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changeset 0:1e677d6b1aaf draft

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IWTomics v1.0 uploaded
author fabio
date Tue, 02 May 2017 11:05:18 -0400
parents
children 79efc29b7680
files ._loadandplot.R ._loadandplot.xml ._plotwithscale.R ._plotwithscale.xml ._testandplot.R ._testandplot.xml examples/.Rhistory examples/._.DS_Store examples/._ETn_example examples/._paper_example examples/ETn_example/._Control.bed examples/ETn_example/._ETn_fixed.bed examples/ETn_example/._Recombination_hotspots.txt examples/ETn_example/._features.header examples/ETn_example/._regions.header examples/ETn_example/Control.bed examples/ETn_example/ETn_fixed.bed examples/ETn_example/Recombination_hotspots.txt examples/ETn_example/features.header examples/ETn_example/regions.header examples/easy/._.DS_Store examples/easy/features/._Feature1.bed examples/easy/features/._Feature1.txt examples/easy/features/._Feature2.bed examples/easy/features/._Feature2.txt examples/easy/features/._features.header.bed.txt examples/easy/features/._features.header.txt examples/easy/features/Feature1.bed examples/easy/features/Feature1.txt examples/easy/features/Feature2.bed examples/easy/features/Feature2.txt examples/easy/features/features.header.bed.txt examples/easy/features/features.header.txt examples/easy/regions/._Controls_regions.bed examples/easy/regions/._Elements1_regions.bed examples/easy/regions/._Elements2_regions.bed examples/easy/regions/._Elements3_regions.bed examples/easy/regions/._regions.header.txt examples/easy/regions/Controls_regions.bed examples/easy/regions/Elements1_regions.bed examples/easy/regions/Elements2_regions.bed examples/easy/regions/Elements3_regions.bed examples/easy/regions/regions.header.txt examples/hard-withNAs/._.DS_Store examples/hard-withNAs/._Controls_regions.bed examples/hard-withNAs/._Elements1_regions.bed examples/hard-withNAs/._Elements2_regions.bed examples/hard-withNAs/._Elements3_regions.bed examples/hard-withNAs/._Feature1.bed examples/hard-withNAs/._Feature2.bed examples/hard-withNAs/Controls_regions.bed examples/hard-withNAs/Elements1_regions.bed examples/hard-withNAs/Elements2_regions.bed examples/hard-withNAs/Elements3_regions.bed examples/hard-withNAs/Feature1.bed examples/hard-withNAs/Feature2.bed examples/paper_example/._control.bed examples/paper_example/._elem1.bed examples/paper_example/._elem2.bed examples/paper_example/._elem3.bed examples/paper_example/._feature1.txt examples/paper_example/._feature2.txt examples/paper_example/._features.header.txt examples/paper_example/._regions.header.txt examples/paper_example/control.bed examples/paper_example/elem1.bed examples/paper_example/elem2.bed examples/paper_example/elem3.bed examples/paper_example/feature1.txt examples/paper_example/feature2.txt examples/paper_example/features.header.txt examples/paper_example/regions.header.txt loadandplot.R loadandplot.xml plotwithscale.R plotwithscale.xml testandplot.R testandplot.xml
diffstat 78 files changed, 25668 insertions(+), 0 deletions(-) [+]
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Binary file ._loadandplot.R has changed
Binary file ._loadandplot.xml has changed
Binary file ._plotwithscale.R has changed
Binary file ._plotwithscale.xml has changed
Binary file ._testandplot.R has changed
Binary file ._testandplot.xml has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/.Rhistory	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,3 @@
+regionsheader
+row.names(regionsheader)
+regionsFeatures
Binary file examples/._.DS_Store has changed
Binary file examples/._ETn_example has changed
Binary file examples/._paper_example has changed
Binary file examples/ETn_example/._Control.bed has changed
Binary file examples/ETn_example/._ETn_fixed.bed has changed
Binary file examples/ETn_example/._Recombination_hotspots.txt has changed
Binary file examples/ETn_example/._features.header has changed
Binary file examples/ETn_example/._regions.header has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/ETn_example/Control.bed	Tue May 02 11:05:18 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/ETn_example/ETn_fixed.bed	Tue May 02 11:05:18 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/ETn_example/Recombination_hotspots.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2438 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/ETn_example/features.header	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,1 @@
+Recombination_hotspots.txt	Recomb_hot	Recombination hotspots
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/ETn_example/regions.header	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2 @@
+Control.bed	Control	Control
+ETn_fixed.bed	ETn_fixed	ETn fixed
\ No newline at end of file
Binary file examples/easy/._.DS_Store has changed
Binary file examples/easy/features/._Feature1.bed has changed
Binary file examples/easy/features/._Feature1.txt has changed
Binary file examples/easy/features/._Feature2.bed has changed
Binary file examples/easy/features/._Feature2.txt has changed
Binary file examples/easy/features/._features.header.bed.txt has changed
Binary file examples/easy/features/._features.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/Feature1.bed	Tue May 02 11:05:18 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/Feature1.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,108 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/Feature2.bed	Tue May 02 11:05:18 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/Feature2.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,108 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/features.header.bed.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.bed	ftr1	Feature 1
+Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/features/features.header.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.txt	ftr1	Feature 1
+Feature2.txt	ftr2	Feature 2
\ No newline at end of file
Binary file examples/easy/regions/._Controls_regions.bed has changed
Binary file examples/easy/regions/._Elements1_regions.bed has changed
Binary file examples/easy/regions/._Elements2_regions.bed has changed
Binary file examples/easy/regions/._Elements3_regions.bed has changed
Binary file examples/easy/regions/._regions.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/regions/Controls_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,35 @@
+chr1	91399892	91499892
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+chr21	45089115	45189115
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+chrX	37029585	37129585
+chrX	103593349	103693349
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/regions/Elements1_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,25 @@
+chr2	49960150	50060150
+chr2	55912445	56012445
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/regions/Elements2_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,20 @@
+chr1	65942901	66042901
+chr1	117128102	117228102
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/regions/Elements3_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,28 @@
+chr1	49721616	49821616
+chr1	95059425	95159425
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/easy/regions/regions.header.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,4 @@
+Elements1_regions.bed	elem1	Elements 1
+Elements2_regions.bed	elem2	Elements 2
+Elements3_regions.bed	elem3	Elements 3
+Controls_regions.bed	control	Controls
\ No newline at end of file
Binary file examples/hard-withNAs/._.DS_Store has changed
Binary file examples/hard-withNAs/._Controls_regions.bed has changed
Binary file examples/hard-withNAs/._Elements1_regions.bed has changed
Binary file examples/hard-withNAs/._Elements2_regions.bed has changed
Binary file examples/hard-withNAs/._Elements3_regions.bed has changed
Binary file examples/hard-withNAs/._Feature1.bed has changed
Binary file examples/hard-withNAs/._Feature2.bed has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Controls_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,35 @@
+chr1	91399892	91499892
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+chr6	99727306	99827306
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+chr7	120999784	121099784
+chr8	126860366	126960366
+chr8	127636547	127736547
+chr11	41362564	41462564
+chr11	101741527	101841527
+chr12	15210277	15310277
+chr13	91106037	91206037
+chr13	91518822	91618822
+chr13	98963030	99055030
+chr15	39087176	39187176
+chr17	58542142	58642142
+chr18	12199823	12299823
+chr20	8173704	8273704
+chr21	16255112	16355112
+chr21	45089115	45189115
+chrX	23898983	23998983
+chrX	37029585	37129585
+chrX	103593349	103693349
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Elements1_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,25 @@
+chr2	49960150	50060150
+chr2	55914445	56010445
+chr3	140330750	140422750
+chr4	41774201	41870201
+chr4	70633719	70725719
+chr4	109344735	109432735
+chr5	15027389	15123389
+chr5	43032888	43124888
+chr5	58233354	58329354
+chr5	91279761	91375761
+chr5	119466508	119558508
+chr6	85317170	85401170
+chr6	85764072	85860072
+chr6	134625363	134717363
+chr6	147472164	147564164
+chr7	77197798	77293798
+chr7	77884914	77976914
+chr7	114807399	114903399
+chr10	46352885	46444885
+chr10	67835078	67931078
+chr12	27724692	27820692
+chr12	95522506	95614506
+chr12	117869466	117957466
+chr14	100464166	100564166
+chrX	29266748	29362748
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Elements2_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,20 @@
+chr1	65942901	66042901
+chr1	117128102	117228102
+chr1	190338169	190438169
+chr2	227365478	227465478
+chr6	50856764	50956764
+chr6	135703067	135803067
+chr7	38228726	38328726
+chr7	51115898	51215898
+chr7	150325760	150425760
+chr8	25475691	25575691
+chr9	73374609	73474609
+chr11	55092625	55192625
+chr11	86581661	86681661
+chr12	12795284	12895284
+chr12	48151882	48251882
+chr12	83109951	83209951
+chr15	31430278	31530278
+chr15	65610815	65710815
+chr17	40766223	40866223
+chr20	17245048	17345048
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Elements3_regions.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,28 @@
+chr1	49721616	49821616
+chr1	95059425	95159425
+chr1	207236313	207336313
+chr2	73790843	73890843
+chr3	134465321	134565321
+chr4	43433669	43533669
+chr4	122032777	122132777
+chr5	12701747	12801747
+chr5	58501529	58601529
+chr5	152853250	152953250
+chr6	136085023	136185023
+chr6	147019529	147119529
+chr7	14192964	14292964
+chr7	125519883	125619883
+chr8	77652872	77752872
+chr8	108375665	108475665
+chr9	2984971	3084971
+chr10	978822	1078822
+chr11	18395046	18495046
+chr12	47273592	47373592
+chr12	60095778	60195778
+chr12	84854096	84954096
+chr12	95157539	95257539
+chr14	23982000	24082000
+chr16	1875335	1975335
+chr16	66789863	66889863
+chr18	64644131	64744131
+chr21	15966609	16066609
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Feature1.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2700 @@
+chr2	49960150	49964150	0.98
+chr2	49964150	49968150	1.11
+chr2	49968150	49972150	1.03
+chr2	49972150	49976150	0.87
+chr2	49976150	49980150	0.94
+chr2	49980150	49984150	0.99
+chr2	49984150	49988150	1.08
+chr2	49988150	49992150	NA
+chr2	49992150	49996150	1.00
+chr2	49996150	50000150	0.87
+chr2	50000150	50004150	1.04
+chr2	50004150	50008150	1.04
+chr2	50008150	50012150	1.11
+chr2	50012150	50016150	0.91
+chr2	50016150	50020150	0.95
+chr2	50020150	50024150	0.94
+chr2	50024150	50028150	0.92
+chr2	50028150	50032150	1.02
+chr2	50032150	50036150	0.89
+chr2	50036150	50040150	0.90
+chr2	50040150	50044150	1.11
+chr2	50044150	50048150	1.07
+chr2	50048150	50052150	0.96
+chr2	50052150	50056150	1.07
+chr2	50056150	50060150	1.02
+chr2	55912445	55916445	0.98
+chr2	55916445	55920445	0.96
+chr2	55920445	55924445	0.98
+chr2	55924445	55928445	NA
+chr2	55928445	55932445	0.99
+chr2	55932445	55936445	0.91
+chr2	55936445	55940445	0.86
+chr2	55940445	55944445	1.10
+chr2	55944445	55948445	0.98
+chr2	55948445	55952445	0.88
+chr2	55952445	55956445	1.06
+chr2	55956445	55960445	1.17
+chr2	55960445	55964445	0.93
+chr2	55964445	55968445	0.97
+chr2	55968445	55972445	1.09
+chr2	55972445	55976445	0.92
+chr2	55976445	55980445	1.06
+chr2	55980445	55984445	1.07
+chr2	55984445	55988445	1.02
+chr2	55988445	55992445	0.95
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+chr2	55996445	56000445	0.99
+chr2	56000445	56004445	0.89
+chr2	56004445	56008445	0.83
+chr2	56008445	56012445	1.04
+chr3	140326750	140330750	1.00
+chr3	140330750	140334750	1.12
+chr3	140334750	140338750	1.09
+chr3	140338750	140342750	1.09
+chr3	140342750	140346750	1.12
+chr3	140346750	140350750	0.94
+chr3	140350750	140354750	1.00
+chr3	140354750	140358750	0.93
+chr3	140358750	140362750	0.83
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+chr3	140366750	140370750	1.09
+chr3	140370750	140374750	1.00
+chr3	140374750	140378750	1.02
+chr3	140378750	140382750	NA
+chr3	140382750	140386750	0.91
+chr3	140386750	140390750	0.97
+chr3	140390750	140394750	1.02
+chr3	140394750	140398750	0.97
+chr3	140398750	140402750	1.14
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+chr3	140406750	140410750	1.01
+chr3	140410750	140414750	1.08
+chr3	140414750	140418750	1.01
+chr3	140418750	140422750	1.02
+chr3	140422750	140426750	1.04
+chr4	41772201	41776201	1.02
+chr4	41776201	41780201	0.91
+chr4	41780201	41784201	0.96
+chr4	41784201	41788201	0.97
+chr4	41788201	41792201	NA
+chr4	41792201	41796201	0.92
+chr4	41796201	41800201	1.06
+chr4	41800201	41804201	1.00
+chr4	41804201	41808201	NA
+chr4	41808201	41812201	0.90
+chr4	41812201	41816201	0.86
+chr4	41816201	41820201	1.01
+chr4	41820201	41824201	1.02
+chr4	41824201	41828201	1.03
+chr4	41828201	41832201	NA
