -1,6 +1,6 @@
-genotypename: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt
--- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt	Thu May 20 12:38:35 2010 -0400
@@ -1,14 +1,14 @@
-Reading genotypes for 40 subjects and 5 markers
+Reading genotypes for 40 subjects and 25 markers
 Calculating 780 pairs...
 Estimated time is 0.00 to 0.00 seconds ...
-T1:  0.00482821464539	T2:  0.0623338222504	T3:  0.000771522521973	TOT: 0.0691449642181	0 pairs with no (or not enough) comparable genotypes (0.0%)
-Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23
-Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22
-Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24
-Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+T1:  0.00254368782043	T2:  0.018296957016	T3:  0.000444173812866	TOT: 0.022047996521	0 pairs with no (or not enough) comparable genotypes (0.0%)
+Relstate dupe (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parentchild (n=26): mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+Relstate sibpairs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate halfsibs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parents (n=40): mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+Relstate unrelated (n=714): mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+Relstate unknown (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
 780 pairs are available of 780
 Outliers: 0
 Plotting ...
\ No newline at end of file
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1.html
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html	Thu May 20 12:38:35 2010 -0400
@@ -9,39 +9,26 @@
 </head>
 <body>
 <div class="document">
-<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br>
+<h4><div>Output from rgGRR.py run at 19/05/2010 15:14:41<br>
 </h4>
 If you need to rerun this analysis, the command line was
-<pre>'/share/shared/galaxy/tools/rgenetics/rgGRR.py' '/share/shared/galaxy/test-data/tinywga' 'tinywga' '/share/shared/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/share/shared/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6' 'true'</pre>
+<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre>
 </div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol>
 <li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li>
 <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li>
+<li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li>
 <li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li>
-<li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li>
-</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers
-
+</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers
 Calculating 780 pairs...
-
 Estimated time is 0.00 to 0.00 seconds ...
-
-T1:  0.00482821464539	T2:  0.0623338222504	T3:  0.000771522521973	TOT: 0.0691449642181	0 pairs with no (or not enough) comparable genotypes (0.0%)
-
-Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-
-Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23
-
-Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-
-Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-
-Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22
-
-Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24
-
-Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-
+T1:  0.00254368782043	T2:  0.018296957016	T3:  0.000444173812866	TOT: 0.022047996521	0 pairs with no (or not enough) comparable genotypes (0.0%)
+Relstate dupe (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parentchild (n=26): mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+Relstate sibpairs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate halfsibs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parents (n=40): mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+Relstate unrelated (n=714): mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+Relstate unknown (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
 780 pairs are available of 780
-
 Outliers: 0
-
 Plotting ...</pre><hr></div></body></html>
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1.svg
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg	Thu May 20 12:38:35 2010 -0400
@@ -17,7 +17,7 @@
           var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12};
           var dist = 12;
           var yOffset = 4;
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+
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}
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           }
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@@ -247,103 +247,492 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls	Thu May 20 12:38:35 2010 -0400
@@ -1,781 +1,781 @@
-fid1 iid1	fid2 iid2	mean	sdev	zmean	zsdev	geno	relcode
-101_1	101_2	1.400000	0.894427	1.351962	-1.627597	5	5
-101_1	101_3	1.400000	0.894427	0.105472	0.511563	5	5
-101_1	105_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	105_2	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	105_3	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	112_1	1.400000	0.894427	-0.219631	1.712469	5	5
-101_1	112_2	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	112_3	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	117_1	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	117_2	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	117_3	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	12_1	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	12_2	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	12_3	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	13_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	13_2	1.400000	0.894427	-0.219631	1.712469	5	5
-101_1	13_3	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	1334_1	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	1334_10	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1334_11	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1334_12	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1334_13	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1334_2	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1340_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1340_10	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1340_11	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1340_12	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	1340_2	1.400000	0.894427	-1.260908	-0.397216	5	5
-101_1	1340_9	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1341_1	1.400000	0.894427	0.821646	-0.397216	5	5
-101_1	1341_11	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1341_12	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_1	1341_13	1.400000	0.894427	-0.219631	1.712469	5	5
-101_1	1341_14	1.400000	0.894427	-0.219631	1.712469	5	5
-101_1	1341_2	1.400000	0.894427	-0.219631	1.712469	5	5
-101_1	1344_1	1.400000	0.894427	-1.260908	1.532838	5	5
-101_1	1344_12	1.400000	0.894427	-1.260908	-0.397216	5	5
-101_1	1344_13	1.400000	0.894427	-1.260908	-0.397216	5	5
-101_1	1345_12	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_2	101_3	1.400000	0.894427	-0.132290	0.048238	5	5
