[galaxy-commits] [hg] galaxy 3759: SNP/WGA tool changes only

10 May 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/6aa1379d35e0
changeset: 3759:6aa1379d35e0
user:      fubar/ross period lazarus at gmail d0t com
date:      Mon May 10 10:17:11 2010 -0400
description:
SNP/WGA tool changes only
Updates to functional test outputs
Minor tweaks to some tests
All now pass when run using -sid but there's something busted when a full functional test is run
diffstat:
static/welcome.html                                           |     5 +-
 test-data/rgCaCotest1_CaCo_log.txt                            |    20 +-
 test-data/rgGLMtest1_GLM_log.txt                              |    28 +-
 test-data/rgQQtest1.pdf                                       |    52 +-
 test-data/rgTDTtest1_TDT_log.txt                              |    18 +-
 test-data/rgtestouts/rgClean/rgCleantest1.log                 |    28 +-
 test-data/rgtestouts/rgEigPCA/Rplots.pdf                      |    46 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R                 |     2 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html              |    35 +-
 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf       |    50 +-
 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                 |     8 +-
 test-data/rgtestouts/rgGRR/rgGRRtest1.html                    |    14 +-
 test-data/rgtestouts/rgGRR/rgGRRtest1.svg                     |   118 +-
 test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls               |  1560 +++++-----
 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    |    14 +-
 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS   |    10 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed             |     2 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim             |     4 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log             |    96 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map             |     4 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped             |    80 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in        |     4 +-
 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out       |     4 +-
 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png            |     0 
 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png               |     0 
 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png          |     0 
 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png             |     0 
 test-data/rgtestouts/rgManQQ/rgManQQtest1.R                   |     4 +-
 test-data/rgtestouts/rgManQQ/rgManQQtest1.html                |     4 +-
 test-data/rgtestouts/rgPedSub/rgPedSubtest1.log               |     8 +-
 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-data/rgtestouts/rgfakePed/rgfakePedtest1.lped            |     2 +-
 test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped             |    80 +-
 test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe            |    80 +-
 tool-data/annotation_profiler_options.xml.sample              |     2 +-
 tool_conf.xml.sample                                          |   231 -
 tools/rgenetics/rgGRR.py                                      |    12 +-
 tools/rgenetics/rgGRR.xml                                     |    10 +-
 tools/rgenetics/rgHaploView.xml                               |     4 +-
 tools/rgenetics/rgQC.xml                                      |     2 +-
 tools/rgenetics/rgtest.sh                                     |     6 +-
 tools/rgenetics/rgutils.py                                    |    20 +-
 81 files changed, 2045 insertions(+), 2007 deletions(-)
diffs (truncated from 5750 to 3000 lines):
diff -r acaf971320bd -r 6aa1379d35e0 static/welcome.html

--- a/static/welcome.html	Mon May 10 10:03:00 2010 -0400
+++ b/static/welcome.html	Mon May 10 10:17:11 2010 -0400
@@ -8,12 +8,11 @@
 <body>
     <div class="document">
         <div class="warningmessagelarge">
-            <strong>Hello world! It's running...</strong>
+            <strong>Welcome to Galaxy at the Channing Laboratory</strong>
             <hr>
-            To customize this page edit <code>static/welcome.html</code>
         </div>
         <br/>
-        <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />
+        <img src="images/Armitagep_manhattan.png" alt="manhattan plot" 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 acaf971320bd -r 6aa1379d35e0 test-data/rgCaCotest1_CaCo_log.txt
--- a/test-data/rgCaCotest1_CaCo_log.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgCaCotest1_CaCo_log.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,6 +1,6 @@
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -10,24 +10,24 @@
Skipping web check... [ --noweb ] 
 Writing this text to log file [ rgCaCotest1.log ]
-Analysis started: Thu Mar 25 21:01:31 2010
+Analysis started: Sun May  9 21:23:49 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/tinywga
+	--bfile /share/shared/galaxy/test-data/tinywga
    --out rgCaCotest1
    --model
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
 Before frequency and genotyping pruning, there are 25 SNPs
 27 founders and 13 non-founders found
@@ -40,7 +40,7 @@
 Full-model association tests, minimum genotype count: --cell 5
 Writing full model association results to [ rgCaCotest1.model ]
-Analysis finished: Thu Mar 25 21:01:31 2010
+Analysis finished: Sun May  9 21:23:49 2010
###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772
-Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31
+Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgGLMtest1_GLM_log.txt
--- a/test-data/rgGLMtest1_GLM_log.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgGLMtest1_GLM_log.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,11 +1,11 @@
-rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff']
-vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear']
-xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls
+rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff']
+vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear']
+xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls
 ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -15,31 +15,31 @@
Skipping web check... [ --noweb ] 
 Writing this text to log file [ tinywga.log ]
-Analysis started: Thu Mar 25 21:01:31 2010
+Analysis started: Sun May  9 21:23:49 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/tinywga
+	--bfile /share/shared/galaxy/test-data/tinywga
    --pheno-name c1
-	--pheno /opt/galaxy/test-data/tinywga.pphe
+	--pheno /share/shared/galaxy/test-data/tinywga.pphe
    --out tinywga
    --mind 1
    --geno 1
    --maf 0
    --linear
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
-Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] 
+Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 
 40 individuals with non-missing alternate phenotype
 Assuming a quantitative trait
 Missing phenotype value is -9
@@ -54,5 +54,5 @@
 Converting data to Individual-major format
 Writing linear model association results to [ tinywga.assoc.linear ]
-Analysis finished: Thu Mar 25 21:01:31 2010
+Analysis finished: Sun May  9 21:23:49 2010
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgQQtest1.pdf
--- a/test-data/rgQQtest1.pdf	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgQQtest1.pdf	Mon May 10 10:17:11 2010 -0400
@@ -2,8 +2,8 @@
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diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgTDTtest1_TDT_log.txt
--- a/test-data/rgTDTtest1_TDT_log.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgTDTtest1_TDT_log.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,6 +1,6 @@
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -10,25 +10,25 @@
Skipping web check... [ --noweb ] 
 Writing this text to log file [ rgTDTtest1.log ]
-Analysis started: Thu Mar 25 21:01:31 2010
+Analysis started: Sun May  9 21:23:49 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/tinywga
+	--bfile /share/shared/galaxy/test-data/tinywga
    --out rgTDTtest1
    --mind 0.5
    --tdt
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