+chr4	41832201	41836201	0.90
+chr4	41836201	41840201	0.94
+chr4	41840201	41844201	1.06
+chr4	41844201	41848201	1.02
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+chr4	70629719	70633719	1.13
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+chr4	70637719	70641719	1.05
+chr4	70641719	70645719	0.87
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+chr4	70649719	70653719	1.17
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+chr4	70717719	70721719	0.88
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+chr4	109340735	109344735	1.00
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+chr4	109408735	109412735	1.05
+chr4	109412735	109416735	1.07
+chr4	109416735	109420735	NA
+chr4	109420735	109424735	0.99
+chr4	109424735	109428735	1.02
+chr4	109428735	109432735	1.02
+chr4	109432735	109436735	0.97
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+chr5	15025389	15029389	1.12
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+chr5	43028888	43032888	0.99
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+chr5	58303354	58307354	1.03
+chr5	58307354	58311354	0.96
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+chr5	58319354	58323354	1.07
+chr5	58323354	58327354	0.95
+chr5	58327354	58331354	1.13
+chr5	91277761	91281761	1.04
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+chr5	91297761	91301761	1.05
+chr5	91301761	91305761	0.94
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+chr5	91313761	91317761	1.09
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+chr5	91325761	91329761	1.05
+chr5	91329761	91333761	0.96
+chr5	91333761	91337761	0.98
+chr5	91337761	91341761	1.04
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+chr5	91345761	91349761	0.99
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+chr5	119464508	119468508	1.00
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+chr6	85357170	85361170	0.96
+chr6	85361170	85365170	0.88
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+chr6	85762072	85766072	1.05
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+chr6	134621363	134625363	0.94
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+chr6	134629363	134633363	0.89
+chr6	134633363	134637363	1.06
+chr6	134637363	134641363	1.00
+chr6	134641363	134645363	1.00
+chr6	134645363	134649363	1.02
+chr6	134649363	134653363	NA
+chr6	134653363	134657363	NA
+chr6	134657363	134661363	1.03
+chr6	134661363	134665363	1.08
+chr6	134665363	134669363	0.98
+chr6	134669363	134673363	0.98
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+chr6	134713363	134717363	1.06
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+chr6	147470164	147474164	0.93
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+chr6	147486164	147490164	1.05
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+chr6	147498164	147502164	0.89
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+chr6	147506164	147510164	0.93
+chr6	147510164	147514164	0.87
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+chr6	147518164	147522164	1.08
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+chr6	147530164	147534164	0.99
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/hard-withNAs/Feature2.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,5401 @@
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Binary file examples/paper_example/._control.bed has changed
Binary file examples/paper_example/._elem1.bed has changed
Binary file examples/paper_example/._elem2.bed has changed
Binary file examples/paper_example/._elem3.bed has changed
Binary file examples/paper_example/._feature1.txt has changed
Binary file examples/paper_example/._feature2.txt has changed
Binary file examples/paper_example/._features.header.txt has changed
Binary file examples/paper_example/._regions.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/control.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,35 @@
+chr1	91399892	91499892
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+chr12	15210277	15310277
+chr13	91106037	91206037
+chr13	91518822	91618822
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+chr17	58542142	58642142
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+chr21	45089115	45189115
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+chrX	37029585	37129585
+chrX	103593349	103693349
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/elem1.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,25 @@
+chr2	49960150	50058150
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+chr6	147472164	147566164
+chr7	77197798	77293798
+chr7	77884914	77976914
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+chr10	46352885	46446885
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+chr12	95522506	95614506
+chr12	117869466	117957466
+chr14	100464166	100562166
+chrX	29266748	29364748
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/elem2.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,20 @@
+chr1	65942901	66042901
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+chr8	25475691	25575691
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/elem3.bed	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,28 @@
+chr1	49721616	49821616
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/feature1.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,108 @@
+chr2	49960150	50058150	NA	0.94262393	0.781642204	0.892165843	1.125914428	0.794702705	1.189725645	1.093851314	1.111683966	0.792379914	0.992690747	0.950415463	0.902397696	NA	1.103429799	0.939850937	1.084582974	1.029612124	1.065450723	1.227229075	1.23306801779749	1.06754194708522	1.03042670698303	1.21000942996344	1.27106402217427	1.27378353582558	1.22008143403318	0.919197201681516	1.0113523996945	0.918139743559695	0.789399804	0.877614552	0.938689617	1.023859386	1.089562776	0.91275793	1.083397157	1.18376341	0.900444988	1.080563235	0.959463578	0.849602699	1.014094534	0.944870837	0.889909954	0.907349556	0.945458245	1.218876455	0.965712384	0.955782111
+chr2	55914445	56010445	NA	0.997520895	1.161945571	0.975966044	0.810432058	1.012036267	1.046274443	1.054287541	0.939107794	1.234992499	1.130447455	0.826938145	0.954778392	1.125009683	0.724496099	1.108436018	1.03161832	1.047116257	1.023861504	1.133802208	1.07669242138214	1.11615676539188	0.946639104382872	1.2152082328117	1.02666905530112	1.16940823370869	1.06861643096178	1.0167684822112	0.919265631844583	1.04144387443392	1.166706942	1.032902267	1.072657048	1.01108553	0.932459047	0.983388281	1.005086891	1.033576232	0.910766248	1.173153733	1.008185187	1.022832698	0.958712482	0.781899645	1.119467755	0.978860832	1.04698641	0.96035837	0.97868521	NA
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+chr7	77197798	77293798	NA	0.850723552	0.977913352	0.942508431	1.057193106	1.064357391	1.074901049	1.055744716	0.862989204	0.96879308	0.856682075	1.046356507	1.199615354	1.044230904	0.960589051	0.945323538	1.03912311	1.011444952	1.023078472	0.78117618	1.09319081976958	1.13697301497374	1.24786889078218	1.12306242917941	1.16990796543967	1.15950495585202	1.05109067327952	0.939074445618681	1.00897937681108	0.939606828719063	0.975854112	1.031436305	0.924525105	0.846569348	1.04316829	0.905661779	1.010324215	0.963521941	1.00844752	1.022518995	0.877387638	1.19944264	1.063971209	1.014423348	0.892611145	1.034894826	0.993720512	0.965792993	0.924506508	NA
+chr7	77884914	77976914	NA	NA	1.011961691	0.996087309	0.963162804	1.00612635	0.947370574	0.964245654	0.80056759	0.827200317	1.000526195	0.966212977	1.07262732	0.965866243	0.975538163	1.169099467	0.873063342	1.030130615	1.259743179	1.020293478	0.999768957611843	1.05879024996116	0.995438979381504	1.04464920933337	1.15777894853378	0.967085455525553	1.32069583425323	1.16865786279717	0.990432170207904	1.03530716468167	0.838375649	1.09612042	0.946533354	0.956019679	0.96904314	1.020529114	0.990066279	1.203176199	1.024623129	0.711275798	0.814813561	0.876342049	0.972907783	0.991058567	0.894369779	1.115845668	0.865655345	0.983108083	NA	NA
+chr7	114807399	114903399	NA	0.964466749	1.087832323	0.95262689	1.094181455	1.007784567	0.959723061	1.01054528	1.147461809	0.890409726	0.992691736	0.975112261	1.107540115	1.17793438	0.919941259	1.128207008	0.956563553	0.947317069	1.014939171	0.896213052	1.03510594062663	1.08574251071093	0.978855631373129	1.08894328259578	1.27821874991299	1.07558918797887	1.25589287921032	1.25107232122767	1.01279079627128	0.855224215753633	1.02012231	0.870497685	0.878604434	0.950553222	0.932229648	1.139159645	0.93891176	0.987400634	0.887997451	0.999617429	0.903292638	0.906751088	1.193126935	1.113160401	1.078691324	0.899335498	1.089005699	0.837114582	0.865836227	NA
+chr10	46352885	46446885	NA	NA	0.93738844	0.976716317	0.61070122	0.917148727	0.935181136	0.959287025	1.074651707	0.883343285	1.058574068	0.99354137	0.934891561	0.709206511	1.067635596	1.194376089	0.953695181	1.03552619	NA	0.991474049	1.07743478619478	1.06155474326872	1.0629269445119	1.11489842394783	1.1621465351679	1.1520341608585	1.17407030997939	0.991837015887024	1.10237410519364	1.19854673531051	0.945076798	0.949856263	1.066197583	1.012151455	1.102086849	1.004475476	1.145208783	1.010111894	1.338164648	0.876248402	1.104605618	0.992752384	1.095237822	0.985620623	1.028790125	0.927074254	1.039350206	1.057769863	1.098595963	NA
+chr10	67835078	67931078	NA	0.754164754	0.879774215	0.906324351	1.236996624	0.952857388	1.070407478	0.790608099	1.11657116	0.887394087	1.012573809	1.136515965	1.094322956	1.055665433	0.875170787	1.221311072	0.906978156	0.945694966	0.89808076	1.050780555	0.903707572840347	1.08406278932974	1.16558818508156	1.38137722697738	1.24113794053324	1.31155336502451	1.33415452756821	1.07027148799376	1.07135718384936	1.10559958454014	1.009083056	0.953340096	1.089501229	1.038298277	1.147472324	0.952947284	1.058428587	1.014484842	1.105776781	1.009283799	1.09193063	1.023083535	1.079543194	1.032295095	1.013772763	0.943409302	0.932904461	0.771069131	0.887278633	NA
+chr12	27724692	27820692	NA	1.015018946	0.979910721	1.077201438	1.042176262	1.136547785	1.071282051	0.933189358	0.97389937	1.102683223	1.081814152	1.097688351	1.029903211	1.039816138	1.1484144	1.028167505	1.003454063	1.050279376	0.849515903	1.089662647	1.09944026944761	1.24232558529913	1.04147676324668	0.875924988135612	1.28912889422738	1.07983759214475	1.02244765008603	1.22856742143639	0.92489202854728	1.12489600373254	0.865896906	0.982478422	0.972507206	1.00177427	0.829667232	1.095968241	1.009621838	1.278520192	0.831725389	0.874245804	1.00795286	0.935140518	0.896635358	1.040388099	0.860368035	0.95764349	0.997706195	0.954654447	0.936781229	NA
+chr12	95522506	95614506	NA	NA	1.031666546	1.087808985	0.935597802	1.095580733	1.124058894	0.954635256	0.935366476	0.938578896	0.996753386	1.201681295	0.999254286	0.817017809	1.067874325	1.01534144	0.940595173	1.019345283	0.902362428	1.170811135	0.979181029627138	1.12814017362747	1.14897517666761	1.00157524824404	1.14991754752564	1.08632146588707	1.01294233263679	1.08498488081707	0.950606644139543	1.25544067457317	0.95488923	0.996231006	0.952752724	0.901139723	0.915796936	1.165234624	1.087905694	0.970586503	0.964751006	1.064665337	0.814878255	1.175673464	1.136955556	0.886237754	0.959103389	1.032784031	1.037247365	1.014171063	NA	NA
+chr12	117869466	117957466	NA	NA	NA	0.993747372	0.841093963	0.908192224	1.179806973	1.001629184	1.014673812	0.914327382	0.964149728	0.849804307	0.787482738	1.073736664	1.086001528	0.947957342	1.002082487	1.054502193	0.96592535	1.044302596	0.967208218295743	1.14810368944227	1.07518993594522	1.13922686435708	1.12371290433016	1.01256574386892	1.06063275251922	1.25335997497325	1.02629124180965	1.12016984553498	0.92184014	0.937299566	1.156617896	1.046655895	0.852891162	1.04835169	1.140728084	0.94601641	1.058617444	1.014097291	1.060850261	0.880892433	1.068462543	0.94759119	0.975690352	0.982800926	0.977627949	NA	NA	NA
+chr14	100464166	100562166	NA	1.148973318	1.069684179	0.933394715	1.200644994	0.995147072	1.014456557	1.010270069	1.213793771	1.090105964	1.024308027	0.910265043	1.204164307	0.962205148	1.006878482	1.091468123	1.008907789	1.031151666	0.821555411	1.131775078	1.01625035922959	1.09546665116566	1.18065283125577	1.25276271380631	0.985114263004505	1.14537210220487	1.17402484133491	1.22924236788014	0.954271178646421	1.07272676300765	1.125706077	0.940649646	1.186380338	1.188637727	0.954876677	0.989332064	1.021986088	1.048798044	1.024117591	1.180388008	0.853789498	1.019676143	1.084298334	1.054422335	0.983137019	0.99301192	0.964023342	1.050010145	1.014806155	1.024565791
+chrX	29266748	29364748	NA	0.998146716	1.065576857	1.06999614	1.034773158	0.996452821	0.989102002	0.954337784	1.025052926	1.123062045	1.035990999	1.026787747	1.128633907	0.907754085	0.960094207	0.948883086	1.000720729	0.907040338	0.886843339	1.145121591	0.944890875983844	1.0934627556323	1.11256881357545	0.968442332595534	1.16194480279721	1.04174686732022	1.12511397085779	1.28509124196251	1.02785523416341	1.01100129531262	0.940463203	0.960207039	0.928384772	0.913917826	1.039510025	0.86914871	0.957290398	0.849009824	1.014513156	0.801240842	1.166336876	0.931134534	0.95919341	0.998325168	0.942213087	1.139644702	0.947916342	0.961696839	1.032069802	1.175444307
+chr1	65942901	66042901	NA	1.302221024	1.506098279	1.61587923	1.353075211	1.504981174	1.558581932	1.428164803	1.432707687	1.468903307	1.61590509	1.544818755	1.27545703	1.568466866	1.474753455	1.431158482	1.560166374	1.499815147	1.624067662	1.59810127	1.576863444	1.585501696	1.465141844	1.554057769	1.688479409	1.475457698	1.317496056	1.3880323	1.387169638	1.397978376	1.513177343	1.70166773	1.370494516	1.496616974	1.637296044	1.544647117	1.613824019	1.570946063	1.460657175	1.428547565	1.503809993	1.368158208	1.551154254	1.540993021	1.649572717	1.575530773	1.603139665	1.368021191	1.548699353	1.579569203