-101_2	105_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-101_2	105_2	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	105_3	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	112_1	1.400000	0.894427	0.196880	1.267018	5	5
-101_2	112_2	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	112_3	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	117_1	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	117_2	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	117_3	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	12_1	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	12_2	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	12_3	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	13_1	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	13_2	1.400000	0.894427	-0.219631	1.712469	5	5
-101_2	13_3	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	1334_1	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	1334_10	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1334_11	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1334_12	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1334_13	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1334_2	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1340_11	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	1340_2	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_2	1340_9	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-101_2	1341_11	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-101_2	1341_13	1.400000	0.894427	0.196880	1.267018	5	5
-101_2	1341_14	1.400000	0.894427	0.196880	1.267018	5	5
-101_2	1341_2	1.400000	0.894427	0.196880	1.267018	5	5
-101_2	1344_1	1.400000	0.894427	-0.636142	1.267018	5	5
-101_2	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_2	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_2	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-101_3	105_1	1.400000	0.894427	-1.260908	1.532838	5	5
-101_3	105_2	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	105_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	112_1	1.400000	0.894427	-1.469163	1.023277	5	5
-101_3	112_2	1.400000	0.894427	-2.302185	1.712469	5	5
-101_3	112_3	1.400000	0.894427	0.196880	-0.195857	5	5
-101_3	117_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	117_2	1.400000	0.894427	1.029902	-0.619941	5	5
-101_3	117_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	12_1	1.400000	0.894427	1.029902	-0.619941	5	5
-101_3	12_2	1.400000	0.894427	1.029902	-0.619941	5	5
-101_3	12_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	13_1	1.400000	0.894427	0.196880	-0.195857	5	5
-101_3	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-101_3	13_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	1334_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	1334_10	1.400000	0.894427	0.196880	-0.195857	5	5
-101_3	1334_11	1.400000	0.894427	-2.302185	1.712469	5	5
-101_3	1334_12	1.400000	0.894427	-0.636142	1.267018	5	5
-101_3	1334_13	1.400000	0.894427	-1.469163	-0.619941	5	5
-101_3	1334_2	1.400000	0.894427	-0.636142	1.267018	5	5
-101_3	1340_1	1.400000	0.894427	-1.469163	-0.619941	5	5
-101_3	1340_10	1.400000	0.894427	-1.469163	-0.619941	5	5
-101_3	1340_11	1.400000	0.894427	-1.469163	-0.619941	5	5
-101_3	1340_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	1340_2	1.400000	0.894427	-2.302185	0.476644	5	5
-101_3	1340_9	1.400000	0.894427	-0.636142	1.267018	5	5
-101_3	1341_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-101_3	1341_11	1.400000	0.894427	-2.302185	1.712469	5	5
-101_3	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-101_3	1341_13	1.400000	0.894427	-1.469163	1.023277	5	5
-101_3	1341_14	1.400000	0.894427	-1.469163	1.023277	5	5
-101_3	1341_2	1.400000	0.894427	-1.469163	1.023277	5	5
-101_3	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-101_3	1344_12	1.400000	0.894427	-2.302185	0.476644	5	5
-101_3	1344_13	1.400000	0.894427	-2.302185	0.476644	5	5
-101_3	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-105_1	105_2	1.400000	0.894427	0.105472	0.511563	5	5
-105_1	105_3	1.400000	0.894427	0.105472	0.511563	5	5
-105_1	112_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	112_2	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	112_3	1.400000	0.894427	-0.219631	1.712469	5	5
-105_1	117_1	1.400000	0.894427	-1.260908	-0.397216	5	5
-105_1	117_2	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	117_3	1.400000	0.894427	-1.260908	-0.397216	5	5
-105_1	12_1	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	12_2	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	12_3	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	13_1	1.400000	0.894427	-0.219631	1.712469	5	5
-105_1	13_2	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	13_3	1.400000	0.894427	-1.260908	-0.397216	5	5
-105_1	1334_1	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1334_10	1.400000	0.894427	-0.219631	1.712469	5	5
-105_1	1334_11	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1334_12	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	1334_13	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1334_2	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	1340_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1340_10	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1340_11	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1340_12	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1340_2	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1340_9	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	1341_1	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1341_11	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1341_12	1.400000	0.894427	-0.219631	1.712469	5	5
-105_1	1341_13	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1341_14	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1341_2	1.400000	0.894427	-0.219631	-0.070847	5	5
-105_1	1344_1	1.400000	0.894427	-1.260908	1.532838	5	5
-105_1	1344_12	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1344_13	1.400000	0.894427	0.821646	-0.397216	5	5
-105_1	1345_12	1.400000	0.894427	-0.219631	1.712469	5	5
-105_2	105_3	1.400000	0.894427	1.883560	-2.485480	5	5
-105_2	112_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	112_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	112_3	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	117_1	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	117_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	117_3	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	12_1	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	12_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	12_3	1.400000	0.894427	1.862924	-2.506901	5	5
-105_2	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	13_2	1.400000	0.894427	0.821646	-0.397216	5	5
-105_2	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1334_1	1.400000	0.894427	1.862924	-2.506901	5	5
-105_2	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1334_11	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1334_12	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1334_13	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1334_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1340_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1340_10	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1340_12	1.400000	0.894427	1.862924	-2.506901	5	5