 Before frequency and genotyping pruning, there are 25 SNPs
 27 founders and 13 non-founders found
@@ -48,6 +48,6 @@
 0 Mendel errors detected in total
 Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ]
-Analysis finished: Thu Mar 25 21:01:31 2010
+Analysis finished: Sun May  9 21:23:49 2010
###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgClean/rgCleantest1.log
--- a/test-data/rgtestouts/rgClean/rgCleantest1.log	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.log	Mon May 10 10:17:11 2010 -0400
@@ -1,7 +1,7 @@
-rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0
+rgClean.py started, called as /share/shared/galaxy/tools/rgenetics/rgClean.py /share/shared/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /share/shared/galaxy/test-data/rgtestouts/rgClean 0 0 0 0
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -10,14 +10,14 @@
 @----------------------------------------------------------@
Skipping web check... [ --noweb ]
-Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ]
-Analysis started: Thu Mar 25 21:01:24 2010
+Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ]
+Analysis started: Sun May  9 21:23:43 2010
Options in effect:
 --noweb
---bfile /opt/galaxy/test-data/tinywga
+--bfile /share/shared/galaxy/test-data/tinywga
 --make-bed
---out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1
+--out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1
 --set-hh-missing
 --mind 1
 --geno 1
@@ -25,16 +25,16 @@
 --hwe 0
 --me 1 1
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ]
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ]
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ]
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ]
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ]
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ]
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ]
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ]
 Detected that binary PED file is v1.00 SNP-major mode
 Before frequency and genotyping pruning, there are 25 SNPs
 27 founders and 13 non-founders found
@@ -57,10 +57,10 @@
 0 Mendel errors detected in total
 0 families ( 0 individuals ) removed due to Mendel errors
 0 markers removed due to Mendel errors, 25 remaining
-Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ]
-Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ]
-Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ]
+Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ]
+Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ]
+Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ]
 Using (default) SNP-major mode
 Converting data to SNP-major format
-Analysis finished: Thu Mar 25 21:01:24 2010
+Analysis finished: Sun May  9 21:23:43 2010
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/Rplots.pdf
--- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf	Mon May 10 10:03:00 2010 -0400
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diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R	Mon May 10 10:17:11 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 25/03/2010 21:01:25
+#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:43
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html	Mon May 10 10:17:11 2010 -0400
@@ -9,30 +9,27 @@
 </head>
 <body>
 <div class="document">
-<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/>
+<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/>
 </h4>
-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>
+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>
 <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_eval.xls">rgEigPCAtest1_eval.xls  (507 B)</a></li>
-<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par  (311 B)</a></li>
+<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>
+<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_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_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_log.txt">rgEigPCAtest1_log.txt  (6.0 KB)</a></li>
-<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li>
-<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt  (257 B)</a></li>
-<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps  (13.6 KB)</a></li>
-<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec  (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls  (1.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf  (7.9 KB)</a></li>
-<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt  (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf  (2.1 KB)</a></li>
-<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R  (1.6 KB)</a></li>
-<li><a href="Rplots.pdf">Rplots.pdf  (813 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: /opt/galaxy/test-data/tinywga.ped
-snpname: /opt/galaxy/test-data/tinywga.map
-indivname: /opt/galaxy/test-data/tinywga.ped
+genotypename: /share/shared/galaxy/test-data/tinywga.ped
+snpname: /share/shared/galaxy/test-data/tinywga.map
+indivname: /share/shared/galaxy/test-data/tinywga.ped
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
@@ -156,5 +153,5 @@
 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 /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/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 /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
 <p/></div></body></html>
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf	Mon May 10 10:17:11 2010 -0400
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diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,9 +1,9 @@
 parameter file: rgEigPCAtest1_pca.xls.par
 ### THE INPUT PARAMETERS
 ##PARAMETER NAME: VALUE
-genotypename: /opt/galaxy/test-data/tinywga.ped
-snpname: /opt/galaxy/test-data/tinywga.map
-indivname: /opt/galaxy/test-data/tinywga.ped
+genotypename: /share/shared/galaxy/test-data/tinywga.ped
+snpname: /share/shared/galaxy/test-data/tinywga.map
+indivname: /share/shared/galaxy/test-data/tinywga.ped
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls	Mon May 10 10:17:11 2010 -0400
@@ -3,43 +3,43 @@
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diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par	Mon May 10 10:17:11 2010 -0400
@@ -1,6 +1,6 @@
-genotypename: /opt/galaxy/test-data/tinywga.ped
-snpname: /opt/galaxy/test-data/tinywga.map
-indivname: /opt/galaxy/test-data/tinywga.ped
+genotypename: /share/shared/galaxy/test-data/tinywga.ped
+snpname: /share/shared/galaxy/test-data/tinywga.map
+indivname: /share/shared/galaxy/test-data/tinywga.ped
 evecoutname: rgEigPCAtest1_pca.xls.evec
 evaloutname: rgEigPCAtest1_eval.xls
 altnormstyle: NO
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt
--- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,13 +1,13 @@
 Reading genotypes for 40 subjects and 5 markers
 Calculating 780 pairs...
 Estimated time is 0.00 to 0.00 seconds ...
-T1:  0.00229454040527	T2:  0.0166795253754	T3:  0.000442743301392	TOT: 0.0201091766357	0 pairs with no (or not enough) comparable genotypes (0.0%)
+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)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22
+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)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29
-Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22
+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
 780 pairs are available of 780
 Outliers: 0
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.html
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html	Mon May 10 10:17:11 2010 -0400
@@ -9,34 +9,34 @@
 </head>
 <body>
 <div class="document">
-<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br>
+<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br>
 </h4>
 If you need to rerun this analysis, the command line was
-<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>
+<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>
 </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="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li>
 <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li>
-<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</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
Calculating 780 pairs...
Estimated time is 0.00 to 0.00 seconds ...