+chr1	117128102	117228102	1.632676937	1.353615912	1.403677392	1.61622503	1.524694952	1.273228747	1.595607867	1.476472348	1.466733325	1.483964615	1.361794708	1.520544817	1.452362482	1.352957143	1.327651789	1.367710354	1.405211607	1.487797682	1.605594306	1.605994635	1.564933338	1.410120741	1.656245352	1.547550031	1.497304449	1.324927781	1.465402382	1.508671603	1.626798534	1.550887883	1.529265504	1.539948143	1.322044105	1.452441485	1.420807784	1.537680949	1.452361524	1.514281747	1.53625711	1.620631611	1.474678614	1.533993801	1.416551008	1.384051967	1.53954691	1.519675373	1.478475529	1.652722495	1.376811267	1.280003236
+chr1	190338169	190438169	1.285951585	1.60062706	1.399167528	1.49478459	1.593256098	1.384997076	1.319266748	1.527563297	1.486234468	1.5783802	1.327015859	1.579899803	1.503158077	1.655071064	1.564234075	1.456961704	1.556691767	1.3571462	1.280703487	1.553091236	1.537090071	1.613860872	1.567871832	1.507686908	1.341320669	1.597945674	1.453033582	1.531200499	1.470046275	1.344365624	1.443755626	1.645972706	1.771498412	1.509869307	1.375187683	1.438431551	1.438961151	1.627165635	1.487139365	1.338109904	1.484812419	1.465051459	1.366784877	1.359974937	1.689786377	1.42252905	1.471916906	1.712330566	1.466280228	1.604600885
+chr2	227365478	227465478	1.538609097	1.547007001	1.546968022	1.519621079	1.414818193	1.413211559	1.54884838	1.410811613	1.482248654	1.66856628	1.448285368	1.369637679	1.52084653	1.551191154	1.736892951	1.44296511	1.406410709	1.479286525	1.696746538	1.422221993	1.543670792	1.3928711	1.398786271	1.691985187	1.50091168	1.476051191	1.646277648	1.605090133	1.546124601	1.554926538	1.376629664	1.404211265	1.5178526	1.607012017	1.374016728	1.522859006	1.418454997	1.714845122	1.595263998	1.280997445	1.558116522	1.428088399	1.589211049	1.431012622	1.609792328	1.474982409	1.380782091	1.458749217	1.458940712	1.691484724
+chr6	50856764	50956764	1.323899281	1.673677808	1.513609276	1.37616716	1.516464433	1.660656188	1.460087776	1.528491354	1.395661343	1.394049583	1.27190825	1.420503922	1.361895949	1.552814985	1.47066692	1.46450148	1.44412503	1.587294877	1.576988209	1.600904956	1.36890695	1.664299275	1.42659893	1.531735207	1.40572023	1.57021002	1.469188212	1.580491826	1.43470749	1.396287271	1.642166677	1.351396917	1.453760989	1.409687033	1.42064418	1.364076403	1.445916595	1.554484595	1.544618012	1.260999525	1.420490408	1.522044897	1.447663247	1.592453786	1.408701949	1.342112196	1.466355617	1.40531773	1.642830966	1.709380403
+chr6	135703067	135803067	1.748549982	1.580388824	1.441652741	1.486425249	1.404877337	1.436224608	1.443038894	1.467101115	1.46631933	1.388094672	1.450664264	1.483390368	1.322518331	1.567700736	1.368576803	1.381131196	1.375031249	1.538540534	1.506738842	1.389003785	1.557344145	1.383140022	1.499821547	1.462109208	1.540438797	1.462868198	1.62461282	1.459833753	1.400463017	1.657797516	1.558543148	1.444334038	1.439519833	1.372113726	1.531853052	1.442860676	1.394302014	1.499831478	1.674434948	1.43014948	1.537228183	1.495251184	1.469370711	1.619484849	1.440539199	1.604950854	1.554777175	1.498862545	1.588496177	1.29933242
+chr7	38228726	38328726	1.551833971	1.639745193	1.533187266	1.595484275	1.481693685	1.459112413	1.429647405	1.545968454	1.470090162	1.338855399	1.682489216	1.686976003	1.486726996	1.27434842	1.493545657	1.408259798	1.473880562	1.562366219	1.429460936	1.490114624	1.539147129	1.573836405	1.556053342	1.587785068	1.53249915	1.57292032	1.418600826	1.40651673	1.355542337	1.517232263	1.517409727	1.480004793	1.443410417	1.541619503	1.39821003	1.361042143	1.493724623	1.533424022	1.390168176	1.44926387	1.54695119	1.531275379	1.453895725	1.474310486	1.4926172	1.548665621	1.510373761	1.652194715	1.327399982	1.501582272
+chr7	51115898	51215898	1.55515168	1.416457183	1.463412214	1.535297415	1.579911195	1.602282422	1.475421431	1.518570565	1.438820764	1.530311218	1.471873934	1.404220277	1.460961112	1.601498315	1.557918019	1.392486875	1.611806328	1.796675351	1.367591565	1.461475311	1.618684407	1.540946004	1.376802446	1.548438856	1.393291425	1.448106655	1.545631764	1.666210804	1.537339033	1.408037648	1.440972855	1.468285993	1.459195577	1.435489195	1.563128867	1.498600797	1.346594207	1.392882696	1.54690653	1.319511464	1.529005999	1.431423342	NA	1.287023633	1.408301964	1.451621065	1.382214154	1.510724475	1.534065639	1.415039397
+chr7	150325760	150425760	1.530242873	1.409102693	1.451951902	1.583115936	1.446558506	1.522528799	1.721963053	1.6358471	1.369476141	NA	1.430878326	1.54221283	1.60404339	1.598144271	1.50188904	1.508713551	1.323258818	1.48520884	1.381436217	1.661081636	1.479449293	1.439864914	1.54757744	1.494276578	1.556910938	1.434318944	1.578707936	1.57194963	1.457977608	1.468256563	1.517622839	1.531137342	1.476905662	1.617960537	1.485477069	1.600391958	1.323086177	1.655503964	1.526179253	1.584202425	1.485136683	1.441964921	1.512824614	1.429162912	1.411731126	1.359695733	1.489453952	1.400782675	1.436733965	1.589605802
+chr8	25475691	25575691	1.48286218	1.489094935	1.507267839	1.290483149	1.446769262	1.628727871	1.546665365	1.549852103	1.464835554	1.507618199	1.548281113	1.577613605	1.402268892	1.511868999	1.513669032	1.462606524	1.58192377	1.640858629	1.37853497	1.403689299	1.637207584	1.36658794	1.433938202	NA	1.461835001	1.419831683	1.576634041	1.37664095	1.381544196	1.615682549	1.375085149	1.61696042	1.573351385	1.472411464	1.502104655	1.564947386	1.484803154	1.439785582	1.446926739	1.380794764	1.451536505	1.425704713	1.46174997	1.304249541	1.327977576	1.620229886	1.449191799	1.31387036	1.54215976	1.369651421
+chr9	73374609	73474609	1.577460233	1.501005648	1.601775513	1.453546711	1.447826479	1.332782072	1.532515829	1.737826626	1.513049243	1.368907653	1.612201564	1.611197713	1.445448405	1.682815034	1.382930571	1.462057528	1.602268339	1.363286043	1.684940812	1.390062199	1.379531825	1.501382843	1.659733019	1.328542428	1.475803149	1.420212578	1.532536211	1.417724914	1.674650225	1.461039881	1.420667412	1.403032232	1.367029746	1.809207595	1.431942126	1.568689784	1.39074308	1.542460408	1.601295748	1.565230038	1.42550521	1.459688459	1.573347637	1.652263642	1.58610571	1.648057676	1.478707761	1.491492048	1.491324068	1.476970999
+chr11	55092625	55192625	1.495567909	1.441868228	1.560760314	1.624711615	1.439076268	1.413381208	1.263007528	1.428914376	1.576871163	1.52887114	1.464159659	1.540536795	1.53048213	1.758067261	1.476072728	1.635630599	1.476714089	1.520913213	1.497706312	1.469525587	1.522770485	1.451098235	1.586453115	1.323853682	1.59520522	1.358197336	1.786089784	1.474434113	1.484887501	1.695983922	1.277912745	1.506234288	1.518892866	1.458626446	1.650890242	1.611460792	1.620192368	1.436102457	1.658616709	1.422321619	1.605146049	1.421380255	1.51973205	1.595603105	1.534803502	1.578288077	1.629329834	1.637058148	1.64408725	1.381395488
+chr11	86581661	86681661	1.583969064	1.504825856	1.50897549	1.464132686	1.526649933	1.584467498	1.428778384	1.59608294	1.386950491	1.526380073	1.508441296	1.547707612	1.571638589	1.476560433	1.308381944	1.291114043	1.538773729	1.450346997	1.62871574	1.578361221	1.397594731	1.382836467	1.475862259	1.539431829	1.455035705	1.296875512	1.449340433	1.548363785	1.377366151	1.471205684	1.52314755	1.528956501	1.557401745	1.601277231	1.486809957	1.508365075	1.479499378	1.25854246	1.502560644	1.416060148	1.433320143	1.54120141	1.507213586	1.467656699	1.384317762	1.372205196	1.491647966	1.576372981	1.507932413	1.386216654
+chr12	12795284	12895284	1.473755142	1.461496983	1.598254487	1.319746229	1.457412438	1.565818821	1.484780209	1.529445756	1.636885982	1.358667935	1.435035839	1.548745764	1.595216084	1.427006993	1.592423067	1.404092263	1.559514057	1.390219873	1.457299163	1.45098846	1.423264161	1.542821786	1.528242305	1.619917472	1.401374155	1.572142551	1.584953796	1.462544527	1.483255566	1.652472721	1.51079275	1.556494024	1.524402611	1.774031537	1.62076488	1.545281171	1.590622557	1.446925534	1.501787273	1.711678187	1.610910654	1.446160753	1.461021071	1.454411044	1.469713977	1.495393155	1.357873001	1.409840941	1.299381781	1.630689712
+chr12	48151882	48251882	1.518262718	1.408012435	1.415608866	1.582053434	1.504350046	1.436261323	1.462825066	1.503734781	1.558538141	1.596544673	1.357716374	1.504503722	1.588429008	1.358182422	1.473481881	1.514742233	1.442363773	1.403059125	1.438680404	1.392827011	1.488566071	1.418811027	1.494958387	1.463255661	1.412890435	1.485247146	1.410915033	1.258036226	1.457365283	1.437739203	1.438977147	1.388071488	1.454307394	1.54649175	1.545205043	1.377582823	1.60614025	1.464530125	1.475592002	1.488764059	1.363348963	1.465807493	1.437463033	1.602792105	1.612990888	1.601173736	1.462634082	1.298014672	1.629004758	1.537251872
+chr12	83109951	83209951	1.577133687	1.470264719	1.619770752	1.443194576	1.443189908	1.553340717	1.634669284	1.421784983	1.684583484	1.572641121	1.493028888	1.582872469	1.463693111	1.412885539	1.552816186	1.586447231	1.253385692	1.612148766	1.43895151	1.618943301	1.589650911	1.393079376	1.620235671	1.646878807	1.450107356	1.679076972	1.371139536	1.443558325	1.398089369	1.590649672	1.382042275	1.414847852	1.408878808	1.62483684	1.3640673	1.604040674	1.599542417	1.374028383	1.540071832	1.577551621	1.424052801	1.573223563	1.58604064	1.622310034	1.378954643	1.58108881	1.399936985	1.49913733	1.424181877	1.340143787
+chr15	31430278	31530278	1.537051898	1.395955138	1.420100983	1.446080555	1.476236757	1.536475753	1.599647375	1.501897522	1.392236068	1.396061387	1.636990263	1.537480569	1.37047357	1.568024465	1.362604994	1.638266594	1.417156447	1.627866944	1.495617521	1.422518351	1.483673854	1.613248237	1.528448165	1.415066957	1.349690556	1.461715948	1.459589316	1.362118809	1.44795037	1.491271775	1.48340194	1.427969363	1.606149529	1.429842765	1.501053137	1.724713773	1.509676899	1.605456676	1.532588586	1.345496158	1.571427218	1.417438862	1.655293151	1.691911882	1.485638704	1.413441099	1.380861204	1.736041563	1.487303582	1.434729671
+chr15	65610815	65710815	1.482643719	1.360755545	1.615645407	1.420556889	1.602121515	1.369420275	1.626249597	1.366047004	1.492788757	1.467066883	1.460279633	1.484123951	1.420985054	1.610940384	1.364070801	1.525381298	1.616404652	1.566421904	1.540784093	1.531020592	1.445097673	1.487162357	1.546664772	1.544604866	1.612179487	1.384848144	1.564777976	1.616896709	1.658728731	1.405059597	1.56551477	1.473788582	1.504707483	1.466676825	1.474442264	1.465753191	1.366165809	1.640033359	1.656245869	1.559534228	1.3939623	1.523015541	1.557723908	1.505032313	1.781944036	1.543055196	1.412526985	1.718920205	1.527562705	1.392847365
+chr17	40766223	40866223	1.32120959	1.493905284	1.499071789	1.361016062	1.578773451	1.560184424	1.588303229	1.419777607	1.410919263	1.689648823	1.432813801	1.42405505	1.604403383	1.528533941	1.554163756	1.593958074	1.424405591	1.584457049	1.834788665	1.530395618	1.567849758	1.41817979	1.414274148	1.438788837	1.423339572	1.505296364	1.626259227	1.557311535	1.588823585	1.802708481	1.534642553	1.505552499	1.741668445	1.528256803	1.553678336	1.467728217	1.457327202	1.681308924	1.529424612	1.44998504	1.482506494	1.632324957	1.400771086	1.58227473	1.507986347	1.598812504	1.412288378	1.614085797	1.489418485	1.467671633
+chr20	17245048	17345048	1.401959908	1.700879562	1.447844163	1.450934463	1.433641664	1.512319651	1.686287375	1.573092917	1.318204326	1.423752173	1.570824703	1.562901595	1.337686289	1.244050219	1.842917129	1.445386727	1.446416279	1.613778358	1.524747312	1.3351262	1.351768968	1.518918291	1.649076754	1.315420816	1.416079442	1.503853502	1.42514588	1.60437914	1.632469641	1.575637517	1.471095506	1.73322496	1.392861692	1.470313054	1.653250052	1.545100133	1.383478542	1.548299318	1.503419289	1.588671952	1.411015797	1.460389071	1.528538072	1.577227319	1.326101462	1.511956386	1.429028793	1.523547057	1.517710551	1.330007402
+chr1	49721616	49821616	0.774506524	1.09937788	1.063668995	1.408230447	1.087925504	0.922182889	0.821698045	0.965599315	1.106169081	1.065904344	0.939668209	1.129120638	0.931054847	1.037334472	0.78560402	1.623765644	1.725334295	1.411241283	1.384129796	1.388783552	1.747030529	1.374630045	1.514570819	1.506060702	1.494695415	1.416430393	1.495005399	1.598046711	1.554617944	1.558067485	1.610782998	1.575123599	1.495087934	1.486714521	1.635026913	0.81254344	0.920674626	0.92653306	1.207262936	0.969626435	1.188185098	0.736090629	1.305914244	1.11373631	1.03095872	1.029227912	1.258053244	0.896957247	1.17720094	0.670684164
+chr1	95059425	95159425	0.934734195	0.876218247	1.011308881	1.019556911	1.196670463	0.822218218	0.756406525	0.798442191	0.92882957	1.106866266	0.797293611	1.172904372	1.070959046	0.986491761	1.178288104	1.463209261	1.299401345	1.422061243	1.421143797	1.435273857	1.076800237	1.469294022	1.631741443	1.711088608	1.523146446	1.498227745	1.392247563	1.616686342	1.62956496	1.412124734	1.349524051	1.359128999	1.704614626	1.485797634	1.291210534	1.232733537	1.192208241	0.983477354	1.054667954	1.250317032	1.179893641	0.730158695	0.828163463	0.712228339	1.108666148	1.226119859	1.389100252	1.05895099	0.850100777	1.043891531
+chr1	207236313	207336313	1.197307256	0.972235993	1.187587088	1.149621296	0.859586792	1.021613584	0.826902018	0.942651435	1.044419719	0.70417538	0.903667203	1.042385577	0.915435541	0.944525114	0.736123138	1.5355935	1.052246691	1.694944171	1.360288449	1.578905775	1.447841736	1.514265083	1.335717522	1.506714734	1.438165845	1.380173908	1.518642081	1.366641491	1.659397049	1.489863977	1.797500818	1.426229922	1.442736956	1.390772712	1.575310878	0.973181277	1.100789783	0.77893716	1.008209272	0.958121788	1.013105532	1.145640463	1.264695537	1.025245865	1.152206528	1.235155626	1.230134741	0.898785689	0.818622054	0.785453395