-105_2	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1340_9	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1341_1	1.400000	0.894427	1.862924	-2.506901	5	5
-105_2	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-105_2	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-105_2	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-105_2	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	112_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	112_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	112_3	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	117_1	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	117_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	117_3	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	12_1	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	12_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	12_3	1.400000	0.894427	1.862924	-2.506901	5	5
-105_3	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	13_2	1.400000	0.894427	0.821646	-0.397216	5	5
-105_3	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1334_1	1.400000	0.894427	1.862924	-2.506901	5	5
-105_3	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1334_11	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1334_12	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1334_13	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1334_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1340_1	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1340_10	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1340_12	1.400000	0.894427	1.862924	-2.506901	5	5
-105_3	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1340_9	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1341_1	1.400000	0.894427	1.862924	-2.506901	5	5
-105_3	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-105_3	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-105_3	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-105_3	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	112_2	1.400000	0.894427	0.354770	0.285726	5	5
-112_1	112_3	1.400000	0.894427	-0.642422	0.715736	5	5
-112_1	117_1	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	117_2	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	117_3	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	12_1	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	12_2	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	12_3	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	13_1	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	13_2	1.400000	0.894427	1.862924	-2.506901	5	5
-112_1	13_3	1.400000	0.894427	-0.636142	1.267018	5	5
-112_1	1334_1	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1334_10	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1334_11	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1334_12	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1334_13	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1334_2	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1340_11	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1340_2	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_1	1340_9	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1341_11	1.400000	0.894427	1.029902	-0.619941	5	5
-112_1	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-112_1	1341_13	1.400000	0.894427	1.862924	-2.506901	5	5
-112_1	1341_14	1.400000	0.894427	1.862924	-2.506901	5	5
-112_1	1341_2	1.400000	0.894427	1.862924	-2.506901	5	5
-112_1	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-112_1	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_1	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_1	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	112_3	1.400000	0.894427	-1.140216	1.652064	5	5
-112_2	117_1	1.400000	0.894427	-1.469163	1.023277	5	5
-112_2	117_2	1.400000	0.894427	-1.469163	2.115187	5	5
-112_2	117_3	1.400000	0.894427	-1.469163	1.023277	5	5
-112_2	12_1	1.400000	0.894427	-1.469163	2.115187	5	5
-112_2	12_2	1.400000	0.894427	-1.469163	2.115187	5	5
-112_2	12_3	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	13_1	1.400000	0.894427	-0.636142	1.267018	5	5
-112_2	13_2	1.400000	0.894427	0.821646	-0.397216	5	5
-112_2	13_3	1.400000	0.894427	-1.469163	1.023277	5	5
-112_2	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1334_10	1.400000	0.894427	-0.636142	1.267018	5	5
-112_2	1334_11	1.400000	0.894427	1.862924	-2.506901	5	5
-112_2	1334_12	1.400000	0.894427	0.196880	1.267018	5	5
-112_2	1334_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_2	1334_2	1.400000	0.894427	0.196880	1.267018	5	5
-112_2	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_2	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_2	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_2	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1340_9	1.400000	0.894427	0.196880	1.267018	5	5
-112_2	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1341_11	1.400000	0.894427	1.862924	-2.506901	5	5
-112_2	1341_12	1.400000	0.894427	-0.636142	1.267018	5	5
-112_2	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-112_2	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-112_2	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-112_2	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-112_2	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-112_2	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	117_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_3	117_2	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	117_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_3	12_1	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	12_2	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	12_3	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	13_1	1.400000	0.894427	1.862924	-2.506901	5	5
-112_3	13_2	1.400000	0.894427	-0.219631	-0.070847	5	5
-112_3	13_3	1.400000	0.894427	-0.636142	-0.195857	5	5
-112_3	1334_1	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1334_10	1.400000	0.894427	1.862924	-2.506901	5	5
-112_3	1334_11	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	1334_12	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1334_13	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1334_2	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1340_11	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1340_2	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	1340_9	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-112_3	1341_11	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	1341_12	1.400000	0.894427	1.862924	-2.506901	5	5
-112_3	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-112_3	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-112_3	1344_12	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	1344_13	1.400000	0.894427	-0.636142	1.267018	5	5
-112_3	1345_12	1.400000	0.894427	1.862924	-2.506901	5	5
-117_1	117_2	1.400000	0.894427	-0.642422	0.715736	5	5
-117_1	117_3	1.400000	0.894427	1.351962	-1.627597	5	5