-T1:  0.00229454040527	T2:  0.0166795253754	T3:  0.000442743301392	TOT: 0.0201091766357	0 pairs with no (or not enough) comparable genotypes (0.0%)
+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)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22
+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)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29
+Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22
-Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, 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
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.svg
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg	Mon May 10 10:17:11 2010 -0400
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diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls	Mon May 10 10:17:11 2010 -0400
@@ -1,781 +1,781 @@
 fid1 iid1	fid2 iid2	mean	sdev	zmean	zsdev	geno	relcode
-101_1	101_2	1.600000	0.547723	1.257561	-1.479131	5	5
-101_1	101_3	1.600000	0.547723	-0.500320	0.746448	5	5
-101_1	105_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	105_2	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	105_3	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	112_1	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	112_2	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	112_3	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	117_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	117_2	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	117_3	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	12_1	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	12_2	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	12_3	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	13_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	13_2	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	13_3	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_10	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_11	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_12	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_13	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1334_2	1.600000	0.547723	-1.538609	1.903891	5	5
-101_1	1340_1	1.600000	0.547723	-2.634984	-2.447598	5	5
-101_1	1340_10	1.600000	0.547723	-2.634984	-2.447598	5	5
-101_1	1340_11	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1340_12	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	1340_2	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	1340_9	1.600000	0.547723	-2.634984	1.263364	5	5
-101_1	1341_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1341_11	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	1341_12	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	1341_13	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	1341_14	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	1341_2	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_1	1344_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_1	1344_12	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	1344_13	1.600000	0.547723	0.654139	-0.175107	5	5
-101_1	1345_12	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_2	101_3	1.600000	0.547723	-0.100609	0.062138	5	5
-101_2	105_1	1.600000	0.547723	-0.442235	0.176448	5	5
-101_2	105_2	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	105_3	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	112_1	1.600000	0.547723	-0.880785	0.041791	5	5
-101_2	112_2	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	112_3	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	117_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	117_2	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	117_3	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	12_1	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	12_2	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	12_3	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	13_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	13_2	1.600000	0.547723	-1.538609	-0.175107	5	5
-101_2	13_3	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_10	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_12	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_13	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1334_2	1.600000	0.547723	-0.880785	1.617557	5	5
-101_2	1340_1	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_2	1340_10	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_2	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	1340_9	1.600000	0.547723	-1.757884	1.355006	5	5
-101_2	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	1341_12	1.600000	0.547723	-0.880785	0.041791	5	5
-101_2	1341_13	1.600000	0.547723	-0.880785	0.041791	5	5
-101_2	1341_14	1.600000	0.547723	-0.880785	0.041791	5	5
-101_2	1341_2	1.600000	0.547723	-0.880785	0.041791	5	5
-101_2	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_2	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-101_2	1345_12	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	105_1	1.600000	0.547723	-1.538609	1.903891	5	5
-101_3	105_2	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	105_3	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	112_1	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	112_2	1.600000	0.547723	-0.003685	0.041791	5	5
-101_3	112_3	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	117_1	1.600000	0.547723	-1.757884	1.355006	5	5
-101_3	117_2	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	117_3	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	12_1	1.600000	0.547723	0.873414	-0.415020	5	5
-101_3	12_2	1.600000	0.547723	0.873414	-0.415020	5	5
-101_3	12_3	1.600000	0.547723	0.873414	-0.415020	5	5
-101_3	13_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_3	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-101_3	13_3	1.600000	0.547723	-0.003685	0.041791	5	5
-101_3	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-101_3	1334_10	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-101_3	1334_12	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1334_13	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1334_2	1.600000	0.547723	-2.634984	0.766189	5	5
-101_3	1340_1	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1340_10	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1340_11	1.600000	0.547723	-1.757884	-0.415020	5	5
-101_3	1340_12	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1340_2	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1340_9	1.600000	0.547723	-1.757884	1.355006	5	5
-101_3	1341_1	1.600000	0.547723	-1.757884	1.355006	5	5
-101_3	1341_11	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1341_12	1.600000	0.547723	-2.634984	0.766189	5	5
-101_3	1341_13	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1341_14	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1341_2	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1344_1	1.600000	0.547723	-1.757884	1.355006	5	5
-101_3	1344_12	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1344_13	1.600000	0.547723	-0.880785	0.041791	5	5
-101_3	1345_12	1.600000	0.547723	-2.634984	0.766189	5	5
-105_1	105_2	1.600000	0.547723	-0.500320	0.746448	5	5
-105_1	105_3	1.600000	0.547723	-2.258200	1.090746	5	5
-105_1	112_1	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	112_2	1.600000	0.547723	-0.442235	2.097383	5	5
-105_1	112_3	1.600000	0.547723	-0.442235	0.176448	5	5
-105_1	117_1	1.600000	0.547723	1.750514	-2.447598	5	5
-105_1	117_2	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	117_3	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	12_1	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	12_2	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	12_3	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	13_1	1.600000	0.547723	-2.634984	1.263364	5	5
-105_1	13_2	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	13_3	1.600000	0.547723	-2.634984	1.263364	5	5
-105_1	1334_1	1.600000	0.547723	-0.442235	2.097383	5	5
-105_1	1334_10	1.600000	0.547723	-0.442235	0.176448	5	5
-105_1	1334_11	1.600000	0.547723	-0.442235	2.097383	5	5
-105_1	1334_12	1.600000	0.547723	-0.442235	0.176448	5	5
-105_1	1334_13	1.600000	0.547723	-0.442235	0.176448	5	5
-105_1	1334_2	1.600000	0.547723	-1.538609	1.903890	5	5
-105_1	1340_1	1.600000	0.547723	-2.634984	1.263364	5	5
-105_1	1340_10	1.600000	0.547723	-2.634984	1.263364	5	5
-105_1	1340_11	1.600000	0.547723	-0.442235	0.176448	5	5
-105_1	1340_12	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1340_2	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1340_9	1.600000	0.547723	-2.634984	2.800494	5	5
-105_1	1341_1	1.600000	0.547723	1.750514	-2.447598	5	5
-105_1	1341_11	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1341_12	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1341_13	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	1341_14	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	1341_2	1.600000	0.547723	-1.538609	1.903891	5	5