+chr2	73790843	73890843	0.888687083	1.080218946	1.171330935	1.10293533	1.219875881	1.060280435	0.795139476	1.289851814	1.284518622	0.909845884	1.190723426	0.869369349	1.264177928	1.213535483	1.246832353	1.534847491	1.16881159	1.342942104	1.538452198	1.656930492	1.478489214	1.383296588	1.125127056	1.372621401	1.328525567	1.477389598	1.326670848	1.565466817	1.446539461	1.818090349	1.64655537	1.505904118	1.546069479	1.563565454	1.737354886	1.299431657	0.813401638	0.915194812	1.172889314	1.172931652	1.078050762	1.107833217	1.178544561	0.875100273	0.901845125	1.045542532	0.902101054	0.907343633	0.753221984	1.041305772
+chr3	134465321	134565321	0.86550842	1.069796845	0.688774921	0.783120486	1.090862446	1.043463382	1.370135229	1.102775153	0.893684683	1.129282797	1.239897899	1.103004515	0.918282779	1.083039171	1.254228846	1.57948429	1.291883082	1.535344824	1.552551419	1.427124312	1.641592294	1.413979964	1.570512434	1.500917868	1.461545197	1.368984788	1.694049502	1.290075776	1.631447277	1.124200828	1.606774787	1.400592071	1.484098138	1.62775977	1.296948541	0.835181041	1.121747955	1.119762621	1.048144474	1.242114799	1.214755754	1.177673274	0.964596187	1.040978304	0.962176761	1.151339231	0.951187335	0.828513125	0.839885893	1.003248636
+chr4	43433669	43533669	0.886517143	1.227863754	0.839802591	1.00350265	1.06214504	0.944423477	1.096030654	0.921828419	1.017534408	0.962226182	0.832326975	1.334745343	1.18119748	1.032167259	0.77803692	1.421420911	1.513881437	1.411222811	1.364848561	1.58802428	1.565243898	1.709008996	1.668075551	1.724084791	1.707605195	1.270300225	1.598966103	1.436942105	1.60535287	1.341940515	1.677176981	1.38933626	1.575681067	1.667194584	1.711212263	0.993366784	1.084485027	1.009726508	1.157728879	1.063798307	1.185006549	0.937423712	1.003977043	0.997670455	1.24318738	1.183696636	1.157260191	1.104977319	0.998504995	0.974062168
+chr4	122032777	122132777	0.843845378	0.924690306	1.045229019	1.261257384	1.082345089	0.776440531	1.176756481	0.974664146	1.048422531	0.9965978	0.892779057	0.968065799	0.998777269	1.208061583	1.201598007	1.830502002	1.466520877	1.410699455	1.651808985	NA	NA	1.444820251	1.604197501	1.236953648	1.765086093	1.507351906	1.094886884	1.498472486	1.694009166	1.35154288	1.674590233	1.298740176	1.638881555	1.520860589	1.439582881	1.148077553	1.194599726	1.19756491	1.170776585	0.993885431	0.81439652	1.083976371	0.839829927	0.873399096	1.0072539	1.125497893	1.172817113	1.194065319	1.127489896	1.114827366
+chr5	12701747	12801747	0.854532525	0.772815574	1.001589766	0.915362415	0.799031132	0.934643197	0.972559477	0.583612596	0.85439399	0.81849105	0.7513821	0.97393926	0.489791424	0.97782212	1.067591737	1.416170186	1.353612855	1.370574445	1.496093741	1.368704748	1.713783294	1.616838596	1.474430876	1.593144169	1.443656637	1.515007224	1.655397845	1.422109396	1.482720455	1.622547822	1.508274373	1.701759306	1.505856547	1.628875324	1.272733899	0.932658994	0.896010526	0.781156085	0.712130622	1.048881761	1.093805612	1.037542099	0.919216943	1.275913268	0.937463349	0.987927404	0.953037409	1.172989802	0.926135445	0.839608899
+chr5	58501529	58601529	1.14444322	0.816838776	1.159212267	1.049591734	1.338408749	0.867632576	1.460718086	0.998554921	1.078845217	1.447644287	1.025782909	0.904847164	1.009269175	0.973616701	1.145597168	1.70734173	1.717380823	1.363210838	1.858861683	1.631026119	1.497361731	1.703733751	1.640186171	1.622595749	1.735178793	1.777645777	1.570460415	1.231681806	1.592825107	1.528549432	1.372202732	1.703823598	1.413502554	1.539912377	1.726912865	1.30915751	0.899096318	0.832285359	1.106869956	0.995799169	1.064581561	0.820353975	1.016729393	1.238078218	1.114955041	0.964576289	0.921700883	0.850995186	1.119141247	0.912827652
+chr5	152853250	152953250	0.939953327	1.183566989	1.210047275	0.958606944	1.024347614	1.251227139	0.956321141	1.079555563	1.00589087	0.894006808	1.209737773	1.061233646	0.929415416	1.370204791	0.891472616	1.753804675	1.403206605	1.605379076	1.403570545	1.534285507	1.566745845	1.636608153	1.360126035	1.600529142	1.536844354	1.51019584	1.536900475	1.589339208	1.545699974	1.71846112	1.598614953	1.638429831	1.369330284	1.781598941	1.43941903	1.012253522	1.200235284	0.826883009	0.449273656	1.173246297	1.05034578	1.031418913	1.249293992	0.954957111	0.850972895	1.223107745	1.180347266	0.886011129	1.052509996	1.157287632
+chr6	136085023	136185023	1.073646064	0.982507118	1.040660002	1.009995425	1.156614727	1.145709666	0.819621664	0.977756352	1.067359194	1.015800556	0.870374933	0.832111697	0.987661754	1.072852573	1.109385237	1.422946351	1.305508594	1.347465895	1.27247551	1.480728779	1.418907546	1.558687133	1.565534057	1.600770142	1.424620734	1.489959506	1.346859369	1.630080278	1.316662652	1.576726975	1.609785128	1.164849763	1.553612203	1.694567815	1.715251706	0.844926679	1.098703988	0.964531326	0.698862153	1.054871348	1.095641485	0.893974079	1.02224911	1.079137169	1.029194171	0.974879043	0.829590201	1.132664587	0.779804477	1.091310438
+chr6	147019529	147119529	1.147088489	1.077382517	0.883261728	1.031181846	1.128169011	0.927436213	1.099398357	0.766836152	1.047292595	0.893808454	0.978161432	1.023451038	1.043024573	1.015047802	1.292591698	1.4569859	1.590801329	1.483592503	1.375100954	1.351570271	1.598799161	1.665625687	1.500037874	1.670698565	1.269682426	1.339646415	1.601877938	1.376896627	1.72462736	1.438482518	1.610753135	1.59775866	1.550182256	1.451065498	1.532063414	0.971735251	0.937564066	0.805906628	0.89319445	0.786231757	0.877687254	1.105553472	0.928675491	1.107155556	1.173147599	0.819918656	1.084172884	1.10705634	1.253091594	1.069614102
+chr7	14192964	14292964	1.011424118	0.897666885	0.968536029	1.106187551	1.225355836	0.938801544	1.196835432	0.994942895	1.088373951	1.015660067	1.055652092	1.244818428	1.076710088	1.205509279	0.990555345	1.64880969	1.416613832	1.634012553	1.483978096	1.596726234	1.49490893	1.532746056	1.398785857	1.66381857	1.382958541	1.602372029	1.535016295	1.490285673	1.459605822	1.202125679	1.626755745	1.612444442	1.28498573	1.35024346	1.545292301	0.864180555	1.264249768	0.843733389	1.086255377	0.801396774	0.915607443	0.863665425	0.812190775	1.029208171	0.993334896	1.04935205	0.8583245	1.064990425	0.807108002	0.928763107
+chr7	125519883	125619883	0.990074941	0.943126676	0.996926878	0.918549045	1.04349092	1.120895489	1.131348319	1.235415232	1.230802226	0.938678934	1.073823713	1.045707063	0.799169121	1.073723902	0.953143382	1.456794597	1.52897821	1.316436093	1.459544061	1.226799211	1.508676217	1.371883924	1.578593207	1.438664134	1.657046576	1.579421624	1.19439758	1.428590049	1.423441419	1.266592988	1.338203684	1.551136792	1.56584353	1.398506888	1.239076751	1.270449389	0.948641881	1.251005856	1.009630258	0.823795171	1.109779733	1.23527628	1.244933846	1.092071022	0.982884261	0.837382332	1.127838473	1.404895511	1.121410783	0.906482054
+chr8	77652872	77752872	1.017345061	1.022105951	1.076478391	0.73233191	1.02420071	1.039311995	1.064312046	1.047704726	0.763368408	1.136723851	1.184268483	0.835797178	0.914512022	0.817940221	0.863148892	1.437580662	1.923988012	1.28383743	1.380289076	1.65743048	1.560966271	1.574154458	1.737056109	1.593532406	1.584322169	1.500546364	1.37672679	1.177651659	1.505791841	1.433922355	1.658288865	1.455434691	1.471050508	1.728750929	1.60800757	1.116250812	1.012984085	0.884785938	0.842300959	0.900204743	1.034634621	1.008454824	1.132171415	1.362828596	1.272296946	0.855499969	0.650162482	0.945561035	1.01433972	1.082221186
+chr8	108375665	108475665	0.957633639	0.882782341	0.823089043	1.064049753	1.035252722	1.024237171	0.654566275	0.865485334	1.09899247	1.013361138	1.065010609	0.844012616	0.96244761	1.327477519	0.970242632	1.38862222	1.616893667	1.391257175	1.447485453	1.576754216	1.593875046	1.402073594	1.439799369	1.249572668	1.577382036	1.380470588	1.480834764	1.526676603	1.441585532	1.54267876	1.145275691	1.539067877	1.154373878	1.353486963	1.666442552	0.940420497	0.876818658	0.976057859	0.958287876	0.947626467	1.160422696	1.179994939	1.048759283	1.121808274	0.810731959	1.131726956	0.963874638	1.055927869	0.890997962	1.190993149
+chr9	2984971	3084971	1.00840325	1.036322247	0.902773422	0.723208659	0.825324488	0.788931382	1.126437117	1.07334083	0.786457248	1.164924539	0.96252058	1.100080731	1.101772482	1.030838096	1.245950422	1.399277176	1.245218084	1.699923846	1.660046163	1.197411127	1.534235918	1.586418175	1.580834757	1.375276564	1.4078256	1.483882897	1.430069974	1.394274655	NA	1.493110492	1.75814408	1.46650891	1.426370234	1.498430735	1.434236214	0.994219779	0.973355626	1.116723756	0.884999404	1.005542583	0.790688193	1.153181614	0.859684043	0.854894683	1.377504155	1.089417122	1.005014313	1.092256987	0.984623563	0.860642987
+chr10	978822	1078822	0.935260532	1.277943258	1.222436275	1.062097694	0.967247129	1.038001631	0.817764662	0.85896528	1.034891625	1.043663734	1.10754271	0.993358094	1.197491704	1.241788338	1.058014308	1.657146914	1.263407706	1.340677175	1.543766743	1.467400257	1.696390134	1.601375785	1.626096985	1.33411574	1.416491499	1.343233527	NA	1.502156	1.351366466	1.31859933	1.418727086	1.529253504	1.409172834	1.679055636	1.496059511	1.335456552	1.047520988	0.894382243	0.748159852	0.89252298	1.084667827	1.001182342	1.127927399	0.838416992	1.094103497	1.215536073	0.757644313	1.081820765	0.999400216	0.983370771
+chr11	18395046	18495046	1.010775703	1.170014282	1.024495821	1.136185046	1.303739619	1.077148946	0.980345487	0.753323012	0.999663554	1.061277094	0.987580426	1.323031136	1.020811456	1.083825233	1.055211107	1.469645454	1.347846858	1.641576592	1.346259724	1.518375276	1.511621853	1.197881336	1.268010017	1.256157954	1.665167562	1.557640119	1.518562444	1.373608997	1.547351988	1.593496765	1.250681949	1.254411392	1.589076745	1.778138288	1.556355662	1.084782406	1.009288125	0.840868892	0.947623846	0.941748648	1.01843877	0.896289689	1.076114832	1.078463082	1.037570679	0.959708489	1.051208819	1.061464005	1.138695667	0.996313982
+chr12	47273592	47373592	0.965662969	1.048697886	1.007978755	1.109836092	1.038182239	0.794399413	0.809805801	1.068296065	0.881743838	0.966975027	0.882682447	0.940560238	0.709193122	0.969473291	0.93709906	1.363124392	1.564489123	1.422951193	1.507966554	1.592911148	1.670738354	1.508060553	1.383886894	1.786184113	1.544713862	1.520570699	1.619398513	1.674814775	1.652736203	1.44681823	1.412502068	1.6376281	1.49373581	1.312752939	1.472918026	1.248938098	0.916406317	1.068515075	1.117503503	0.87000034	0.926190613	0.833963778	1.008954909	1.106002181	0.68065084	0.922129855	0.925991553	0.980115336	1.412194158	1.144432586
+chr12	60095778	60195778	1.103715996	1.010702555	1.113916369	0.703151382	1.190147116	0.959698464	0.877186479	0.872841644	1.044721883	1.209553481	1.228342441	0.988047514	0.785645238	0.880489852	0.861517041	1.432828531	1.481606383	1.362091609	1.341148909	1.531147151	1.467928403	1.533141689	1.403448703	NA	1.466775647	1.497722161	1.673242368	1.263090075	1.358880953	1.555962338	1.522552356	1.453170683	1.67053864	1.581026236	1.828913061	0.93892384	0.91832223	0.929327625	1.105451265	0.828202415	1.123767397	1.110651569	0.877223589	1.130396449	1.09696945	1.050221408	0.971559904	1.016732858	1.036274716	0.924379322
+chr12	84854096	84954096	0.817068468	0.986795279	1.090934056	1.066826242	0.9218162	1.142360288	0.900600187	1.104902843	0.609110618	1.245372315	0.970953624	1.00138356	1.19827467	1.141679518	0.877622481	1.657947398	1.268699868	1.679689132	1.405426319	1.249216787	1.422905636	1.583041671	1.703856929	1.608253473	1.397708008	1.812852459	1.458405035	1.488742855	1.526259834	1.568283332	1.464668861	1.687103859	1.647815812	1.518464941	1.54369183	1.041051647	0.950660577	1.039268966	0.929469423	0.734338785	1.033401336	0.901854426	0.892342984	0.949857034	1.211968406	1.147660735	0.987069859	0.903823944	0.721047754	0.857862071
+chr12	95157539	95257539	1.0359623	1.222592717	0.91683142	0.952029062	1.111491676	1.114598558	1.071695813	1.033642966	0.556151645	1.16217199	1.086146856	0.943589832	1.3189785	0.845895209	1.121463782	1.597044175	1.561037945	1.538152325	1.47255592	1.333554298	1.295445904	1.499294818	1.529044094	1.480630449	1.394590234	1.807298453	1.294379469	1.302236227	1.674430457	1.434776099	1.540540853	1.296083599	1.651760933	1.322393405	1.579002179	0.837840564	0.778855563	0.882637729	0.596843384	1.239596178	0.805306986	1.019084036	0.952750574	0.901702228	0.976299992	1.06546102	1.082320465	0.801531543	0.683496424	1.007877207
+chr14	23982000	24082000	0.951371723	1.089598264	1.056084056	1.044878611	0.810140089	1.066007599	1.070004179	1.02748732	0.9990729	1.024576628	0.821532503	1.209345039	0.994569733	0.808516872	1.337006735	1.466385023	1.619469343	1.64595918	1.588577067	1.319456933	1.477627745	1.291969594	1.64549925	1.436778894	1.429542693	1.407597029	1.696540322	1.316669654	1.267741834	1.521446279	1.382287165	1.412104362	1.672062141	1.437193417	1.677421663	0.883193594	0.79935424	0.957824837	0.969530346	1.281093285	0.904698142	1.051782736	1.110371021	0.840645601	0.956171704	1.138627072	0.88019072	0.966437688	1.061262385	0.814126939
+chr16	1875335	1975335	0.792894667	0.884153508	1.18784207	0.991490463	0.625860911	1.006802168	1.231720434	1.231966422	1.332796977	1.097935546	0.73925416	0.782421769	0.833989158	1.170745216	1.011924236	1.365116764	1.760429899	1.536363844	1.364005372	1.439116366	1.56924511	1.704693788	1.34572901	1.363329169	1.521984836	1.470503734	1.588114655	1.408328852	1.73908358	1.451148757	1.730767784	1.52487597	1.627147094	1.785377404	1.486381747	0.862437907	0.987084014	1.416995001	0.65959045	1.126151026	0.80622999	1.002264418	0.666941899	0.920857732	0.94724938	0.754814281	0.995567495	0.935044081	0.781716111	1.235753204