-117_1	12_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	12_2	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	12_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	13_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_1	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-117_1	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1334_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_1	1334_11	1.400000	0.894427	-1.469163	1.023277	5	5
-117_1	1334_12	1.400000	0.894427	-1.469163	1.023277	5	5
-117_1	1334_13	1.400000	0.894427	1.029902	-0.619941	5	5
-117_1	1334_2	1.400000	0.894427	-1.469163	1.023277	5	5
-117_1	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_1	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_1	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-117_1	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1340_9	1.400000	0.894427	-1.469163	1.023277	5	5
-117_1	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1341_11	1.400000	0.894427	-1.469163	1.023277	5	5
-117_1	1341_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_1	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-117_1	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-117_1	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-117_1	1344_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-117_1	1345_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_2	117_3	1.400000	0.894427	-0.132290	0.048238	5	5
-117_2	12_1	1.400000	0.894427	1.862924	-2.506901	5	5
-117_2	12_2	1.400000	0.894427	1.862924	-2.506901	5	5
-117_2	12_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_2	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-117_2	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-117_2	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_2	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_2	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-117_2	1334_11	1.400000	0.894427	-1.469163	2.115187	5	5
-117_2	1334_12	1.400000	0.894427	0.196880	1.267018	5	5
-117_2	1334_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_2	1334_2	1.400000	0.894427	0.196880	1.267018	5	5
-117_2	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_2	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_2	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_2	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-117_2	1340_2	1.400000	0.894427	-1.469163	1.023277	5	5
-117_2	1340_9	1.400000	0.894427	0.196880	1.267018	5	5
-117_2	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_2	1341_11	1.400000	0.894427	-1.469163	2.115187	5	5
-117_2	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-117_2	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-117_2	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-117_2	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-117_2	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-117_2	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-117_2	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-117_2	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-117_3	12_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	12_2	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	12_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	13_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_3	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-117_3	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1334_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_3	1334_11	1.400000	0.894427	-1.469163	1.023277	5	5
-117_3	1334_12	1.400000	0.894427	-1.469163	1.023277	5	5
-117_3	1334_13	1.400000	0.894427	1.029902	-0.619941	5	5
-117_3	1334_2	1.400000	0.894427	-1.469163	1.023277	5	5
-117_3	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_3	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_3	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-117_3	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1340_9	1.400000	0.894427	-1.469163	1.023277	5	5
-117_3	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1341_11	1.400000	0.894427	-1.469163	1.023277	5	5
-117_3	1341_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-117_3	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-117_3	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-117_3	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-117_3	1344_1	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-117_3	1345_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_1	12_2	1.400000	0.894427	1.351962	-1.627597	5	5
-12_1	12_3	1.400000	0.894427	-0.642422	0.715736	5	5
-12_1	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-12_1	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-12_1	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-12_1	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-12_1	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-12_1	1334_11	1.400000	0.894427	-1.469163	2.115187	5	5
-12_1	1334_12	1.400000	0.894427	0.196880	1.267018	5	5
-12_1	1334_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_1	1334_2	1.400000	0.894427	0.196880	1.267018	5	5
-12_1	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_1	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_1	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_1	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-12_1	1340_2	1.400000	0.894427	-1.469163	1.023277	5	5
-12_1	1340_9	1.400000	0.894427	0.196880	1.267018	5	5
-12_1	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-12_1	1341_11	1.400000	0.894427	-1.469163	2.115187	5	5
-12_1	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-12_1	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-12_1	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-12_1	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-12_1	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-12_1	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-12_1	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-12_1	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-12_2	12_3	1.400000	0.894427	-0.132290	0.048238	5	5
-12_2	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-12_2	13_2	1.400000	0.894427	-1.260908	1.532838	5	5
-12_2	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-12_2	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-12_2	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-12_2	1334_11	1.400000	0.894427	-1.469163	2.115187	5	5
-12_2	1334_12	1.400000	0.894427	0.196880	1.267018	5	5
-12_2	1334_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_2	1334_2	1.400000	0.894427	0.196880	1.267018	5	5
-12_2	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_2	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_2	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-12_2	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-12_2	1340_2	1.400000	0.894427	-1.469163	1.023277	5	5
-12_2	1340_9	1.400000	0.894427	0.196880	1.267018	5	5
-12_2	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-12_2	1341_11	1.400000	0.894427	-1.469163	2.115187	5	5