-105_1	1344_1	1.600000	0.547723	1.750514	-2.447598	5	5
-105_1	1344_12	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1344_13	1.600000	0.547723	0.654139	-0.175107	5	5
-105_1	1345_12	1.600000	0.547723	0.654139	-0.175107	5	5
-105_2	105_3	1.600000	0.547723	0.846302	-0.286640	5	5
-105_2	112_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	112_2	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	112_3	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	117_1	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	117_2	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	117_3	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	12_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	12_2	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	12_3	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	13_1	1.600000	0.547723	-0.880785	0.041791	5	5
-105_2	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-105_2	13_3	1.600000	0.547723	-0.880785	0.041791	5	5
-105_2	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1334_10	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1334_12	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1334_13	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1334_2	1.600000	0.547723	-0.003685	1.617557	5	5
-105_2	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-105_2	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-105_2	1340_11	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1340_12	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	1340_2	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-105_2	1341_1	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1341_11	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	1341_12	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-105_2	1344_1	1.600000	0.547723	0.873414	-0.415020	5	5
-105_2	1344_12	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	1344_13	1.600000	0.547723	1.750514	-2.447598	5	5
-105_2	1345_12	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	112_1	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	112_2	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	112_3	1.600000	0.547723	1.750514	-2.447598	5	5
-105_3	117_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	117_2	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	117_3	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	12_1	1.600000	0.547723	-0.880785	0.041791	5	5
-105_3	12_2	1.600000	0.547723	-0.880785	0.041791	5	5
-105_3	12_3	1.600000	0.547723	-0.880785	0.041791	5	5
-105_3	13_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	13_2	1.600000	0.547723	0.654139	-0.175107	5	5
-105_3	13_3	1.600000	0.547723	-1.757884	-0.415020	5	5
-105_3	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1334_10	1.600000	0.547723	1.750514	-2.447598	5	5
-105_3	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1334_12	1.600000	0.547723	1.750514	-2.447598	5	5
-105_3	1334_13	1.600000	0.547723	1.750514	-2.447598	5	5
-105_3	1334_2	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1340_11	1.600000	0.547723	1.750514	-2.447598	5	5
-105_3	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-105_3	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-105_3	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	112_2	1.600000	0.547723	-0.148744	0.511487	5	5
-112_1	112_3	1.600000	0.547723	-0.148744	0.511487	5	5
-112_1	117_1	1.600000	0.547723	-0.880785	1.617557	5	5
-112_1	117_2	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	117_3	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	12_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	12_2	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	12_3	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	13_1	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	13_2	1.600000	0.547723	1.750514	-2.447598	5	5
-112_1	13_3	1.600000	0.547723	-0.880785	0.041791	5	5
-112_1	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1334_10	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1334_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1334_13	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1334_2	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1340_1	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1340_10	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1340_11	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1340_12	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1340_2	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1340_9	1.600000	0.547723	0.873414	-0.415020	5	5
-112_1	1341_1	1.600000	0.547723	-0.880785	1.617557	5	5
-112_1	1341_11	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1341_12	1.600000	0.547723	-0.003685	1.617557	5	5
-112_1	1341_13	1.600000	0.547723	1.750514	-2.447598	5	5
-112_1	1341_14	1.600000	0.547723	1.750514	-2.447598	5	5
-112_1	1341_2	1.600000	0.547723	1.750514	-2.447598	5	5
-112_1	1344_1	1.600000	0.547723	-0.880785	1.617557	5	5
-112_1	1344_12	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1344_13	1.600000	0.547723	-0.003685	0.041791	5	5
-112_1	1345_12	1.600000	0.547723	-0.003685	1.617557	5	5
-112_2	112_3	1.600000	0.547723	-0.100609	0.062138	5	5
-112_2	117_1	1.600000	0.547723	-0.003685	1.617557	5	5
-112_2	117_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	117_3	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	12_1	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	12_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	12_3	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	13_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	13_2	1.600000	0.547723	0.654139	-0.175107	5	5
-112_2	13_3	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1334_1	1.600000	0.547723	1.750514	-2.447598	5	5
-112_2	1334_10	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1334_11	1.600000	0.547723	1.750514	-2.447598	5	5
-112_2	1334_12	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1334_13	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1334_2	1.600000	0.547723	-0.880785	1.617557	5	5
-112_2	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-112_2	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1340_9	1.600000	0.547723	-0.003685	1.617557	5	5
-112_2	1341_1	1.600000	0.547723	-0.003685	1.617557	5	5
-112_2	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1341_12	1.600000	0.547723	-0.880785	1.617557	5	5
-112_2	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1344_1	1.600000	0.547723	-0.003685	1.617557	5	5
-112_2	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-112_2	1345_12	1.600000	0.547723	-0.880785	1.617557	5	5
-112_3	117_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	117_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	117_3	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	12_1	1.600000	0.547723	-0.880785	0.041791	5	5
-112_3	12_2	1.600000	0.547723	-0.880785	0.041791	5	5
-112_3	12_3	1.600000	0.547723	-0.880785	0.041791	5	5
-112_3	13_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	13_2	1.600000	0.547723	0.654139	-0.175107	5	5
-112_3	13_3	1.600000	0.547723	-1.757884	-0.415020	5	5
-112_3	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1334_10	1.600000	0.547723	1.750514	-2.447598	5	5
-112_3	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1334_12	1.600000	0.547723	1.750514	-2.447598	5	5
-112_3	1334_13	1.600000	0.547723	1.750514	-2.447598	5	5
-112_3	1334_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1340_11	1.600000	0.547723	1.750514	-2.447598	5	5
-112_3	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-112_3	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-112_3	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	117_2	1.600000	0.547723	-0.148744	0.511487	5	5
-117_1	117_3	1.600000	0.547723	-0.148744	0.511487	5	5
-117_1	12_1	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	12_2	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	12_3	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	13_1	1.600000	0.547723	-1.757884	1.355006	5	5
-117_1	13_2	1.600000	0.547723	-1.538609	1.903891	5	5
-117_1	13_3	1.600000	0.547723	-1.757884	1.355006	5	5
-117_1	1334_1	1.600000	0.547723	-0.003685	1.617557	5	5
-117_1	1334_10	1.600000	0.547723	-0.003685	0.041791	5	5
-117_1	1334_11	1.600000	0.547723	-0.003685	1.617557	5	5
-117_1	1334_12	1.600000	0.547723	-0.003685	0.041791	5	5
-117_1	1334_13	1.600000	0.547723	-0.003685	0.041791	5	5
-117_1	1334_2	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	1340_1	1.600000	0.547723	-1.757884	1.355006	5	5
-117_1	1340_10	1.600000	0.547723	-1.757884	1.355006	5	5
-117_1	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-117_1	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1340_9	1.600000	0.547723	-1.757884	2.531179	5	5
-117_1	1341_1	1.600000	0.547723	1.750514	-2.447598	5	5