+chr16	66789863	66889863	1.239312634	1.09817783	1.120963443	0.952887777	0.983098388	1.183910784	0.888674996	0.917506163	0.844134862	1.166572681	1.083046132	0.945986523	0.71426383	0.827219158	0.946726278	1.382370004	1.597465135	1.29302323	1.262760717	1.485305377	1.482766497	1.587267122	1.517360216	1.891973525	1.648473014	1.580637384	1.365750435	1.599744188	1.453453515	1.322277412	1.659312022	1.788544818	1.822600101	1.466099069	1.523599433	0.972959487	0.813890832	1.185919661	0.841418503	0.926559192	1.107426648	1.012271643	1.369332311	0.734353101	1.147288579	0.664215196	0.845493703	0.882147184	0.809127231	0.81628924
+chr18	64644131	64744131	0.769204425	0.966910211	0.809264367	0.70298943	1.14723877	0.973696784	0.910087798	0.94646829	1.058426656	0.927667349	1.187423332	1.222052504	0.880563425	0.914485239	1.010347372	1.622645212	1.482966459	1.286819625	1.534929397	1.588447902	1.490332623	1.31424966	1.453370326	1.352178982	1.775323709	1.603983032	1.693071648	1.542295564	1.681065757	1.487142254	1.552240874	1.366204502	1.576243551	1.443784374	1.378115375	1.065516368	1.040298462	1.101256079	1.162487974	1.102096504	1.127025409	1.061582332	1.245002099	0.834309456	0.75728973	1.104518163	0.922628463	0.804253156	1.001620399	0.956034286
+chr21	15966609	16066609	1.124408016	0.958928875	0.980859325	0.985836855	0.924304227	0.981319441	0.949853799	0.858050928	0.836178837	1.206331966	0.969230627	1.061200613	0.88573303	0.987056693	1.052660198	1.297451365	1.363179721	1.585535219	1.478006594	1.750420113	1.393291367	1.572557443	1.209291025	1.538532322	1.649854815	1.595757498	1.42205669	1.660538021	1.703860863	1.735418789	1.396824914	1.433365898	1.633863172	1.532339251	1.539522416	1.280749612	1.279224092	0.962647374	0.95080745	1.195498451	1.034622003	0.952643344	1.209463212	0.965927028	0.976116335	1.077560044	0.987244607	1.046203554	1.027612409	0.870263756
+chr1	91399892	91499892	0.914729028	1.037886693	1.156950788	1.054339714	1.058272447	1.002161175	0.873489002	0.873100412	0.928712683	0.941325621	1.06739894	0.909275169	1.100938875	1.053429126	NA	NA	1.096492926	0.902578292	0.821718065	0.909063176	1.125986477	0.96299199	0.886361986	1.197357949	1.105858907	1.118309383	0.89184945	0.921613353	0.961394603	0.94212054	1.041792277	0.846036296	0.903782108	0.92632447	1.016177881	1.018719948	0.863466004	0.911534382	0.909397861	0.882437981	1.200227303	1.022867075	1.008249592	1.133872366	0.917808428	1.009801533	1.078007804	1.057892112	0.983519376	1.063014991
+chr1	116449079	116545079	NA	1.049234869	0.972429436	0.943485097	0.877213727	1.076099557	1.059647065	NA	1.103976436	0.879172377	0.952455625	0.872450869	0.734632501	0.975852194	1.159684818	1.03479249	0.958716781	1.008821504	0.894048456	0.862250242	1.085632735	1.035706107	1.282637135	1.053448817	0.958843715	0.907730747	0.964823765	0.972508804	0.964761127	1.210224634	0.870817358	0.970216008	1.098602698	1.019858847	1.041511995	1.105424911	1.066979584	0.972137682	0.900068042	1.009451791	0.910760202	0.960315924	1.055586038	0.920385441	0.94547208	0.825917997	0.803391879	0.861973619	1.077735566	NA
+chr2	231381109	231481109	0.938545921	1.053550999	0.990663048	1.245455475	1.034765837	1.13788663	1.036187514	1.137000159	1.065831916	1.17340059	1.02717029	0.843654669	1.003967015	0.999772218	0.899826992	0.953521216	0.846461151	0.819825257	1.04835666	0.938116991	1.045088574	1.141602118	1.02299139	0.984519737	0.936479392	1.101126338	1.095085048	NA	0.868292018	0.955809714	0.932906363	1.005716987	1.043207539	1.000888605	0.901074615	1.03317671	1.081396012	1.189679188	0.970074554	1.020751855	0.913959553	1.096760355	0.993266118	1.171556261	1.048664621	0.980570286	1.017010153	1.020704917	1.162521431	0.92719112
+chr3	47386633	47486633	1.062076296	0.970223713	0.857507001	0.955413898	0.97513391	0.947918937	0.979505671	0.961090193	NA	1.047936634	0.949493968	0.883167547	0.984016989	1.127854611	1.057587579	0.942516002	0.926117765	NA	0.826483736	0.982811705	0.758443623	0.966492886	0.900090861	1.125094333	1.086001645	0.962300692	1.24245323	0.81638103	1.080519852	NA	0.905734959	0.892682204	0.859544312	1.029005919	1.108887612	1.005043209	0.966707798	1.064774949	1.144266882	0.963403426	0.920338501	1.161040401	1.091159949	1.082416199	1.192985671	0.820435008	0.952040088	1.083844662	1.026328753	0.992115409
+chr3	99195712	99295712	1.270158442	0.995363567	1.009373606	1.063165354	1.077985537	1.017346167	0.914371675	0.831037703	0.960400409	0.970195668	1.206611242	1.143210132	0.971685836	0.952129359	1.161054152	0.751282904	0.882267119	1.094428147	1.036866939	1.085634288	1.051962363	0.834830764	1.032239294	1.010407458	1.00547685	1.125104423	1.09981574	1.053426307	0.938893154	1.03356561	0.801835505	0.979682864	1.208857791	1.033055987	1.074457136	1.072561085	0.924398079	1.055802211	1.018235171	1.09445266	0.950697693	1.249451365	1.156165349	1.045257813	0.920535332	0.840654315	1.018017762	0.860765984	1.021403365	1.068010374
+chr3	116765114	116865114	1.011955736	0.98765743	1.018370615	0.973626745	0.983619287	0.797242931	1.132136785	1.025294949	0.833481735	0.930307034	1.175109735	1.000314335	1.144801004	0.971289786	1.122934947	0.923644877	0.982800145	1.061217333	0.972841216	0.944613741	0.952009223	1.203276335	0.897025771	1.171280902	0.960588413	0.972936487	0.99224173	0.809816433	0.960560685	0.987702466	1.171594079	0.841790062	1.016820338	1.100587198	1.080960555	1.010151231	1.105527512	1.04039984	NA	0.897955139	1.104482838	0.869435803	1.143100693	0.891344695	1.015252497	1.033425813	0.958320359	0.973617629	1.101202439	0.903418169
+chr3	134349017	134439017	NA	NA	NA	0.901861524	0.948306551	0.977357488	0.948991386	0.864337323	1.134167589	1.165142521	1.028823385	1.155476971	0.997362462	0.895489419	1.13502581	1.106020284	0.830848914	1.000364014	1.226289379	0.945891472	0.843971421	0.85973254	0.833548561	0.888844157	0.886433648	1.007030585	0.874160496	1.053381326	0.986145177	0.933349455	0.931832747	1.378088632	0.770057611	0.868137641	1.05435661	0.806668276	0.886176998	0.82183629	1.027860137	1.00939276	1.02480877	1.086388152	1.08573161	1.036136609	0.957746287	0.982099584	0.928757105	1.065783792	NA	NA
+chr4	68064019	68164019	0.987445626	0.988342445	1.08188922	0.876572175	0.821189012	0.937868171	0.905789887	1.029453118	0.877476312	0.941815527	0.91770701	1.264816422	1.179945283	0.875126612	0.893508649	0.880981265	1.092743051	0.949604569	0.8306799	1.049429618	0.922000394	1.016305233	0.894297439	1.031539922	1.061166273	0.880679739	0.885104341	1.018243485	0.913120987	1.008089224	0.983141943	1.04977725	0.96214582	0.863972144	0.945472161	1.097281334	0.917030232	1.055235914	1.042382891	1.01607001	1.014746216	0.933625276	0.873625832	0.831846625	1.162116804	0.984092453	0.978628262	0.985733944	1.006231367	1.10708881
+chr4	137465811	137565811	1.060050527	1.047031617	0.868666952	0.928315013	1.014795595	1.178428425	1.009041423	0.919518677	1.038331513	0.988696597	1.149264659	1.11424249	1.038197617	1.021778678	1.00654938	0.907240256	1.029844058	1.090761552	1.000744276	0.958539871	1.155082984	1.165660409	0.962556475	1.065622279	1.076208758	0.930910521	1.1738051	0.93669891	1.065596918	1.101628498	0.874310082	1.009399238	1.001961146	1.083464825	1.056185933	1.061103167	0.86502318	1.200676736	1.153788359	0.759198252	1.11483377	0.996170494	0.91644432	1.167465883	1.092555333	1.046405464	0.961445055	0.931607465	1.147957647	1.119287239
+chr4	173293016	173393016	1.047565034	1.040902514	0.864028881	0.957061102	0.894159471	1.120136772	1.048714465	1.108382628	1.007684407	1.04607039	0.993684206	1.116214089	0.974887057	0.914892294	1.038778824	1.16173203	0.961858968	0.974977272	1.096123572	1.0818147	1.064611635	0.869308794	1.045805115	0.910994784	1.100235178	1.003461962	1.015930561	0.90858743	0.844162164	1.108120083	1.051114901	1.021908588	1.037515318	1.032546662	1.042075805	0.937427914	0.991194078	0.932885807	0.995898278	0.845646207	0.903065117	1.104393524	1.128828787	0.862876543	0.920517786	1.020336197	0.998157937	1.129664661	0.891510312	0.976494824
+chr5	59044110	59144110	0.970045968	1.035854602	1.076957707	0.868116041	0.943722234	1.01810034	1.082896356	1.173547701	0.940731496	0.922794533	1.097132769	1.035971887	0.918608256	1.139931611	1.028122081	1.08713688	1.005470342	1.097729112	1.054585171	0.970111787	0.986697163	0.968674577	0.788177841	1.051221045	0.983563209	1.009326698	0.84639942	0.929584908	0.964155822	0.987506987	1.064683589	0.980337244	1.000963308	1.097581733	1.127080302	1.059790743	1.290726438	0.908737178	1.049293994	1.0787095	0.926669462	0.84701686	1.021779977	1.112257566	0.946654683	0.85669554	0.997600828	0.97256597	1.078943311	1.018956354
+chr5	94592763	94692763	0.928602456	1.005037589	1.057250105	0.814020845	0.862531638	1.012471033	1.080297723	1.009161792	1.005879001	0.951436155	1.08341646	1.032610539	0.889610093	1.112491305	0.911120757	0.934783159	1.020754024	0.994811881	1.053992426	1.092865891	1.094989867	0.957525274	0.919268006	1.185104537	0.976799603	0.953021143	0.827747807	0.925161678	0.735726392	0.963343194	0.931377999	1.026758032	1.046664938	1.120858014	0.785820754	0.925371237	0.934089148	0.965085762	1.035389464	1.053209248	1.080799805	1.02510273	1.068637237	0.947897996	0.993154687	0.985610712	0.93588839	0.872861497	0.990891669	0.815251113
+chr5	108436006	108536006	0.976777568	1.114317435	1.074294878	1.067811873	0.927200917	1.122791569	0.990458503	0.824568119	1.036172898	0.994967545	0.844142642	1.080725926	1.056030032	1.043489457	1.239087473	1.044573655	1.05149881	1.021278653	1.077580918	1.128425749	0.913103164	0.906677612	0.938278179	1.040788042	0.944339447	0.919893475	0.959450864	0.901883573	0.999593684	1.006764447	0.916830154	0.828742202	0.930393386	1.009075789	1.039012455	0.969632207	0.86797819	0.853184582	1.04870954	1.051494644	0.989970312	1.094537654	0.984437872	1.119510991	0.894016224	1.107975259	0.93353325	1.106413914	1.050239905	0.988529446
+chr5	110836898	110936898	1.016238302	0.859928543	1.069132694	1.080131787	0.846751387	0.93376195	1.123540845	0.990209748	0.880756108	1.117560312	1.139640033	0.852271719	0.925605607	1.120401723	0.925159914	NA	NA	NA	1.092219153	0.966962463	1.165682604	1.001157436	0.897117352	1.060288237	0.997842493	0.954483836	0.958584025	1.02781325	1.071460999	1.092190908	1.025025892	0.697306014	0.962693586	0.936097212	1.034195294	0.958948517	0.905379517	0.959033351	0.8527043	1.028285758	1.025310803	1.136678427	1.008355953	0.924940387	0.910533514	0.942733172	1.213465524	0.908563399	1.082582897	1.007646033
+chr5	146669073	146753073	NA	NA	NA	NA	0.941409053	0.879074162	0.975704916	1.182113923	1.084857652	1.01486748	1.027171377	0.973100075	1.086701223	1.087643832	0.840572785	0.942171473	1.16415223	0.965976752	0.911574418	0.947409112	0.849802802	0.898701955	0.998041244	0.854518159	0.964577142	1.192107775	0.978314217	0.842872613	1.012263246	0.848339746	1.002486202	0.987401668	0.98683414	1.182856597	0.980270013	0.766046299	1.063669332	0.979494111	1.023073785	0.998041848	1.004354924	0.971294794	0.896919534	0.793968271	0.957832572	0.908206903	NA	NA	NA	NA
+chr6	99727306	99827306	1.04163323	1.091997928	0.978060114	1.033992859	0.963823351	1.048397575	1.038155167	0.871379686	0.931780687	0.969235245	1.030309945	1.127994855	1.034616411	0.971594933	1.105190985	0.886570733	0.943790186	1.148648094	0.975506109	1.230209638	0.849296043	0.949088641	0.902232885	0.898018554	0.915111211	0.908299603	0.965961365	0.9425258	1.00542318	0.926189155	0.990176039	0.888136178	0.987182899	1.051381743	0.77060758	0.875543712	1.04224684	1.066931235	0.901480706	0.948260703	0.93078043	1.038106435	0.938329808	0.920533482	0.904269315	0.914690847	1.1041295	0.933002405	1.020502155	1.001979512
+chr7	88291325	88391325	1.157645799	1.053708771	1.056155629	0.925868689	0.936509921	1.257706773	0.960978216	1.071637162	0.96834958	0.877733353	0.90601784	0.945901393	1.005724688	0.900311385	0.99851067	1.196980286	0.926220043	0.927305353	0.935938599	0.781456543	1.005790264	1.035573096	1.076224891	1.045980024	0.962489382	1.080515657	1.053809624	1.143026	0.849358629	0.991330587	1.05551539	1.005324457	1.044663238	1.214387936	0.875654383	1.206789772	1.157634328	0.844240225	0.877658109	1.191713721	1.010479627	0.984994219	1.027423933	1.067833572	0.992211647	1.053494225	0.931717271	1.023507006	0.877417002	1.053462557
+chr7	120999784	121099784	1.023838305	1.027880659	1.035040075	0.837700411	1.039695872	0.919676844	0.991652209	0.978606678	1.162461053	1.054628134	1.0079066	1.021551881	0.998942298	0.908477539	1.069451976	1.075926232	0.973283773	0.899089005	1.077930894	0.930064217	1.114997005	1.195836244	0.952071197	0.952123668	1.044794765	0.899667504	1.101462596	1.044709945	1.198680841	0.953606177	1.020753964	0.991954499	0.862834745	0.970822826	1.090065507	0.929006592	1.148104027	0.926931169	1.045315829	0.925853787	1.056536145	1.161961388	1.010943	0.829965335	0.893979398	0.884033676	0.900094684	1.211609545	1.155290664	0.994098571
+chr8	126860366	126960366	0.884364681	0.932943346	0.828582353	0.908535158	1.102726299	0.981912397	0.839456681	0.884576719	1.014742667	1.014405543	0.93225706	1.05743299	0.914159672	1.044681847	1.03394101	0.923193333	1.072990311	1.112608791	1.058623385	0.968019686	1.018046712	0.894269597	1.075877924	0.935746744	1.150974122	1.236902006	0.785226865	0.819136217	0.866182795	0.708723684	0.979663895	0.842238685	1.098704633	1.175565132	1.020374496	0.921735827	0.95442105	1.014669267	1.21581105	1.063189912	1.079098868	0.96332199	0.908262444	1.132700173	0.7900559	0.904878042	0.882705353	1.107062633	0.937505272	1.007892277
+chr8	127636547	127736547	1.029357928	0.918536414	0.995512291	1.044577563	1.019501153	NA	1.04440564	1.0619479	1.074694175	0.946383953	0.91353213	0.830281166	1.049659439	0.985248033	0.993826335	1.068110005	0.948125951	1.062712393	1.102401928	0.968190902	1.005755362	1.107927369	0.946664528	1.089501737	1.030293411	0.882000747	0.973074572	0.963563569	0.844179926	1.026847205	1.044984637	0.89298441	1.198385601	1.044027494	0.872414846	1.059535668	1.081883757	0.969249595	1.195340364	0.968422568	0.834786958	0.883629162	0.939353917	1.018170662	0.972911692	1.226283837	1.009700805	0.961435994	1.065376785	0.911305817