-12_2	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-12_2	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-12_2	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-12_2	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-12_2	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-12_2	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-12_2	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-12_2	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	13_1	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	13_2	1.400000	0.894427	0.821646	-0.397216	5	5
-12_3	13_3	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1334_1	1.400000	0.894427	1.862924	-2.506901	5	5
-12_3	1334_10	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1334_11	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1334_12	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1334_13	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1334_2	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1340_1	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1340_10	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1340_12	1.400000	0.894427	1.862924	-2.506901	5	5
-12_3	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1340_9	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1341_1	1.400000	0.894427	1.862924	-2.506901	5	5
-12_3	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-12_3	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-12_3	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-12_3	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	13_2	1.400000	0.894427	-1.141018	0.842492	5	5
-13_1	13_3	1.400000	0.894427	-1.639614	0.715736	5	5
-13_1	1334_1	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1334_10	1.400000	0.894427	1.862924	-2.506901	5	5
-13_1	1334_11	1.400000	0.894427	-0.636142	1.267018	5	5
-13_1	1334_12	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1334_13	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1334_2	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1340_11	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1340_2	1.400000	0.894427	-0.636142	1.267018	5	5
-13_1	1340_9	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-13_1	1341_11	1.400000	0.894427	-0.636142	1.267018	5	5
-13_1	1341_12	1.400000	0.894427	1.862924	-2.506901	5	5
-13_1	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-13_1	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-13_1	1344_12	1.400000	0.894427	-0.636142	1.267018	5	5
-13_1	1344_13	1.400000	0.894427	-0.636142	1.267018	5	5
-13_1	1345_12	1.400000	0.894427	1.862924	-2.506901	5	5
-13_2	13_3	1.400000	0.894427	-1.896159	1.943496	5	5
-13_2	1334_1	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1334_10	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1334_11	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1334_12	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1334_13	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1334_2	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1340_1	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1340_10	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1340_11	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1340_12	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1340_2	1.400000	0.894427	-1.260908	-0.397216	5	5
-13_2	1340_9	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1341_1	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1341_11	1.400000	0.894427	0.821646	-0.397216	5	5
-13_2	1341_12	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_2	1341_13	1.400000	0.894427	1.862924	-2.506901	5	5
-13_2	1341_14	1.400000	0.894427	1.862924	-2.506901	5	5
-13_2	1341_2	1.400000	0.894427	1.862924	-2.506901	5	5
-13_2	1344_1	1.400000	0.894427	-3.343462	1.532838	5	5
-13_2	1344_12	1.400000	0.894427	-1.260908	-0.397216	5	5
-13_2	1344_13	1.400000	0.894427	-1.260908	-0.397216	5	5
-13_2	1345_12	1.400000	0.894427	-0.219631	-0.070847	5	5
-13_3	1334_1	1.400000	0.894427	0.196880	-0.195857	5	5
-13_3	1334_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-13_3	1334_11	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1334_12	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1334_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-13_3	1334_2	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1340_1	1.400000	0.894427	1.029902	-0.619941	5	5
-13_3	1340_10	1.400000	0.894427	1.029902	-0.619941	5	5
-13_3	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-13_3	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-13_3	1340_2	1.400000	0.894427	-1.469163	-0.619941	5	5
-13_3	1340_9	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-13_3	1341_11	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1341_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-13_3	1341_13	1.400000	0.894427	-0.636142	1.267018	5	5
-13_3	1341_14	1.400000	0.894427	-0.636142	1.267018	5	5
-13_3	1341_2	1.400000	0.894427	-0.636142	1.267018	5	5
-13_3	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-13_3	1344_12	1.400000	0.894427	-1.469163	-0.619941	5	5
-13_3	1344_13	1.400000	0.894427	-1.469163	-0.619941	5	5
-13_3	1345_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_1	1334_10	1.400000	0.894427	0.354770	0.285726	5	5
-1334_1	1334_11	1.400000	0.894427	-0.642422	0.715736	5	5
-1334_1	1334_12	1.400000	0.894427	-0.132290	0.048238	5	5
-1334_1	1334_13	1.400000	0.894427	0.875635	-0.416708	5	5
-1334_1	1334_2	1.400000	0.894427	-0.132290	0.048238	5	5
-1334_1	1340_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1340_10	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1340_11	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1340_12	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_1	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_1	1340_9	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_1	1341_1	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_1	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_1	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_1	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_1	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_1	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_1	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_10	1334_11	1.400000	0.894427	-1.140216	1.652064	5	5
-1334_10	1334_12	1.400000	0.894427	0.875635	-0.416708	5	5
-1334_10	1334_13	1.400000	0.894427	-0.132290	0.048238	5	5
-1334_10	1334_2	1.400000	0.894427	0.875635	-0.416708	5	5
-1334_10	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1340_11	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_10	1340_2	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_10	1340_9	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_10	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_10	1341_11	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_10	1341_12	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_10	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_10	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-1334_10	1344_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_10	1344_13	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_10	1345_12	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_11	1334_12	1.400000	0.894427	-0.132290	1.652064	5	5
-1334_11	1334_13	1.400000	0.894427	-1.140216	0.048238	5	5
-1334_11	1334_2	1.400000	0.894427	-0.132290	1.652064	5	5