-117_1	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1341_13	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	1341_14	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	1341_2	1.600000	0.547723	-0.880785	1.617557	5	5
-117_1	1344_1	1.600000	0.547723	1.750514	-2.447598	5	5
-117_1	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-117_1	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	117_3	1.600000	0.547723	1.793213	-1.838520	5	5
-117_2	12_1	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	12_2	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	12_3	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	13_1	1.600000	0.547723	-0.880785	0.041791	5	5
-117_2	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-117_2	13_3	1.600000	0.547723	-0.880785	0.041791	5	5
-117_2	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1334_10	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1334_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1334_13	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1334_2	1.600000	0.547723	-0.003685	1.617557	5	5
-117_2	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-117_2	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-117_2	1340_11	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1340_12	1.600000	0.547723	1.750514	-2.447598	5	5
-117_2	1340_2	1.600000	0.547723	1.750514	-2.447598	5	5
-117_2	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-117_2	1341_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1341_11	1.600000	0.547723	1.750514	-2.447598	5	5
-117_2	1341_12	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-117_2	1344_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_2	1344_12	1.600000	0.547723	1.750514	-2.447598	5	5
-117_2	1344_13	1.600000	0.547723	1.750514	-2.447598	5	5
-117_2	1345_12	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	12_1	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	12_2	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	12_3	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	13_1	1.600000	0.547723	-0.880785	0.041791	5	5
-117_3	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-117_3	13_3	1.600000	0.547723	-0.880785	0.041791	5	5
-117_3	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1334_10	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1334_12	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1334_13	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1334_2	1.600000	0.547723	-0.003685	1.617557	5	5
-117_3	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-117_3	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-117_3	1340_11	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1340_12	1.600000	0.547723	1.750514	-2.447598	5	5
-117_3	1340_2	1.600000	0.547723	1.750514	-2.447598	5	5
-117_3	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-117_3	1341_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1341_11	1.600000	0.547723	1.750514	-2.447598	5	5
-117_3	1341_12	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-117_3	1344_1	1.600000	0.547723	0.873414	-0.415020	5	5
-117_3	1344_12	1.600000	0.547723	1.750514	-2.447598	5	5
-117_3	1344_13	1.600000	0.547723	1.750514	-2.447598	5	5
-117_3	1345_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	12_2	1.600000	0.547723	1.257561	-1.479131	5	5
-12_1	12_3	1.600000	0.547723	1.257561	-1.479131	5	5
-12_1	13_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_1	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-12_1	13_3	1.600000	0.547723	0.873414	-0.415020	5	5
-12_1	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_1	1334_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-12_1	1334_12	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1334_13	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1334_2	1.600000	0.547723	-1.757884	1.355006	5	5
-12_1	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1340_11	1.600000	0.547723	-0.880785	0.041791	5	5
-12_1	1340_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1340_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-12_1	1341_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_1	1341_11	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1341_12	1.600000	0.547723	-1.757884	1.355006	5	5
-12_1	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1344_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_1	1344_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1344_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_1	1345_12	1.600000	0.547723	-1.757884	1.355006	5	5
-12_2	12_3	1.600000	0.547723	1.793213	-1.838520	5	5
-12_2	13_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_2	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-12_2	13_3	1.600000	0.547723	0.873414	-0.415020	5	5
-12_2	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_2	1334_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-12_2	1334_12	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1334_13	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1334_2	1.600000	0.547723	-1.757884	1.355006	5	5
-12_2	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1340_11	1.600000	0.547723	-0.880785	0.041791	5	5
-12_2	1340_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1340_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-12_2	1341_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_2	1341_11	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1341_12	1.600000	0.547723	-1.757884	1.355006	5	5
-12_2	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1344_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_2	1344_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1344_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_2	1345_12	1.600000	0.547723	-1.757884	1.355006	5	5
-12_3	13_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_3	13_2	1.600000	0.547723	-0.442235	0.176448	5	5
-12_3	13_3	1.600000	0.547723	0.873414	-0.415020	5	5
-12_3	1334_1	1.600000	0.547723	0.873414	-0.415020	5	5
-12_3	1334_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1334_11	1.600000	0.547723	0.873414	-0.415020	5	5
-12_3	1334_12	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1334_13	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1334_2	1.600000	0.547723	-1.757884	1.355006	5	5
-12_3	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1340_11	1.600000	0.547723	-0.880785	0.041791	5	5
-12_3	1340_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1340_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1340_9	1.600000	0.547723	-0.880785	1.617557	5	5
-12_3	1341_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_3	1341_11	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1341_12	1.600000	0.547723	-1.757884	1.355006	5	5
-12_3	1341_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1341_14	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1341_2	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1344_1	1.600000	0.547723	-0.880785	1.617557	5	5
-12_3	1344_12	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1344_13	1.600000	0.547723	-0.003685	0.041791	5	5
-12_3	1345_12	1.600000	0.547723	-1.757884	1.355006	5	5
-13_1	13_2	1.600000	0.547723	-0.500320	0.746448	5	5
-13_1	13_3	1.600000	0.547723	-1.555048	0.958868	5	5
-13_1	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1334_10	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1334_12	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1334_13	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1334_2	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1340_12	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1340_2	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-13_1	1341_1	1.600000	0.547723	-1.757884	1.355006	5	5
-13_1	1341_11	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1341_12	1.600000	0.547723	-0.880785	1.617557	5	5
-13_1	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-13_1	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-13_1	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-13_1	1344_1	1.600000	0.547723	-1.757884	1.355006	5	5
-13_1	1344_12	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1344_13	1.600000	0.547723	-0.880785	0.041791	5	5
-13_1	1345_12	1.600000	0.547723	-0.880785	1.617557	5	5
-13_2	13_3	1.600000	0.547723	-1.757704	-0.103465	5	5
-13_2	1334_1	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1334_10	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1334_11	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1334_12	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1334_13	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1334_2	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1340_1	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1340_10	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1340_11	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1340_12	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1340_2	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1340_9	1.600000	0.547723	0.654139	-0.175107	5	5