+chr11	41362564	41462564	1.008820676	1.066409144	0.888694378	1.036316392	1.04609798	1.139077813	0.940707228	0.987082259	1.132422318	0.992857069	1.085377204	1.051787982	0.832415632	0.859449819	0.794672671	0.942685377	0.880702646	1.138858814	0.919380791	1.066408809	0.915705078	1.027999511	1.045165447	1.096697533	0.88639158	1.078950047	0.954650741	1.03497876	1.043128394	1.026042357	0.874742378	1.05925962	0.890848054	1.005557543	0.923529329	1.068135779	NA	1.06935397	1.072911803	1.052583684	0.935410209	1.077008958	0.845207708	0.857151679	1.162929721	0.912046529	1.02760565	0.98798691	0.893396708	0.845473274
+chr11	101741527	101841527	0.942359255	1.089415586	0.95962796	1.086020643	0.804735744	0.949953785	0.860643517	0.901069295	1.078502106	1.142577754	0.898006258	0.962207068	1.062820092	0.915224191	1.2245536	1.221909587	1.017638247	0.900236829	1.118932903	0.95774623	1.060416607	1.056930317	0.965482811	0.940023636	1.02377161	0.989756621	1.028709516	0.96778865	0.808453811	1.055195494	0.959349483	0.926905436	0.91275336	1.048022623	0.906544709	0.880093291	1.125019236	1.178249577	1.115574076	1.080330372	0.964662226	0.986228798	0.971028346	0.98093756	0.887887365	1.003302315	0.893245122	1.037853655	1.012259621	0.869775917
+chr12	15210277	15310277	0.944169011	0.866288448	1.032204712	1.076020134	0.998296658	1.072217097	0.983797829	0.952864734	0.973436855	0.969758719	1.103519618	0.940267894	1.079870055	0.854254063	0.99674239	0.968500489	0.941869744	0.989430785	1.02352565	0.939188771	1.038692089	1.030154949	1.033560856	1.019759029	0.961135365	1.002901485	0.956996426	1.092161703	1.04320007	0.98614937	1.000051705	0.968860869	0.9626575	1.061604261	1.161967912	0.933498173	0.95000128	1.041967207	0.907089514	1.05533374	0.878320782	1.110665617	1.074861319	1.110063055	0.989652093	0.875873818	1.001263475	0.95871525	1.04047788	0.990123198
+chr13	91106037	91206037	1.262571776	0.734735991	1.095391967	0.93808342	0.943646564	1.016764901	1.076257711	0.91340799	0.773725217	0.877179005	0.944089177	0.932135594	1.09073639	1.171475272	0.847277034	0.873679195	0.947872224	1.096495555	0.891153819	1.044813657	1.120443638	1.094289139	0.887785295	0.98772	0.730023414	1.01333116	0.919504798	0.929504755	0.998365502	0.939298442	1.053110929	0.875675696	1.193355068	1.118871696	1.013686623	0.985414672	1.077144924	1.073912848	1.057814608	0.92579275	0.906803056	0.926983874	1.05931726	1.069924211	1.103030121	1.03742299	1.13985435	1.031038036	0.647621622	1.027176556
+chr13	91518822	91618822	0.960899438	1.082342887	0.99789296	1.08475727	1.217319579	0.950400644	1.127502974	1.009670828	0.878158897	0.884695487	0.950179332	0.967915323	0.966185856	0.935244046	0.842553541	1.077816919	1.057232253	0.920317829	0.8929266	1.084584372	1.136125371	0.891764372	0.986278036	1.047345444	0.90074013	0.874658634	0.955536126	0.749422854	1.046901182	0.899296201	1.047364576	1.178875606	1.112788723	0.940451913	0.914074588	1.068716376	0.880647677	1.115865959	0.871057152	0.918695368	1.009588011	1.00955855	1.067471226	0.983103684	1.284847545	1.075543346	0.860343571	1.02714843	0.985479642	0.845989848
+chr13	98963030	99055030	NA	NA	0.998124088	0.941233349	1.020516778	1.082098359	1.061763926	0.86715405	0.890546661	1.062189059	1.120522574	0.949540379	1.063080486	0.927945555	0.950233362	1.139649245	0.962486651	1.122056742	0.965504093	0.901575197	0.977554404	0.909824633	NA	1.041517243	0.830846694	1.083339508	0.946254143	1.061817057	1.026686856	0.944602297	1.098756992	1.110115287	0.866377042	0.947826745	1.141915662	1.126549339	1.020088449	1.136977036	0.871538906	1.032255307	0.899455628	0.93392765	1.010541135	0.9187502	0.901022216	0.866013025	0.910701809	0.941822998	NA	NA
+chr15	39087176	39187176	1.075754549	0.984732204	1.017598921	0.926487241	1.081709811	1.134898895	0.989137706	1.112449577	0.967471164	1.176075636	1.105072921	0.997946966	0.953296698	0.761845735	1.068734977	0.86028425	0.978115025	0.892134595	1.027014407	0.96539193	1.106402866	0.929669032	0.932142456	0.923985493	1.167746462	0.91904067	1.036507584	0.897959204	1.015372539	0.97252977	0.796445742	0.921793832	0.922546715	1.095436262	0.821887092	1.091471469	0.944683383	1.03508594	1.006227039	0.969964744	1.083842018	1.000410228	1.148132641	1.053299423	1.02686973	0.986857834	1.099602558	0.907362807	1.005225175	1.074648759
+chr17	58542142	58642142	1.152551451	0.813427107	0.829069799	0.875869268	0.928133603	0.967465743	0.902621356	0.877372441	1.094621847	1.17912888	1.014956933	0.851645933	1.050341137	0.962627858	0.956843417	0.987129683	1.13593474	0.900420294	1.123320125	0.92884971	1.081817641	1.185064263	0.959119041	1.110039712	0.958483624	1.190948203	1.051043364	1.040039908	0.916771865	1.004831251	1.05502407	1.095368983	0.989283483	0.879670448	1.09174434	1.064317641	0.86725729	1.007779226	1.009270559	1.059761551	1.056111543	0.886379787	0.854492309	1.043384065	1.000133905	1.022200835	1.220412256	0.832970316	0.803218042	1.000386525
+chr18	12199823	12299823	1.263654694	0.988269655	1.035978479	1.116959535	0.865032018	1.172649963	0.83698752	1.075913181	1.149530266	1.079699219	0.933023991	1.076489959	1.029621239	0.903293561	0.804310598	1.022997054	1.031882692	0.832547062	0.933932575	1.051815306	1.097535287	1.041913128	0.82933811	1.045265729	1.100145352	0.984170134	0.973632283	1.090727064	1.028455044	0.986754629	0.885206841	0.936002282	1.078601604	1.030277211	0.984574816	1.007336494	0.821501009	0.874013881	1.07621773	0.948910844	1.18818458	0.785530297	1.197901659	0.875093235	1.114923051	1.055820922	1.089244152	1.232197494	1.030509037	0.938091223
+chr20	8173704	8273704	0.970809408	1.117932082	1.06303146	1.007305847	1.012419213	1.114443349	1.037593987	0.997913206	1.124896156	0.795070067	1.126326854	0.885342594	0.893283558	1.080229541	1.043566132	1.064241313	1.073251079	1.164836602	0.77262778	1.091781567	1.066619573	1.141396027	1.032737097	1.013127889	0.964386912	1.056496569	1.007627293	1.085610218	1.032050085	1.019055263	0.943978981	1.034148636	0.990345945	1.014039798	0.922814154	0.881603932	0.827687325	1.083375603	0.946779408	0.939221292	0.819590588	0.790962263	0.999039926	0.92481105	1.035965206	0.852361627	1.181121901	0.994575516	1.060331362	0.983666463
+chr21	16255112	16355112	1.177105519	NA	1.071517224	1.030859496	1.089008921	1.039659673	0.883594013	1.21009346	0.826187452	0.961992291	1.044089309	1.057497966	1.129194301	0.875974161	0.921098831	1.02470614	1.15795123	0.823673836	1.114013422	1.046857781	1.057536457	1.06438401	1.033940269	1.078392268	1.014473553	1.132325796	0.898022689	0.94228443	0.634163551	1.13654097	0.978434334	0.901865446	0.979448392	1.115154429	0.88726117	1.039289778	0.934290937	1.124469328	0.981034716	1.079334172	0.890674582	0.99304165	1.036942115	0.909604473	1.014269152	0.862691129	0.908143072	0.98482788	1.002454774	1.170056591
+chr21	45089115	45189115	1.128766975	1.14005722	0.96116741	1.082705974	0.963650005	0.827323587	1.067023661	0.917567025	0.989751759	1.010219166	1.082917953	1.245031656	1.151150253	0.997437239	0.858137326	0.98198696	0.850794707	0.99180389	1.082099157	1.008377358	1.08751314	1.073916835	1.201830084	1.004069188	1.006114424	0.792034461	1.129284618	1.007236686	1.01976535	1.030684776	1.019549208	0.966675886	1.055072414	1.011617895	0.839540579	0.980997231	1.04627179	0.816653056	1.033705401	1.054165848	1.052020039	0.816863479	1.171636489	1.147925102	1.14014694	1.053253523	0.879102941	0.967322915	0.941265221	1.071801399
+chrX	23898983	23998983	1.095956071	1.035904265	0.757938585	0.954327563	0.928770006	0.847426753	1.089608835	0.955892591	1.130729633	1.082264273	0.958715215	0.90091568	0.942003917	1.010964789	0.940231198	1.180425637	0.950425986	0.950483043	1.051233349	1.048891592	0.776983412	0.910588698	1.239470441	0.95990234	1.076000458	1.025641956	0.947949452	0.804913701	0.910973613	1.022080299	0.980462332	0.96781169	0.932764086	1.190362601	1.027322553	1.149071578	0.889516954	0.935487957	0.946885545	1.073126316	0.980312197	1.043955933	1.101269957	1.064177944	0.923214112	1.089247244	0.884482905	1.029376267	1.157709555	0.984456503
+chrX	37029585	37129585	0.98122434	1.011630647	1.230283632	0.891470471	0.783631045	1.066342819	0.927321445	1.085527539	0.993568587	0.843088512	1.086477024	0.875131243	0.978607197	1.02131458	1.114798021	1.089478532	1.054893683	0.984181112	1.218871163	0.97708926	0.90916199	1.037263452	0.99435055	0.913535387	0.885835686	1.120085293	0.746787617	1.090131115	1.096296609	0.963270724	0.986765333	1.252219318	0.980515077	0.822161692	0.875149266	1.093895114	0.936458408	0.93051396	1.066030352	1.021325533	0.985920595	0.852340716	1.041090942	0.962076024	1.131767695	1.160041034	0.778883063	1.010510275	1.181604274	1.043847295
+chrX	103593349	103693349	0.936415479	0.859715361	0.976667748	1.004099321	0.929985084	0.956524376	0.975445569	0.918743462	0.769553884	0.893753739	1.038432231	0.929975777	0.992950192	0.939068598	0.850373566	1.077598699	0.944390212	0.903804745	0.929229543	0.910550822	0.874731622	1.017930204	1.034993706	1.028853504	0.953183688	0.956823258	1.025889085	0.948570076	1.017572603	1.046571516	1.086105993	1.084022344	1.153320158	1.07270122	1.080699057	1.003759777	0.85552851	0.952183729	1.077855327	1.041314276	0.932338492	1.064333457	0.890314599	1.188471466	1.026837475	0.893522714	1.013810089	0.903361049	0.799854911	1.017848509
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/feature2.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,108 @@
+chr2	49960150	50058150	NA	6.06024603927522	5.66339250643023	5.98491788533868	5.89566164014674	5.67509100885992	6.17718485715483	6.25525988941349	6.13419496045146	6.02309132104361	5.6907852827365	5.97696019147247	6.06898504563158	6.19811248450889	6.11789029560194	5.97378475421173	6.09032932757932	6.119340786178	5.97367320592689	5.91695929095814	5.95788266535406	5.85958975316589	5.92692167975047	5.97530489883431	6.19465295805737	6.07337738045431	6.11984936793537	6.18335296396836	6.27317740607339	5.73683764564453	5.78534168878846	6.0373119165995	6.05861267940555	6.06109416553306	6.24744462437121	6.13770460019817	5.51738475681524	5.88449206940354	5.95431028164373	5.95196302766881	6.27714436237652	5.33466843886919	6.29287732225571	5.98461532145612	5.90741580769078	6.27255947181976	6.16373285780621	6.18430980153562	6.12992725731244	6.19047386112561
+chr2	55914445	56010445	NA	6.13008749558118	5.87352059082773	6.2566521440462	5.92289748004593	6.02398354047441	5.68218631698084	6.08277768737753	5.82779858566119	6.17994880126712	5.97336222591632	6.31857375045222	6.32315934372086	6.06822127014921	5.68691143179597	6.18768497725833	5.87850638348253	5.55565496481075	5.99284618170363	6.05793491041518	6.18620311137425	6.15627335184857	6.24983411318564	5.88945149315978	6.00051893928219	5.8869710901493	5.92380205361588	5.89466003933414	6.05582116637007	5.79486331060924	6.01021601264105	6.43336115522525	6.25277302758657	6.15363689682735	5.79577949256957	6.03590992906734	6.02704208678425	5.80098998550242	6.09201062256286	5.79947850351777	5.71621024240232	6.0743380359125	6.01480553908656	6.11003461894382	5.98852602343237	6.0203716788541	5.89040878553694	5.79214164950517	5.85862014677883	NA
+chr3	140330750	140422750	NA	NA	6.05197882398586	6.22741374393606	5.83933224256848	6.11226992687831	5.88576889843699	5.86422741431383	5.91277666135517	5.71763308970134	5.73001349050373	5.84194980911574	5.87807030743253	6.26556784463186	6.11900466435129	6.37632394453355	6.00778814980201	5.93317480923638	5.79883874966036	5.92435460610702	5.93554445368991	5.84105582597051	6.55204150136781	5.72731711017526	6.23900072962316	5.92117419583373	6.02727335302886	5.81280509729581	6.11366781843796	6.03713234066355	5.71526271793194	6.03524115526765	6.01568435459379	6.09177050579587	6.16654857328973	5.97096374266677	6.01817361499121	5.79133209750679	6.23939035641288	5.85335040572262	5.99313667358934	6.00580935931276	6.35653378859505	5.90288071297678	5.9890580929073	5.95469850679321	6.1035955148999	6.09539004711721	NA	NA
+chr4	41774201	41870201	NA	6.23769336759385	6.06282010045362	6.02229113080518	5.79883154295246	5.8667410913441	6.14529070402206	5.85780595415378	5.92811993165277	5.78214550655575	6.38654556587901	6.07775488202319	5.89840219028158	5.77253067623375	5.86268254067261	6.04383391488889	6.097159187772	6.01055206661177	6.226406947123	5.52157214409182	6.02362873829766	6.21076232715197	6.12173187816025	5.48784328596158	5.88431847324102	6.12201261235468	6.07737456286197	6.14807535922196	6.24756314471972	5.52958689569075	6.12080083468414	5.50996984059744	5.74740750171817	5.82598295520573	6.06297975011948	6.12048088597781	5.90867150534097	5.79732770058305	5.7780755736448	6.45096219345197	5.56090313902356	6.02895973985621	5.79124250049178	6.11257330636146	5.80801868448084	6.02815102402724	6.11755434284472	5.93005204397862	6.45930367182979	NA
+chr4	70633719	70725719	NA	NA	5.93490064286332	6.09788160336497	6.30189459143248	6.46363044361727	5.98552304794787	5.81547299871371	5.97765881870882	5.64623437037155	6.13995985733723	6.05847065349694	5.9973396606636	6.11463035071014	6.14801997146825	5.89903818624257	6.19674970140611	6.13360773252033	6.09294118446684	5.85947056598473	6.0050032379306	5.53990495729871	6.04112459209713	5.87968227089722	5.76676000355971	5.88725587687006	6.04936693427577	5.69713042780102	6.23966996193731	5.64900256618959	5.67995023578089	5.98803102337478	6.06678621466185	5.94386208419068	5.89731290311462	6.48984431364225	6.03664863641087	6.10833113716289	6.35496309675517	6.00923049110908	6.0919918934351	5.89020167668789	5.97368758551073	5.86874194330179	5.86551200327721	5.97985461722694	6.02692080783279	6.21464069484212	NA	NA