-1334_11	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_11	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_11	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_11	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_11	1340_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_11	1340_9	1.400000	0.894427	0.196880	1.267018	5	5
-1334_11	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_11	1341_11	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_11	1341_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_11	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_11	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_11	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_11	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-1334_11	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_11	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_11	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1334_12	1334_13	1.400000	0.894427	-1.140216	0.048238	5	5
-1334_12	1334_2	1.400000	0.894427	1.351962	-1.627597	5	5
-1334_12	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_12	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_12	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_12	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_12	1340_2	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_12	1340_9	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_12	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_12	1341_11	1.400000	0.894427	0.196880	1.267018	5	5
-1334_12	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_12	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_12	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_12	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_12	1344_1	1.400000	0.894427	-3.135207	2.115187	5	5
-1334_12	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_12	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_12	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1334_2	1.400000	0.894427	-1.639614	0.715736	5	5
-1334_13	1340_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1340_10	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1340_11	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_13	1340_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1340_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1340_9	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_13	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1341_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_13	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_13	1344_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_13	1344_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1344_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_13	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_2	1340_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_2	1340_10	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_2	1340_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1334_2	1340_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_2	1340_2	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_2	1340_9	1.400000	0.894427	1.862924	-2.506901	5	5
-1334_2	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1334_2	1341_11	1.400000	0.894427	0.196880	1.267018	5	5
-1334_2	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_2	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_2	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_2	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1334_2	1344_1	1.400000	0.894427	-3.135207	2.115187	5	5
-1334_2	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_2	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-1334_2	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_1	1340_10	1.400000	0.894427	1.351962	-1.627597	5	5
-1340_1	1340_11	1.400000	0.894427	-0.132290	0.048238	5	5
-1340_1	1340_12	1.400000	0.894427	0.875635	-0.416708	5	5
-1340_1	1340_2	1.400000	0.894427	-1.140216	0.048238	5	5
-1340_1	1340_9	1.400000	0.894427	-1.639614	0.715736	5	5
-1340_1	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_1	1341_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_1	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_1	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_1	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_1	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_1	1344_1	1.400000	0.894427	-2.302185	0.476644	5	5
-1340_1	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_1	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_1	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_10	1340_11	1.400000	0.894427	-0.132290	0.048238	5	5
-1340_10	1340_12	1.400000	0.894427	0.875635	-0.416708	5	5
-1340_10	1340_2	1.400000	0.894427	-1.140216	0.048238	5	5
-1340_10	1340_9	1.400000	0.894427	-1.140216	0.048238	5	5
-1340_10	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_10	1341_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_10	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_10	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_10	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_10	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_10	1344_1	1.400000	0.894427	-2.302185	0.476644	5	5
-1340_10	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_10	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_10	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_11	1340_12	1.400000	0.894427	0.875635	-0.416708	5	5
-1340_11	1340_2	1.400000	0.894427	0.354770	0.285726	5	5
-1340_11	1340_9	1.400000	0.894427	-1.140216	0.048238	5	5
-1340_11	1341_1	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_11	1341_11	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_11	1341_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_11	1341_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_11	1341_14	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_11	1341_2	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_11	1344_1	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_11	1344_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_11	1344_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_11	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_12	1340_2	1.400000	0.894427	-0.642422	0.715736	5	5
-1340_12	1340_9	1.400000	0.894427	-0.132290	0.048238	5	5
-1340_12	1341_1	1.400000	0.894427	1.862924	-2.506901	5	5
-1340_12	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_12	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_12	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_12	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_12	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_12	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-1340_12	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_12	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_12	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_2	1340_9	1.400000	0.894427	-2.148141	1.384838	5	5
-1340_2	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_2	1341_11	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_2	1341_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1340_2	1341_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_2	1341_14	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_2	1341_2	1.400000	0.894427	-0.636142	-0.195857	5	5