-13_2	1341_1	1.600000	0.547723	-1.538609	1.903891	5	5
-13_2	1341_11	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1341_12	1.600000	0.547723	-0.442235	2.097383	5	5
-13_2	1341_13	1.600000	0.547723	1.750514	-2.447598	5	5
-13_2	1341_14	1.600000	0.547723	1.750514	-2.447598	5	5
-13_2	1341_2	1.600000	0.547723	1.750514	-2.447598	5	5
-13_2	1344_1	1.600000	0.547723	-1.538609	1.903891	5	5
-13_2	1344_12	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1344_13	1.600000	0.547723	-0.442235	0.176448	5	5
-13_2	1345_12	1.600000	0.547723	-0.442235	2.097383	5	5
-13_3	1334_1	1.600000	0.547723	-0.003685	0.041791	5	5
-13_3	1334_10	1.600000	0.547723	-1.757884	-0.415020	5	5
-13_3	1334_11	1.600000	0.547723	-0.003685	0.041791	5	5
-13_3	1334_12	1.600000	0.547723	-1.757884	-0.415020	5	5
-13_3	1334_13	1.600000	0.547723	-1.757884	-0.415020	5	5
-13_3	1334_2	1.600000	0.547723	-2.634984	0.766189	5	5
-13_3	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-13_3	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-13_3	1340_11	1.600000	0.547723	-1.757884	-0.415020	5	5
-13_3	1340_12	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1340_2	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1340_9	1.600000	0.547723	-1.757884	1.355006	5	5
-13_3	1341_1	1.600000	0.547723	-1.757884	1.355006	5	5
-13_3	1341_11	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1341_12	1.600000	0.547723	-2.634984	0.766189	5	5
-13_3	1341_13	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1341_14	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1341_2	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1344_1	1.600000	0.547723	-1.757884	1.355006	5	5
-13_3	1344_12	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1344_13	1.600000	0.547723	-0.880785	0.041791	5	5
-13_3	1345_12	1.600000	0.547723	-2.634984	0.766189	5	5
-1334_1	1334_10	1.600000	0.547723	-1.555048	0.958868	5	5
-1334_1	1334_11	1.600000	0.547723	1.257561	-1.479131	5	5
-1334_1	1334_12	1.600000	0.547723	-0.100609	0.062138	5	5
-1334_1	1334_13	1.600000	0.547723	-0.100609	0.062138	5	5
-1334_1	1334_2	1.600000	0.547723	-1.047521	1.265241	5	5
-1334_1	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_1	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_1	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_1	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1340_9	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_1	1341_1	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_1	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1341_12	1.600000	0.547723	-0.880785	1.617557	5	5
-1334_1	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1344_1	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_1	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_1	1345_12	1.600000	0.547723	-0.880785	1.617557	5	5
-1334_10	1334_11	1.600000	0.547723	-0.100609	0.062138	5	5
-1334_10	1334_12	1.600000	0.547723	1.793213	-1.838520	5	5
-1334_10	1334_13	1.600000	0.547723	1.793213	-1.838520	5	5
-1334_10	1334_2	1.600000	0.547723	0.846302	-0.286640	5	5
-1334_10	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_10	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_10	1340_11	1.600000	0.547723	1.750514	-2.447598	5	5
-1334_10	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_10	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_10	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_10	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_10	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1334_12	1.600000	0.547723	-0.100609	0.062138	5	5
-1334_11	1334_13	1.600000	0.547723	-0.100609	0.062138	5	5
-1334_11	1334_2	1.600000	0.547723	-1.047521	1.265241	5	5
-1334_11	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_11	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_11	1340_11	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_11	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1340_9	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_11	1341_1	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_11	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1341_12	1.600000	0.547723	-0.880785	1.617557	5	5
-1334_11	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1344_1	1.600000	0.547723	-0.003685	1.617557	5	5
-1334_11	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_11	1345_12	1.600000	0.547723	-0.880785	1.617557	5	5
-1334_12	1334_13	1.600000	0.547723	1.793213	-1.838520	5	5
-1334_12	1334_2	1.600000	0.547723	-0.148744	0.511487	5	5
-1334_12	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_12	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_12	1340_11	1.600000	0.547723	1.750514	-2.447598	5	5
-1334_12	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_12	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_12	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_12	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_12	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1334_2	1.600000	0.547723	-0.148744	0.511487	5	5
-1334_13	1340_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_13	1340_10	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_13	1340_11	1.600000	0.547723	1.750514	-2.447598	5	5
-1334_13	1340_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1340_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1340_9	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_13	1341_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_13	1341_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1341_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1341_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1341_14	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1341_2	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1344_1	1.600000	0.547723	-0.003685	0.041791	5	5
-1334_13	1344_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1344_13	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_13	1345_12	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_2	1340_1	1.600000	0.547723	-0.880785	0.041791	5	5
-1334_2	1340_10	1.600000	0.547723	-0.880785	0.041791	5	5
-1334_2	1340_11	1.600000	0.547723	0.873414	-0.415020	5	5
-1334_2	1340_12	1.600000	0.547723	-0.003685	1.617557	5	5
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+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
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG
Binary file test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
--- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt	Mon May 10 10:17:11 2010 -0400
@@ -1,7 +1,7 @@
-PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
+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
 ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## 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 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 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_03
+Haploview 4.2	Java Version: 1.6.0_13
 *****************************************************
-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
+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
Max LD comparison distance = 200000kb
-Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+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
 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_03
+Haploview 4.2	Java Version: 1.6.0_13
 *****************************************************
-Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/opt/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
+Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/share/shared/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
Max LD comparison distance = 200000kb
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/alljoin.pdf
Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/allnup.pdf
Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html	Mon May 10 10:17:11 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=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
+</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
## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## 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 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 mogrify -resize 800x400! *.PNG returned 0
@@ -51,7 +51,7 @@
*****************************************************
-Haploview 4.2	Java Version: 1.6.0_03
+Haploview 4.2	Java Version: 1.6.0_13
*****************************************************
@@ -59,7 +59,7 @@
-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
+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
@@ -67,9 +67,9 @@
Max LD comparison distance = 200000kb
-Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
+Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
10 out of 10 markers passed the MAF threshold.