+chr4	109344735	109434735	NA	NA	NA	6.08713058383544	5.88606742415739	5.93611109962382	6.08246584090018	6.05517050907905	6.11304558656689	6.35861887782231	6.14804261777474	5.35151027338729	6.14253459554676	5.59576445178488	6.15022167009356	5.82773905557357	6.18100740191119	6.08688335954126	5.54920285147277	5.64728053429768	6.11751505624223	6.20116059054184	6.21540963930682	5.90176566062083	6.04714494971578	6.02564431323902	5.59739918755751	6.18581140273619	5.97176965832817	5.89323792210806	6.04648589002548	5.67611118111376	6.13377902502804	5.99242873063704	6.00918864280005	5.77858604322927	5.79836200826469	5.88683021447347	6.00063555545614	6.00400990416582	6.37718621540332	6.00190554236244	6.16001635660319	5.8817491813174	6.04106392843705	6.21093109114137	6.19751233379476	6.24789215055588	NA	NA
+chr5	15027389	15121389	NA	NA	6.14918565000235	5.66270594488457	5.93691506064313	5.66773142684048	5.63824758148985	5.9836710137783	5.86754982840678	5.75026482030362	5.95523144477664	6.06657755449352	6.12071871890893	5.9763911530301	5.94763749544786	5.80343198271318	5.78069213991773	5.86758104863239	5.98560948088585	5.65193800715905	6.11133938307552	6.04380346613573	6.39924786744423	5.95896685312244	5.88141041868381	6.45834592105559	6.09257484648593	5.51530621033745	6.19440993487116	5.79841837894238	6.08075552073458	6.06364828341391	5.90819626017009	6.14834452939599	5.99207122891425	5.93712383763256	5.84509986842274	5.72027795912808	6.08804588392838	5.99298845879201	5.92804949584247	5.99186406444421	5.70703698754775	6.20967621790208	5.90342694981502	6.1028098040124	6.00336243488415	5.93668331648391	5.93889432406945	NA
+chr5	43032888	43124888	NA	NA	6.40699457331794	6.13932282854157	5.97909959191179	6.04511055361314	6.36921893451242	6.07800240425351	6.28987222656568	5.76098188450095	6.29218506171759	6.13762455076927	5.77935007705354	5.84069432939518	6.20037974876812	6.06947348791888	6.19137447186285	6.0918514830094	5.79427696948596	5.96028569802399	5.97253047807671	6.20035615853316	6.03458941316247	6.13772462952198	5.8792774367363	5.95949184713602	6.4610569735247	6.22209351159204	6.22876150674964	6.26222635583059	5.70175075622823	6.03192129366895	6.16360052638377	5.82241564813318	6.32896123592442	6.08061287184316	6.20165964531106	5.78587444293323	5.81021239929512	5.94225655003481	5.71716129838189	6.14893950874423	5.77202552127982	6.23692631558779	5.84090675585788	5.69519401121138	5.60863623775338	6.0055850289001	NA	NA
+chr5	58233354	58329354	NA	6.21680884021598	6.22996794875741	5.84114611585246	5.82554950588044	5.80217338811548	5.83953121813085	5.89664934349622	5.71725252406577	5.88436272755021	6.04278627955942	5.89022502391158	6.2640997687469	6.111744728198	5.89165658573726	6.09685348631085	5.97801256748634	6.03498512487042	6.1142195082128	6.12398500023757	5.71337441848092	6.01368803918114	6.24862938071079	5.66629558936369	6.21093106612612	6.38915464114333	6.0846666031506	5.96018749508897	5.99198406277026	6.20237473685111	6.09023587838496	5.95368742079795	5.96248427453032	5.87622987504699	5.92529548306921	6.36266727797388	5.9238619396859	6.25821388370053	6.03948001748453	6.50698797310783	6.13141219737989	6.06406504208688	6.15367148411836	5.60152356799767	6.14542136982484	6.13206628886504	6.07011441609992	5.87233518232006	6.10040229177398	NA
+chr5	91279761	91375761	NA	6.02499356344929	5.8713665869611	5.91660470886917	5.8336421152092	5.98946083026561	6.26757007575073	6.12472106845108	5.87400196944181	5.95284563789073	5.66385047968765	6.51172722613417	6.12782537695571	6.17849753619703	6.03559388250791	5.73594622756571	5.94255977840377	5.84624186178317	6.14178616214932	6.13019280902178	6.07935969649543	6.14282219270824	5.74442189918916	6.04230635487554	6.0903863703551	6.21534441621095	5.72788867069658	6.06416027580911	5.80375370931739	5.95132074156791	5.73939438896955	6.23515837013303	6.0278744023511	5.98398820758868	6.31735452505542	6.12623967027066	6.45967386193093	5.79564386517137	6.05863893567495	6.24988869149702	5.89635781118807	6.15419871239184	5.60814755481555	6.24940348785605	6.30573044247507	6.00340571912687	6.07798949593425	6.28491200828968	6.21755037716474	NA
+chr5	119466508	119560508	NA	NA	5.96720945470285	6.08567303342837	6.15688204252074	6.19153922654758	6.15143554958969	5.92438305036925	5.97125103940539	6.10220226972274	5.9412436930865	5.74222095183566	6.0780289598028	5.90773986632603	5.8944926664527	5.66725418470793	5.74397383940193	6.21835390748566	5.89282193344686	5.86052892589622	5.92478382711161	5.73194371737588	6.01791767828602	5.86873397735794	6.25743314934407	5.67858025316207	6.34503338437181	5.77290979526894	5.92087135575906	5.91465860757508	6.27774334213012	5.83295104953991	6.15756389567458	6.44550474060662	5.87340559865791	6.21692329170108	6.15985895527915	5.98273068644207	6.07874188471922	5.63875446501823	5.74750876572831	6.17462873700597	5.75972872415717	5.92955155565074	6.27354744011164	6.23188540104021	5.97381580904862	5.66642517706744	5.74530504235376	NA
+chr6	85317170	85401170	NA	NA	NA	NA	5.95250791906938	6.26251919640056	5.83495224062006	6.14037334299037	5.85325126167988	5.88120836083681	5.87881791162013	6.2327148963679	6.10508488866758	6.27146003409123	5.8953563027665	6.04223223866615	6.17155471648976	6.13268362310437	5.7153707645606	6.10172944529558	5.89109104892256	5.94662256480916	5.91157336055305	6.04862229276348	5.80603806031882	6.08983534108936	5.69378576111834	6.04079478353162	5.7893996276714	5.65927483973026	6.24369606289394	5.92224640926996	6.09778636744187	6.35012409039764	5.8474602369248	6.26563430443633	6.10099467515689	5.82278764212531	6.18571936071223	6.1179097524803	5.89866185206393	5.76536250070608	6.20095585470612	5.84591868042	5.8120077127825	6.09620267844601	NA	NA	NA	NA
+chr6	85764072	85860072	NA	5.69238110048465	5.85426448283789	5.92022822839347	5.70830329759298	6.05568336791787	6.23563673336774	6.03389801842733	5.92194815165856	5.75686258361811	5.99411117733685	6.02698944080882	6.20747077187878	5.96971198377738	6.21275142574368	6.25423127473327	6.04195079759378	5.74768607993255	5.83707084918428	6.25387241091309	6.35081246825793	5.92686845482654	6.24174050036721	5.91623755326312	5.99764246674976	6.14579955089683	5.93340140357211	5.92314446409054	6.04497890479666	6.02283744863704	5.78029437720634	5.81060776402762	6.3298915151129	5.68925347889016	6.10210006694241	6.35137613986755	5.78297312454232	6.06515007736227	5.64764927758603	6.12523303198794	6.14912398816557	5.63455387387583	6.06990123572138	6.3337581824825	6.04196340041895	6.23271459696765	5.86447248604534	6.24854783273281	5.90703234471243	NA
+chr6	134625363	134717363	NA	NA	5.78193965513596	5.99215192605036	5.83929209912987	6.02731359620953	5.8480837261023	5.88886281712703	6.1795858858624	6.08842742596916	6.10504633662557	5.98825051335539	5.97285887358799	5.84579863966886	5.58768480253958	6.06042966137122	5.971950696879	6.44511267382348	5.98240722782151	5.60322024493025	5.89253719249739	5.80286845037158	5.83058863267161	5.93750265452778	5.83736171804464	5.90415190673883	5.81813777001774	6.25544356493167	5.93434009458769	5.61971941928661	5.63660593043029	5.98378469641064	5.73299586517188	5.99046841815475	6.01902991885533	6.26061610651907	5.79436468845125	5.85173463757597	5.81334081173234	6.36130036153617	5.75882073235174	5.93185136438332	6.51650708261353	6.29212035604194	6.07701300438996	6.31217778559645	6.36502148361029	6.08912119497155	NA	NA
+chr6	147472164	147566164	NA	NA	5.93481404178876	6.4748907699245	6.23573648245292	6.34818883889366	5.67154238619839	5.78715298325328	5.96963566098236	5.99863340667947	6.08354905731188	5.55681740760493	6.12760719726262	6.24815234773768	5.95294855088405	6.04687724699929	6.14478175359064	6.22603950496347	6.10326960932923	6.12740727322243	5.98122561298521	6.12276670311487	5.78307480825563	6.26080352037076	5.95789182671572	5.85947893694888	6.31121488131286	6.14307166465805	5.69193540922882	5.85360557841706	6.56973307515196	6.20880976014734	5.59074972652885	6.07340138983583	5.76124460746892	5.99327372693956	6.20549472134977	6.31844597813828	5.81429617354563	6.21313056299527	5.96843760198057	6.07085687722673	5.89715580229413	6.1753539232179	6.21479400153689	6.14115960262049	5.96846712865322	6.29818957168218	6.0584175103083	NA
+chr7	77197798	77293798	NA	6.12432828648021	6.12282496497518	6.18601754504167	6.34157953888768	6.03567765125441	6.20944114680283	5.83082804034806	6.00704171874142	6.50046291515189	5.9968677094463	5.83572320251824	6.06389549361408	5.95429228461869	6.15197741117348	5.65985526281074	6.01586604211278	5.63143570108842	5.75080503452279	6.04447561687804	5.90314415366141	6.29965287587188	5.77038244988803	5.95128854530728	5.7227655008728	5.89688289640741	6.02566351065108	6.12723627158864	6.23065146272588	6.07322204104053	6.02404524297403	6.42187034532305	6.50593911458669	6.06143407144268	6.01408131851912	6.27410320640135	6.24466022312551	6.12842052223441	5.92150606843914	5.92859048777683	6.18365530467204	5.98805872309414	5.60438502582858	6.07732057639457	5.82175590782366	5.69982485296028	6.26318545074961	6.20540119794392	6.26021118551878	NA
+chr7	77884914	77976914	NA	NA	6.16454531059211	5.91403503605771	5.77684793815293	5.7792742221869	6.17498362565548	5.91146590458262	5.78501509347671	5.90555853817734	5.87566145860105	5.86830717935879	5.86385959998618	5.92492122236097	6.11252209843118	6.15424339066783	6.00025813559036	5.58756415027772	6.12436637615239	6.34445517332649	5.63352652067402	5.90044517769743	6.08728362001937	6.28192173647343	5.64506755062004	5.77837163033859	5.83577151842439	5.87976799849791	5.71108890470799	5.93133205273333	5.81149407149367	6.18063583746201	5.74791847574657	6.09563727621243	6.01313942041135	5.80706989626738	5.83877892776804	6.07888284065755	5.69646463408165	5.66491314226579	6.31278648561342	5.87587945613497	5.95001980060995	5.98146393435987	6.15219318494556	5.76981730402022	5.95565602196671	5.81386985613113	NA	NA
+chr7	114807399	114903399	NA	5.71119476571233	6.08960893033331	6.07993742617547	5.71010650629566	5.94464284393192	5.77106284835484	5.84638657626847	6.14195328361561	5.84586205068742	5.57491494449769	5.93339507250449	6.2039859702134	6.35354701080782	5.65264349283586	6.31477989400729	5.96183717310291	5.93097570118194	5.97697688202355	5.78568910672774	5.80579257124306	5.8170817127604	5.9414102759623	6.15085074938494	5.96431210442786	5.87739965695141	6.18645522487438	6.23834290443401	5.70017440673617	6.09816620529248	6.09817278445132	6.19286646102846	5.83236046254061	6.01494406368342	6.02387013494154	6.037815868061	5.93306863132332	5.92702640703342	5.86459726385887	6.30527699101482	5.93776780868183	6.01446029198131	6.03902407615326	5.90955294311793	5.73325556634565	6.16430379170309	5.74692113088161	6.35898590779701	6.34634678462867	NA
+chr10	46352885	46446885	NA	NA	5.87508165788373	5.74658516838793	6.04726233311768	6.35617984606127	5.92250099015258	6.0945863302659	6.13950408021386	6.07127294097309	5.96229817081291	5.58468608360333	6.27500173332615	5.8830577473122	6.11480031811464	6.03633019666554	6.19553297260939	5.99697388206106	5.84616595837604	6.04198519604549	6.137019084798	5.66852549472543	5.91657437473972	5.92949040064377	5.81729745268194	6.03617081432437	5.72740533016046	6.04068169813716	6.30608626959371	5.80680567903247	6.16875984645014	5.96318854174169	5.6948102438987	5.83724920575296	5.94413532447169	6.35793318022285	6.24602225736724	6.15164141011457	6.17501193224289	6.27216942064629	6.34928471500425	5.88176779550989	5.83555428869058	6.14876802910978	6.02308617200278	6.42764767378428	5.88560159544415	6.26653467128986	6.35573662585662	NA
+chr10	67835078	67931078	NA	5.80954472726726	5.87083283850804	5.9960615380456	5.85487499251487	5.91250139383921	6.07328302021994	5.80309647932193	6.42480594919367	6.07919534918975	5.78641867104587	6.32545396878279	6.30786058380672	6.26591503008456	6.08760019058386	6.06029670575787	6.02077542025913	6.09302782321394	5.62029890156444	6.15725429976084	5.83636291721716	6.15204989197792	5.82977827273962	5.75223626028816	5.87611917164382	5.78328604785247	5.85131061429551	6.06182824755766	5.81374025720563	5.91889497687323	5.88943579086872	5.66615563847761	6.08007874465645	5.80811011402326	6.20009386205121	6.27363948313469	6.12272063489225	5.84397595496728	6.28029000369565	5.98457738703383	6.31658940904419	5.75956429639046	6.1302388917103	6.18692138821273	6.18163667358954	5.72951951840217	5.67207676901117	5.86981630259466	6.01441685159722	NA
+chr12	27724692	27820692	NA	6.15932139669026	6.10101563418686	6.00470092587826	6.23123363976754	5.91057350274107	6.21159035661668	6.22794792823149	5.8632127319506	6.10882424978632	5.95980648415469	6.36318927506813	6.33133138575094	6.18262615200429	5.8901397388124	5.78687069375753	6.23348956431378	6.11778851394807	6.05251702931471	5.97499771074319	5.98498606111708	6.23847703143396	5.85743326303633	5.90592879480332	6.06350129144793	5.77738365739388	6.21316008969454	6.17982724288831	6.51074652010973	5.93056556566489	6.10083744907351	6.61988458270184	6.0775639839262	5.84605103926069	5.90357454269242	6.09703489000837	5.91462443694251	5.81447529697405	5.89785940059557	5.88209923950204	6.05862546908079	5.86676819891907	5.81985061347805	5.9970123773808	6.41374836953901	6.12512494562196	6.22174790945756	6.04245040444281	5.87954617397827	NA
+chr12	95522506	95614506	NA	NA	5.90261676943481	5.79807342775931	6.06843025991209	6.59940493630893	5.88693508267531	6.11198230068627	5.94347089608267	6.061115431612	6.29379557878124	6.00023599393709	5.85708002306134	6.01752283688481	6.0024321284035	5.96770342960308	5.97041384136112	6.3459561182103	6.01584071120683	5.90812421791462	6.33337026794075	6.1588616227695	6.52624731613717	5.76569756326845	5.82899724685364	5.959959212293	5.96945619580813	6.17654255028048	5.93017557230842	5.74761823057831	6.21424494115506	5.9844056050485	6.09922724857438	5.92269192741938	5.70490734403477	6.03593482803033	5.6853567294886	5.87866596795876	6.19932360287127	6.21344159715381	5.96716480088724	5.82016281021254	6.00834364979348	6.06462729430496	5.82036458798317	5.86294116516996	5.73454503818392	6.16021889407882	NA	NA