-1340_2	1344_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_2	1344_12	1.400000	0.894427	1.862924	-2.506901	5	5
-1340_2	1344_13	1.400000	0.894427	1.862924	-2.506901	5	5
-1340_2	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1340_9	1341_1	1.400000	0.894427	0.196880	-0.195857	5	5
-1340_9	1341_11	1.400000	0.894427	0.196880	1.267018	5	5
-1340_9	1341_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_9	1341_13	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_9	1341_14	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_9	1341_2	1.400000	0.894427	1.029902	-0.619941	5	5
-1340_9	1344_1	1.400000	0.894427	-3.135207	2.115187	5	5
-1340_9	1344_12	1.400000	0.894427	-1.469163	1.023277	5	5
-1340_9	1344_13	1.400000	0.894427	-1.469163	1.023277	5	5
-1340_9	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1341_1	1341_11	1.400000	0.894427	-0.642422	0.715736	5	5
-1341_1	1341_12	1.400000	0.894427	0.354770	0.285726	5	5
-1341_1	1341_13	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_1	1341_14	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_1	1341_2	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_1	1344_1	1.400000	0.894427	-1.469163	1.023277	5	5
-1341_1	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_1	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_1	1345_12	1.400000	0.894427	1.029902	-0.619941	5	5
-1341_11	1341_12	1.400000	0.894427	-1.140216	1.652064	5	5
-1341_11	1341_13	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_11	1341_14	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_11	1341_2	1.400000	0.894427	0.875635	-0.416708	5	5
-1341_11	1344_1	1.400000	0.894427	-1.469163	2.115187	5	5
-1341_11	1344_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_11	1344_13	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_11	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1341_12	1341_13	1.400000	0.894427	-0.132290	0.048238	5	5
-1341_12	1341_14	1.400000	0.894427	-0.132290	0.048238	5	5
-1341_12	1341_2	1.400000	0.894427	-0.132290	0.048238	5	5
-1341_12	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-1341_12	1344_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1341_12	1344_13	1.400000	0.894427	-0.636142	1.267018	5	5
-1341_12	1345_12	1.400000	0.894427	1.862924	-2.506901	5	5
-1341_13	1341_14	1.400000	0.894427	1.883560	-2.485480	5	5
-1341_13	1341_2	1.400000	0.894427	1.351962	-1.627597	5	5
-1341_13	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-1341_13	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_13	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_13	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_14	1341_2	1.400000	0.894427	1.351962	-1.627597	5	5
-1341_14	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-1341_14	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_14	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_14	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1341_2	1344_1	1.400000	0.894427	-2.302185	1.712469	5	5
-1341_2	1344_12	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_2	1344_13	1.400000	0.894427	-0.636142	-0.195857	5	5
-1341_2	1345_12	1.400000	0.894427	0.196880	-0.195857	5	5
-1344_1	1344_12	1.400000	0.894427	-0.642422	0.715735	5	5
-1344_1	1344_13	1.400000	0.894427	-0.642422	0.715735	5	5
-1344_1	1345_12	1.400000	0.894427	-2.302185	1.712469	5	5
-1344_12	1344_13	1.400000	0.894427	1.883560	-2.485480	5	5
-1344_12	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
-1344_13	1345_12	1.400000	0.894427	-0.636142	1.267018	5	5
+fid1_iid1	fid2_iid2	mean	sdev	zmean	zsdev	geno	relcode	pid1	mid1	pid2	mid2
+101_1	101_2	1.200000	0.577350	1.693329	-2.011511	25	parentchild	3	2	0	0
+101_1	101_3	1.200000	0.577350	-0.717628	0.612530	25	parentchild	3	2	0	0
+101_1	105_1	1.200000	0.577350	0.670010	-0.504142	25	unrelated	3	2	3	2
+101_1	105_2	1.200000	0.577350	0.870921	-0.566551	25	unrelated	3	2	0	0
+101_1	105_3	1.200000	0.577350	1.071833	-0.655899	25	unrelated	3	2	0	0
+101_1	112_1	1.200000	0.577350	-0.736371	0.779435	25	unrelated	3	2	3	2
+101_1	112_2	1.200000	0.577350	-0.937282	0.679102	25	unrelated	3	2	0	0
+101_1	112_3	1.200000	0.577350	-0.535459	-0.655899	25	unrelated	3	2	0	0
+101_1	117_1	1.200000	0.577350	0.067275	0.077804	25	unrelated	3	2	3	2
+101_1	117_2	1.200000	0.577350	0.469098	-0.467231	25	unrelated	3	2	0	0
+101_1	117_3	1.200000	0.577350	0.469098	0.077804	25	unrelated	3	2	0	0
+101_1	12_1	1.200000	0.577350	0.469098	-0.467230	25	unrelated	3	2	3	2
+101_1	12_2	1.200000	0.577350	0.469098	-0.467230	25	unrelated	3	2	0	0
+101_1	12_3	1.200000	0.577350	1.071833	-0.655899	25	unrelated	3	2	0	0
+101_1	13_1	1.200000	0.577350	-0.133637	-0.504142	25	unrelated	3	2	3	2
+101_1	13_2	1.200000	0.577350	-0.255930	0.042025	25	unrelated	3	2	0	0
+101_1	13_3	1.200000	0.577350	1.071832	-0.655899	25	unrelated	3	2	0	0
+101_1	1334_1	1.200000	0.577350	-0.133636	0.045908	25	unrelated	3	2	10	11
+101_1	1334_10	1.200000	0.577350	-0.334548	-0.566551	25	unrelated	3	2	0	0
+101_1	1334_11	1.200000	0.577350	-0.937282	0.679102	25	unrelated	3	2	0	0
+101_1	1334_12	1.200000	0.577350	-0.334548	-0.007823	25	unrelated	3	2	0	0
+101_1	1334_13	1.200000	0.577350	-0.133636	-0.504142	25	unrelated	3	2	0	0
+101_1	1334_2	1.200000	0.577350	-0.736370	1.194476	25	unrelated	3	2	12	13
+101_1	1340_1	1.200000	0.577350	-0.535459	-0.084293	25	unrelated	3	2	9	10
+101_1	1340_10	1.200000	0.577350	-0.535459	-0.084293	25	unrelated	3	2	0	0
+101_1	1340_11	1.200000	0.577350	-0.133636	-0.504142	25	unrelated	3	2	0	0
+101_1	1340_12	1.200000	0.577350	0.469098	-0.467231	25	unrelated	3	2	0	0
+101_1	1340_2	1.200000	0.577350	0.469098	-0.467231	25	unrelated	3	2	11	12
+101_1	1340_9	1.200000	0.577350	-2.142751	0.999931	25	unrelated	3	2	0	0
+101_1	1341_1	1.200000	0.577350	0.163363	-0.455013	25	unrelated	3	2	11	12
+101_1	1341_11	1.200000	0.577350	-0.334549	0.481281	25	unrelated	3	2	0	0
+101_1	1341_12	1.200000	0.577350	-0.937282	-0.925605	25	unrelated	3	2	0	0
+101_1	1341_13	1.200000	0.577350	-0.736371	0.779435	25	unrelated	3	2	0	0
+101_1	1341_14	1.200000	0.577350	-0.736371	0.779435	25	unrelated	3	2	0	0
+101_1	1341_2	1.200000	0.577350	-0.736371	0.779435	25	unrelated	3	2	13	14
+101_1	1344_1	1.200000	0.577350	-0.535459	0.413356	25	unrelated	3	2	12	13
+101_1	1344_12	1.200000	0.577350	0.469098	-0.467231	25	unrelated	3	2	0	0
+101_1	1344_13	1.200000	0.577350	0.469098	-0.467231	25	unrelated	3	2	0	0
+101_1	1345_12	1.200000	0.577350	-0.736370	-0.774446	25	unrelated	3	2	0	0
+101_2	101_3	1.200000	0.577350	0.236040	-0.228179	25	parents	0	0	0	0
+101_2	105_1	1.200000	0.577350	0.670010	-0.504142	25	unrelated	0	0	3	2
+101_2	105_2	1.200000	0.577350	0.943250	-0.598443	25	unrelated	0	0	0	0
+101_2	105_3	1.200000	0.577350	1.136125	-0.693367	25	unrelated	0	0	0	0
+101_2	112_1	1.200000	0.577350	-0.599751	0.780517	25	unrelated	0	0	3	2
+101_2	112_2	1.200000	0.577350	-0.792626	0.696771	25	unrelated	0	0	0	0
+101_2	112_3	1.200000	0.577350	-0.406876	-0.598443	25	unrelated	0	0	0	0
+101_2	117_1	1.200000	0.577350	0.171750	0.062100	25	unrelated	0	0	3	2
+101_2	117_2	1.200000	0.577350	0.557499	-0.483424	25	unrelated	0	0	0	0
+101_2	117_3	1.200000	0.577350	0.557499	0.042491	25	unrelated	0	0	0	0