@@ -93,7 +93,7 @@
*****************************************************
-Haploview 4.2	Java Version: 1.6.0_03
+Haploview 4.2	Java Version: 1.6.0_13
*****************************************************
@@ -101,7 +101,7 @@
-Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/opt/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
+Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-log	/share/shared/galaxy/test-data/tinywga.log	-maxDistance	200000	-compressedpng
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG
Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS	Mon May 10 10:17:11 2010 -0400
@@ -9,17 +9,17 @@
 rs3788347	rs3788347	1.0	
 rs756632	rs756632	1.0	
 rs4820539	rs4820539	1.0	
-rs2283804	rs2267006	1.0	
-rs2267006	rs2267006	1.0	
+rs2283804	rs2283804	1.0	
+rs2267006	rs2283804	1.0	
 rs4822363	rs4822363	1.0
Test	Alleles Captured
-rs2267006	rs2267006,rs2283804
-rs4820539	rs4820539
-rs3788347	rs3788347
+rs2283804	rs2267006,rs2283804
 rs756632	rs756632
+rs2283802	rs2283802
+rs4820537	rs4820537
 rs2267000	rs2267000
 rs4822363	rs4822363
-rs2283802	rs2283802
-rs4820537	rs4820537
 rs16997606	rs16997606
+rs3788347	rs3788347
+rs4820539	rs4820539
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS	Mon May 10 10:17:11 2010 -0400
@@ -1,9 +1,9 @@
-rs2267006
-rs4820539
-rs3788347
+rs2283804
 rs756632
+rs2283802
+rs4820537
 rs2267000
 rs4822363
-rs2283802
-rs4820537
 rs16997606
+rs3788347
+rs4820539
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed	Mon May 10 10:17:11 2010 -0400
@@ -1,1 +1,1 @@
-lÿÿÿÿûÿúÿÿÿmÿÿÿýÿÿÿÿÿ:ú¢ÿ¿«¯ü(
\ No newline at end of file
+lú £ïªîþ¨:*»ïêìª,«Àÿÿÿÿûÿúÿÿÿ
\ No newline at end of file
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim	Mon May 10 10:17:11 2010 -0400
@@ -1,3 +1,3 @@
+22	rs3788347	0	21797804	3	1
+22	rs5759608	0	21832708	2	4
 22	rs2267010	0	21864366	3	1
-22	rs12160770	0	21892925	1	3
-22	rs4822375	0	21905642	1	3
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log	Mon May 10 10:17:11 2010 -0400
@@ -1,9 +1,9 @@
-## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 25/03/2010 21:01:24
+## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42
 ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner
-## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1
+## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -12,30 +12,30 @@
 @----------------------------------------------------------@
Skipping web check... [ --noweb ] 
-Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
-Analysis started: Thu Mar 25 21:01:24 2010
+Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
+Analysis started: Sun May  9 21:23:42 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/tinywga
+	--bfile /share/shared/galaxy/test-data/tinywga
    --indep-pairwise 10000 5000 0.1
-	--out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    --mind 1
    --geno 1
    --maf 0
    --hwe 0
    --me 1 1
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
 Before frequency and genotyping pruning, there are 25 SNPs
 27 founders and 13 non-founders found
@@ -60,20 +60,20 @@
 0 markers removed due to Mendel errors, 25 remaining
 Converting data to SNP-major format
 Performing LD-based pruning...
-Writing pruned-in SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ]
-Writing pruned-out SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ]
+Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ]
+Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ]
 Scanning from chromosome 22 to 22
Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]
 For chromosome 22, 22 SNPs pruned out, 3 remaining
-Analysis finished: Thu Mar 25 21:01:24 2010
+Analysis finished: Sun May  9 21:23:42 2010
-## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -82,48 +82,48 @@
 @----------------------------------------------------------@
Skipping web check... [ --noweb ] 
-Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
-Analysis started: Thu Mar 25 21:01:24 2010
+Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
+Analysis started: Sun May  9 21:23:42 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/tinywga
-	--extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in
+	--bfile /share/shared/galaxy/test-data/tinywga
+	--extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in
    --make-bed
-	--out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
-Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
-25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
+25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
-Reading list of SNPs to extract [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read
+Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read
 Before frequency and genotyping pruning, there are 3 SNPs
 27 founders and 13 non-founders found
-Total genotyping rate in remaining individuals is 0.975
+Total genotyping rate in remaining individuals is 1
 0 SNPs failed missingness test ( GENO > 1 )
 0 SNPs failed frequency test ( MAF < 0 )
 After frequency and genotyping pruning, there are 3 SNPs
 After filtering, 10 cases, 30 controls and 0 missing
 After filtering, 21 males, 19 females, and 0 of unspecified sex
-Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
-Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
-Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
+Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
+Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
+Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
 Using (default) SNP-major mode
-Analysis finished: Thu Mar 25 21:01:24 2010
+Analysis finished: Sun May  9 21:23:42 2010
-## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
@----------------------------------------------------------@
-|        PLINK!       |     v1.06      |   24/Apr/2009     |
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
 |----------------------------------------------------------|
 |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 |----------------------------------------------------------|
@@ -132,38 +132,38 @@
 @----------------------------------------------------------@
Skipping web check... [ --noweb ] 
-Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
-Analysis started: Thu Mar 25 21:01:24 2010
+Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
+Analysis started: Sun May  9 21:23:42 2010
Options in effect:
    --noweb
-	--bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+	--bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
    --recode
-	--out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
+	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
-Reading map (extended format) from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
-3 markers to be included from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ]
-Reading pedigree information from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
-40 individuals read from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
+Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
+3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ]
+Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
+40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
 40 individuals with nonmissing phenotypes
 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 Missing phenotype value is also -9
 10 cases, 30 controls and 0 missing
 21 males, 19 females, and 0 of unspecified sex
-Reading genotype bitfile from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
+Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
 Detected that binary PED file is v1.00 SNP-major mode
 Before frequency and genotyping pruning, there are 3 SNPs
 27 founders and 13 non-founders found
-Total genotyping rate in remaining individuals is 0.975
+Total genotyping rate in remaining individuals is 1
 0 SNPs failed missingness test ( GENO > 1 )
 0 SNPs failed frequency test ( MAF < 0 )
 After frequency and genotyping pruning, there are 3 SNPs
 After filtering, 10 cases, 30 controls and 0 missing
 After filtering, 21 males, 19 females, and 0 of unspecified sex
-Writing recoded ped file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] 
-Writing new map file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] 
+Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] 
+Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ]
-Analysis finished: Thu Mar 25 21:01:24 2010
+Analysis finished: Sun May  9 21:23:42 2010
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map	Mon May 10 10:17:11 2010 -0400
@@ -1,3 +1,3 @@
+22	rs3788347	0	21797804
+22	rs5759608	0	21832708
 22	rs2267010	0	21864366
-22	rs12160770	0	21892925
-22	rs4822375	0	21905642
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped	Mon May 10 10:17:11 2010 -0400
@@ -1,40 +1,40 @@
-101 1 3 2 2 2 1 1 0 0 1 3
-101 2 0 0 2 1 1 1 3 3 1 3
-101 3 0 0 1 1 1 1 1 3 3 3
-105 1 3 2 2 2 1 1 0 0 1 1
-105 2 0 0 2 1 1 1 3 3 1 3
-105 3 0 0 1 1 1 1 3 3 1 3
-112 1 3 2 1 2 1 1 3 3 3 3
-112 2 0 0 2 1 1 1 3 3 3 3
-112 3 0 0 1 1 1 1 3 3 1 3
-117 1 3 2 2 2 1 1 3 3 1 1
-117 2 0 0 2 1 1 1 3 3 1 3
-117 3 0 0 1 1 1 1 3 3 1 3
-12 1 3 2 1 2 1 1 3 3 3 3
-12 2 0 0 2 1 1 1 3 3 3 3
-12 3 0 0 1 1 1 1 3 3 3 3
-13 1 3 2 1 2 1 1 3 3 3 3
-13 2 0 0 2 1 1 1 0 0 3 3
-13 3 0 0 1 1 3 1 3 3 3 3
-1334 1 10 11 1 2 1 1 3 3 3 3
-1334 10 0 0 1 1 1 1 3 3 1 3
-1334 11 0 0 2 1 1 1 3 3 3 3
-1334 12 0 0 1 1 1 1 3 3 1 3
-1334 13 0 0 2 1 1 1 3 3 1 3
-1334 2 12 13 2 2 1 1 3 3 1 3
-1340 1 9 10 1 2 3 1 3 3 3 3
-1340 10 0 0 2 1 3 1 3 3 3 3
-1340 11 0 0 1 1 1 1 3 3 1 3
-1340 12 0 0 2 1 1 1 3 3 1 3
-1340 2 11 12 2 2 1 1 3 3 1 3
-1340 9 0 0 1 1 1 1 3 3 3 3
-1341 1 11 12 1 1 1 1 3 3 1 1
-1341 11 0 0 1 1 1 1 3 3 1 3
-1341 12 0 0 2 1 1 1 3 3 1 1
-1341 13 0 0 1 1 1 1 3 3 3 3
-1341 14 0 0 2 1 1 1 3 3 3 3
-1341 2 13 14 2 1 1 1 3 3 3 3
-1344 1 12 13 1 1 1 1 3 3 1 1
-1344 12 0 0 1 1 1 1 3 3 1 3
-1344 13 0 0 2 1 1 1 3 3 1 3
-1345 12 0 0 1 1 1 1 3 3 1 1
+101 1 3 2 2 2 3 3 2 4 1 1
+101 2 0 0 2 1 3 3 2 4 1 1
+101 3 0 0 1 1 3 3 4 4 1 1
+105 1 3 2 2 2 3 1 2 2 1 1
+105 2 0 0 2 1 3 1 2 4 1 1
+105 3 0 0 1 1 3 1 2 4 1 1
+112 1 3 2 1 2 1 1 2 4 1 1
+112 2 0 0 2 1 1 1 2 2 1 1
+112 3 0 0 1 1 3 1 4 4 1 1
+117 1 3 2 2 2 3 3 2 4 1 1
+117 2 0 0 2 1 3 3 4 4 1 1
+117 3 0 0 1 1 3 3 2 4 1 1
+12 1 3 2 1 2 3 3 4 4 1 1
+12 2 0 0 2 1 3 3 4 4 1 1
+12 3 0 0 1 1 3 1 2 4 1 1
+13 1 3 2 1 2 3 1 4 4 1 1
+13 2 0 0 2 1 1 1 2 4 1 1
+13 3 0 0 1 1 3 3 2 4 3 1
+1334 1 10 11 1 2 3 1 2 4 1 1
+1334 10 0 0 1 1 3 1 4 4 1 1
+1334 11 0 0 2 1 1 1 2 2 1 1
+1334 12 0 0 1 1 1 1 4 4 1 1
+1334 13 0 0 2 1 3 1 2 4 1 1
+1334 2 12 13 2 2 1 1 4 4 1 1
+1340 1 9 10 1 2 3 1 2 4 3 1
+1340 10 0 0 2 1 3 1 2 4 3 1
+1340 11 0 0 1 1 3 1 2 4 1 1
+1340 12 0 0 2 1 3 1 2 4 1 1
+1340 2 11 12 2 2 3 1 2 2 1 1
+1340 9 0 0 1 1 1 1 4 4 1 1
+1341 1 11 12 1 1 3 1 2 4 1 1
+1341 11 0 0 1 1 1 1 2 2 1 1
+1341 12 0 0 2 1 3 1 4 4 1 1
+1341 13 0 0 1 1 1 1 2 4 1 1
+1341 14 0 0 2 1 1 1 2 4 1 1
+1341 2 13 14 2 1 1 1 2 4 1 1
+1344 1 12 13 1 1 3 3 2 2 1 1
+1344 12 0 0 1 1 3 1 2 2 1 1
+1344 13 0 0 2 1 3 1 2 2 1 1
+1345 12 0 0 1 1 3 1 4 4 1 1
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in	Mon May 10 10:17:11 2010 -0400
@@ -1,3 +1,3 @@
+rs3788347
+rs5759608
 rs2267010
-rs12160770
-rs4822375
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out
--- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out	Mon May 10 10:17:11 2010 -0400
@@ -2,14 +2,12 @@
 rs2267000
 rs16997606
 rs4820537
-rs3788347
 rs756632
 rs4820539
 rs2283804
 rs2267006
 rs4822363
 rs5751592
-rs5759608
 rs5759612
 rs2267009
 rs5759636
@@ -17,6 +15,8 @@
 rs2267013
 rs6003566
 rs2256725
+rs12160770
 rs5751611
 rs762601
 rs2156921
+rs4822375
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png
Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png
Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png
Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png
Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed
diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R
--- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R	Mon May 10 10:03:00 2010 -0400
+++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R	Mon May 10 10:17:11 2010 -0400
@@ -108,7 +108,7 @@
         if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank())
         plot
 }
-rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), 
+rgqqMan = function(infile="/share/shared/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), 
 title="rgManQQtest1",grey=0) {
 rawd = read.table(infile,head=T,sep='	')

    

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[galaxy-commits] [hg] galaxy 3759: SNP/WGA tool changes only