+101_2	12_1	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	3	2
+101_2	12_2	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	0	0
+101_2	12_3	1.200000	0.577350	1.136124	-0.693367	25	unrelated	0	0	0	0
+101_2	13_1	1.200000	0.577350	-0.021126	-0.483423	25	unrelated	0	0	3	2
+101_2	13_2	1.200000	0.577350	-0.255930	0.042025	25	unrelated	0	0	0	0
+101_2	13_3	1.200000	0.577350	1.136124	-0.693367	25	unrelated	0	0	0	0
+101_2	1334_1	1.200000	0.577350	-0.021125	0.042491	25	unrelated	0	0	10	11
+101_2	1334_10	1.200000	0.577350	-0.214001	-0.528970	25	unrelated	0	0	0	0
+101_2	1334_11	1.200000	0.577350	-0.792626	0.696771	25	unrelated	0	0	0	0
+101_2	1334_12	1.200000	0.577350	-0.214001	0.002982	25	unrelated	0	0	0	0
+101_2	1334_13	1.200000	0.577350	-0.021126	-0.483424	25	unrelated	0	0	0	0
+101_2	1334_2	1.200000	0.577350	-0.599751	1.178851	25	unrelated	0	0	12	13
+101_2	1340_1	1.200000	0.577350	-0.406876	-0.057030	25	unrelated	0	0	9	10
+101_2	1340_10	1.200000	0.577350	-0.406876	-0.057030	25	unrelated	0	0	0	0
+101_2	1340_11	1.200000	0.577350	-0.021126	-0.483424	25	unrelated	0	0	0	0
+101_2	1340_12	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	0	0
+101_2	1340_2	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	11	12
+101_2	1340_9	1.200000	0.577350	-1.949876	1.086115	25	unrelated	0	0	0	0
+101_2	1341_1	1.200000	0.577350	0.268187	-0.455013	25	unrelated	0	0	11	12
+101_2	1341_11	1.200000	0.577350	-0.214002	0.471641	25	unrelated	0	0	0	0
+101_2	1341_12	1.200000	0.577350	-0.792626	-0.816040	25	unrelated	0	0	0	0
+101_2	1341_13	1.200000	0.577350	-0.599751	0.780517	25	unrelated	0	0	0	0
+101_2	1341_14	1.200000	0.577350	-0.599751	0.780517	25	unrelated	0	0	0	0
+101_2	1341_2	1.200000	0.577350	-0.599751	0.780517	25	unrelated	0	0	13	14
+101_2	1344_1	1.200000	0.577350	-0.406876	0.418047	25	unrelated	0	0	12	13
+101_2	1344_12	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	0	0
+101_2	1344_13	1.200000	0.577350	0.557499	-0.483423	25	unrelated	0	0	0	0
+101_2	1345_12	1.200000	0.577350	-0.599751	-0.693367	25	unrelated	0	0	0	0
+101_3	105_1	1.200000	0.577350	-1.540017	1.879362	25	unrelated	0	0	3	2
+101_3	105_2	1.200000	0.577350	0.171750	-0.460872	25	unrelated	0	0	0	0
+101_3	105_3	1.200000	0.577350	-0.792627	-0.242861	25	unrelated	0	0	0	0
+101_3	112_1	1.200000	0.577350	-0.599750	0.780517	25	unrelated	0	0	3	2
+101_3	112_2	1.200000	0.577350	-0.792626	2.157894	25	unrelated	0	0	0	0
+101_3	112_3	1.200000	0.577350	-0.021126	-0.483423	25	unrelated	0	0	0	0
+101_3	117_1	1.200000	0.577350	-0.599751	1.178851	25	unrelated	0	0	3	2
+101_3	117_2	1.200000	0.577350	1.329000	-0.816040	25	unrelated	0	0	0	0
+101_3	117_3	1.200000	0.577350	0.171750	0.062100	25	unrelated	0	0	0	0
+101_3	12_1	1.200000	0.577350	2.486250	-2.592124	25	unrelated	0	0	3	2
+101_3	12_2	1.200000	0.577350	2.486250	-2.592124	25	unrelated	0	0	0	0
+101_3	12_3	1.200000	0.577350	1.136124	-0.693367	25	unrelated	0	0	0	0
+101_3	13_1	1.200000	0.577350	1.521875	-0.969866	25	unrelated	0	0	3	2
+101_3	13_2	1.200000	0.577350	-0.255930	0.546459	25	unrelated	0	0	0	0
+101_3	13_3	1.200000	0.577350	1.136125	-0.693367	25	unrelated	0	0	0	0
+101_3	1334_1	1.200000	0.577350	-0.021126	-0.483424	25	unrelated	0	0	10	11
+101_3	1334_10	1.200000	0.577350	-0.599750	-0.693367	25	unrelated	0	0	0	0
+101_3	1334_11	1.200000	0.577350	-0.792626	2.157894	25	unrelated	0	0	0	0
+101_3	1334_12	1.200000	0.577350	-0.599751	0.345553	25	unrelated	0	0	0	0
+101_3	1334_13	1.200000	0.577350	-0.406876	-0.598443	25	unrelated	0	0	0	0
+101_3	1334_2	1.200000	0.577350	-0.985501	1.388993	25	unrelated	0	0	12	13
+101_3	1340_1	1.200000	0.577350	-0.406876	-0.598443	25	unrelated	0	0	9	10
+101_3	1340_10	1.200000	0.577350	-0.406876	-0.598443	25	unrelated	0	0	0	0
+101_3	1340_11	1.200000	0.577350	-0.406876	-0.598443	25	unrelated	0	0	0	0
+101_3	1340_12	1.200000	0.577350	-0.599750	-0.693367	25	unrelated	0	0	0	0
+101_3	1340_2	1.200000	0.577350	-0.599751	0.345552	25	unrelated	0	0	11	12
+101_3	1340_9	1.200000	0.577350	-0.406876	1.948414	25	unrelated	0	0	0	0
+101_3	1341_1	1.200000	0.577350	-1.339106	0.413355	25	unrelated	0	0	11	12
+101_3	1341_11	1.200000	0.577350	-1.371251	1.881413	25	unrelated	0	0	0	0
+101_3	1341_12	1.200000	0.577350	-1.564126	0.158748	25	unrelated	0	0	0	0
+101_3	1341_13	1.200000	0.577350	-0.599750	0.780517	25	unrelated	0	0	0	0
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+1341_2	1344_12	1.200000	0.577350	-0.021125	-0.483423	25	unrelated	13	14	0	0
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG
Binary file test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
--- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt	Thu May 20 12:38:35 2010 -0400
@@ -1,7 +1,7 @@
-PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin
+PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
 ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
 ## executing mogrify -resize 800x400! *.PNG returned 0
 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
@@ -12,16 +12,16 @@
 ## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0
 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
 *****************************************************
-Haploview 4.2	Java Version: 1.6.0_13
+Haploview 4.2	Java Version: 1.6.0_03
 *****************************************************
-Arguments:	-n	-pairwiseTagging	-pedfile	/share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-log	/share/shared/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng	-chromosome	22
+Arguments:	-n	-pairwiseTagging	-pedfile	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-log	/opt/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng	-chromosome	22
Max LD comparison distance = 200000kb
-Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
+Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
 10 out of 10 markers passed the MAF threshold.
 10 out of 10 markers passed the Mendel threshold.
 10 out of 10 markers passed the genotyping threshold.
@@ -33,11 +33,11 @@
 Writing output to rgHaploViewtest1.ped.TESTS
 Writing output to rgHaploViewtest1.ped.CHAPS
 *****************************************************
-Haploview 4.2	Java Version: 1.6.0_13
+Haploview 4.2	Java Version: 1.6.0_03
 *****************************************************
-Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/share/shared/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
+Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/opt/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
Max LD comparison distance = 200000kb
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/alljoin.pdf
Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/allnup.pdf
Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html	Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html	Thu May 20 12:38:35 2010 -0400
@@ -23,13 +23,13 @@
 <li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li>
 <li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li>
 <li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li>
-</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin
+</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
## executing mogrify -resize 800x400! *.PNG returned 0
@@ -51,7 +51,7 @@

    