+chr12	117869466	117957466	NA	NA	NA	6.15685538773378	6.08011255805692	6.11990135056637	5.72847215583675	6.02914240550561	5.90196960881199	6.11475606793666	5.84211782721453	5.79538240604529	5.8258325800493	6.42119084935805	6.1018013742571	6.25767985229494	6.00697107478066	5.68665553209664	6.49706711122386	5.88509515637677	6.01324997181747	5.95228636418685	6.18256104326381	5.87320730071441	5.91029923008789	6.06716148432686	5.84828641252854	6.01835272876425	6.22939380129629	6.07563223214289	6.43990014778609	6.02335895057837	6.17401019518516	6.12033242095868	5.8898676925233	6.02921843872209	5.92848130736364	5.9308901499322	5.76448075703196	5.57280380745365	5.59414730695184	6.01182760152553	6.00949206380765	6.06841212330484	6.19712307233084	6.02294919407602	5.90160861024188	NA	NA	NA
+chr14	100464166	100562166	NA	5.60682804943688	6.28245158244054	6.02116230311521	5.91820616152514	5.98652875650432	5.9955537425529	6.00720197227542	5.89903435524294	5.91884064308489	6.27929299844479	5.9180678404517	6.12080146177555	6.01682776421343	5.98126581284627	6.27327540224179	5.85676045673914	5.903307788131	5.8390468512539	6.21325951396932	6.10372535910032	6.00136117232987	5.91721770346643	5.93609938583345	5.99456839534261	5.74329064056368	5.82947383724801	5.97407983200761	6.41459234004018	6.11274206622884	5.98021268987596	6.20091797108309	5.9129879924274	6.05537806435014	5.76761083589629	6.12143501156656	5.91331884391527	6.34729025450677	5.81808977635354	6.09830347150065	6.37615241895117	6.06755749766957	6.20592562693079	6.15531932802772	6.55009328757277	6.3829448507699	5.98895722228972	5.76888064399249	5.95816207878075	5.64893735104092
+chrX	29266748	29364748	NA	5.87005612393756	6.07893115128186	5.82630597208156	5.86199243371087	6.34801702721223	6.23019066402505	6.20858728067203	6.21992131349308	6.72674050779152	5.84078537562776	6.10474741955268	6.33647108398051	5.94182255775251	5.84413081970671	5.98224461875325	5.9922144737647	5.9901715157711	6.14308456219524	6.16899291047834	5.98730297955433	6.2447474470771	6.09869626312088	6.00585429284193	6.27883611818289	5.90691524534429	5.97452661956711	6.47847160758146	5.98420306578921	5.85203078239026	5.94903672925218	6.017291712234	5.73967886588707	5.91770410516037	6.01487872453941	6.47507563005148	6.05223138271635	6.01064443738328	5.54500091456524	6.34037363838037	6.16807019223899	5.91721494089766	5.76170994031756	5.75887469058354	5.55744495613199	5.88753687105948	6.19249759217491	5.70900197145095	5.60522478083405	5.78335328158497
+chr1	65942901	66042901	9.71238826359522	5.09472531711167	0.345664145527698	6.98721236507309	0.802520622964948	7.82770713129928	5.47406917896023	7.40537830895575	2.3575309664011	0.995813084300607	5.85329706759608	7.71918054628086	6.20852603556073	1.30448972771949	3.40035203611478	0.826473266351968	0.475970412006931	5.98674674497402	5.17546498661345	0.782028820831329	2.49855509395699	3.11233190798466	9.21890105078828	3.77302507848895	1.31860156776384	0.967504242435098	11.8171455611693	2.43654302321374	6.28718500470227	2.26561059243977	2.06749496981502	5.21218891700214	0.0968020502477884	5.18526261185712	0.89389355154708	3.62260721137232	7.54160002763283	1.01247958140448	14.9089990920367	2.95689933700487	1.27168030020277	14.9261048205633	1.50682077044621	1.46079450612888	1.32108644582331	7.04800209544509	1.21696738329846	2.57038460345939	4.52981605157187	5.95072255914515
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+chr15	39087176	39187176	5.9380286602744	4.44194361960976	7.441612042825	3.52329450344185	3.42742538866283	5.6763845245587	4.80391114444012	4.1427963050881	4.71912548224832	4.27716570400673	7.55751700757309	5.46305979388871	4.55212671897934	3.57774156408239	6.81418966470312	4.56393897018082	7.13892860512953	4.69173672251961	3.89135829308211	3.65479240180669	4.67081396836796	5.09494834999442	4.7954301443578	4.41932222954705	5.5831535193562	3.00509402295291	5.70352193470097	5.11165982116322	3.40714537316494	5.63786285129	7.37199866213544	4.57147590708969	3.41493777434468	4.63554700222071	5.52066893873767	4.70366089811832	5.53610513154471	6.53345946995638	4.5924633705273	4.80718533437821	4.41145336767495	4.27193497249827	6.36174062046137	5.72001067412137	4.67878224322349	6.11230822065739	6.09343190823031	5.26644795168451	5.54282241628461	5.05246990945085
+chr17	58542142	58642142	3.78258369305722	5.24562228929564	5.94130632573582	6.91608706046793	5.3364362752905	4.37970694584912	5.68907029930803	5.06520907852671	4.30558911048558	5.42812464289729	5.76177509139653	3.68359049251118	4.55645055688819	6.50528059743541	2.95252861425896	6.35174137626987	7.01817500569569	2.85304328810294	4.5906697829549	3.98021679978386	4.61467510707699	5.1112857666068	4.64382536604588	5.77407835286214	5.64032233752237	4.35120498506984	5.62098276516905	5.54111548097298	5.63107936263069	2.99702760432823	4.89689668995302	4.03661910252896	4.79448866640442	3.38195053317233	7.7380228985078	5.41947337595238	4.19192861252094	4.31156135339616	4.31759971221873	2.77197395884205	5.44907638856218	4.96289340918086	5.65460754257777	3.32961053989125	3.74490222127652	4.25837596325282	5.86998879697347	3.93438391593542	5.33040889425571	5.60244031628362
+chr18	12199823	12299823	3.25885112477311	6.08955107764397	5.69721921128154	4.97256244635738	6.09938593794046	5.72602743226379	4.84946717750692	3.98641582929357	2.92576093636519	5.03740463169787	4.3316358163762	4.75446479190763	4.92149054541188	6.3964108746247	6.00482615846947	4.42159921287334	5.96964842487217	3.28154659770011	5.14411842155532	5.86492567252118	5.99759949784854	5.48596073141046	5.97187827899397	4.3502858212033	4.94388322090535	4.89862778096948	3.51620588820609	3.78084822230806	5.93057048344767	4.98579243525724	5.58890065086645	4.70108975748617	4.7895697681093	5.33794569146168	4.23206645182713	6.05267429234428	4.62772392874206	4.39012681127604	5.45237328178362	4.28712630447332	5.24131174693575	6.34798793754705	5.68341572365016	5.03127081298831	6.79427837845977	3.72241150451086	4.79041439287781	3.14136405520943	4.96199911850649	6.81277325630767
+chr20	8173704	8273704	6.43382787231238	4.20629312905753	4.46704298206844	6.03222816987749	4.30147168787313	5.00517531995266	5.09890065941488	6.26031225941689	4.74175960956365	5.43517785840117	5.96784189547297	4.34871495389933	5.34437264668666	3.97360814520199	4.9134516695783	6.86224925090763	5.57749452011018	6.03402391278042	3.64296238013594	5.36057203280719	2.6626713886147	5.58543341549492	4.77030457177342	5.23688269173501	4.209373898032	5.51034830372729	5.57204936283687	8.40586121040696	6.09671890380983	6.60793108314687	5.68317759422036	4.30793023751099	4.95321372131636	5.95532668892152	2.72336741800435	3.86592630331189	4.82395422335664	3.96294890340897	4.05911869483061	3.6132323237958	4.433337790893	6.39501873198737	7.06359875392576	5.68256090102556	6.70759111163696	5.82840253042312	6.27966329982408	6.30744486480589	7.23659706262111	5.24973308230756
+chr21	16255112	16355112	5.43485061781405	5.01260461316357	5.19868572560391	6.79953585668401	5.47154247832347	5.57139768490377	4.41977811394674	5.21005178570924	6.23150534339179	4.13234460718945	3.73643444565989	5.49986157710764	4.24692563903457	6.1201445277858	7.6044996484288	4.39195588598509	3.55400067821432	3.01214252591894	4.82895104706437	4.69885569477155	5.13067495449581	5.68065404133829	5.18131478218747	4.90763858672373	5.6284278674907	6.75243100368637	5.60807167993184	4.1705718092553	5.59795968977399	5.64431912129191	3.24228211918138	5.78400308052907	5.95645634545206	6.29434753041243	6.99818513621809	4.39693050048416	4.39972912514096	5.56319404783912	4.37545858545881	4.2214666033019	4.80441799109772	4.12779454100983	5.73512339435638	6.31824123702265	4.7032033915254	6.22103216056679	5.08243178399854	3.46734142237263	4.80237659387963	4.46719465609719
+chr21	45089115	45189115	3.98478216033248	5.89593194020198	5.60303836466821	5.27279159751476	5.80971477436893	5.57408645669357	5.0904942176002	5.7256184681535	6.81239770900896	5.56862426806081	3.43273288641698	7.11590805160377	4.24928169671269	3.50357501542878	5.73431543970818	4.89302943624425	5.20269127776446	3.11276988188827	6.70573206709031	6.31148848612594	4.68095359931436	5.87574218604384	6.20311789316871	6.01684909049701	5.60285980582541	4.17676768545	4.62701336289684	4.46375199037344	5.21311596423713	4.54975356710246	5.23570551842466	5.45654414498341	5.76872463467434	6.07303933349791	3.19345809093903	4.6777044172874	6.90541188117836	3.86595178334009	3.79147868917487	5.18816102518065	6.03731752174302	4.36652391944316	6.92077179572038	4.2097619283708	6.90752823614391	3.057058298432	5.42490485331077	4.76510475192745	2.35894801089037	5.44506436056745
+chrX	23898983	23998983	7.03066685697484	4.80984039818705	6.87648142714197	4.33342068633308	5.44768902071552	5.24377980852063	3.34381613128697	4.7638049709881	5.02176249812415	5.11315199551325	5.63929407699233	5.17277740161745	4.70952678729912	3.19160952471692	6.32011705004979	4.19036613885934	4.80803548700068	4.93855138948318	5.41062021103021	6.35365406267257	3.88299454704151	6.18440349768351	5.75549919132533	3.11049329589525	5.00541173181963	4.96410149704263	6.22653107000682	4.99930836900414	3.94648431409119	3.84392264480142	4.59067873486645	5.77324368629459	2.43794317536001	4.48520079631577	6.64803228254723	3.40954530479405	5.6199652360586	4.95094029088581	6.74172526888294	4.44855412190394	3.51345142660858	5.82909049735773	5.83865369362918	4.5176155810479	4.76737166205064	4.26232717377676	4.46848774389506	2.23103877943527	4.70000784618739	6.27062142842042
+chrX	37029585	37129585	5.08310992835239	5.05191137525634	6.83538337148873	6.22633996158244	5.82903436820541	5.64328251952464	4.75479035782791	4.8878582034319	5.92909465711536	5.9819443997486	6.60670817186802	4.25619142753195	4.66610579347946	6.17234112920904	3.55418205184691	5.11402299557796	3.79230049741539	3.11087618536958	4.58894113645188	3.71717685239281	4.58796696740988	5.59947138638049	6.05734650462578	4.48158179401952	3.84606980112288	5.60036515077628	4.7988860011278	5.72216107507848	4.86913891902086	5.82455803778606	4.16446009380301	4.63404391451533	4.79357306408379	5.14434162104312	4.26547789878118	3.40216484594991	4.74371184978272	5.2129067039706	4.32151841433918	4.90636437901617	5.63036609909793	6.74871839286766	5.86869049479244	4.61355674591477	4.86401145328662	5.86712733709456	5.28490137892296	4.2972056277626	6.12987499929255	3.6075236114256
+chrX	103593349	103693349	6.37340190485477	4.10474288351457	6.02078692162347	6.59348452737096	5.11365716238428	3.62971024923456	5.42856007221458	4.3279027245615	5.07950379344802	5.6907476922242	4.90776693084081	6.23128939684067	3.76134500557007	5.31089684191184	3.27099290965503	4.09777047720062	5.52286959370605	4.21440588097924	6.09499556724381	3.79112962123879	4.2640571911545	4.28724904018904	3.37347033628808	3.61482331330979	4.35575752957776	5.11289775334567	4.17082227412053	4.32059434655099	6.58340150820527	4.09769472659799	5.66833924151096	4.64441521765574	6.03588217585307	4.65670812807146	5.17171577253924	4.37221612406053	6.04105348527609	6.56026680863041	5.12457673118236	4.60592949236729	4.18768432297649	4.34805676009423	7.32776790008722	4.45831876954239	5.414270828553	5.19188276315724	5.78869637333301	4.94708954456459	3.16857310121393	4.28592378866411
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/features.header.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,2 @@
+feature1.txt	ftr1	Feature 1
+feature2.txt	ftr2	Feature 2
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/paper_example/regions.header.txt	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,4 @@
+elem1.bed	elem1	Elements 1
+elem2.bed	elem2	Elements 2
+elem3.bed	elem3	Elements 3
+control.bed	control	Controls
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.R	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,146 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  require(tools,quietly = FALSE)
+  args=commandArgs(TRUE)
+
+  for (i in seq_along(args)) {
+    message(args[[i]])
+  }
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  outrdata=args_values$outrdata
+  outregions=args_values$outregions
+  outfeatures=args_values$outfeatures
+  outpdf=args_values$outpdf
+  regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
+  if("regionsheaderfile" %in% args_names){
+    # the file regionsheaderfile must contain as first column the (unique) regionsfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
+      if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
+        quit(save="no", status=11)
+        stop('Not all regionsfilenames are present in the first column of regionsheader.')
+      }
+      id_regions=regionsheader[regionsfilenames,1]
+      name_regions=regionsheader[regionsfilenames,2]
+    }, error = function(err) {
+      quit(save="no", status=10) #error on header file
+      stop(err)
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
+    id_regions=paste0('data_',regionsgalaxyids)
+    name_regions=paste0('data_',regionsgalaxyids)
+  }
+  featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
+  if("featuresheaderfile" %in% args_names){
+    # the file featuresheaderfile must contain as first column the (unique) featuresfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
+      if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
+        quit(save="no", status=21)
+        stop('Not all featuresfilenames are present in the first column of featuresheader.')
+      }
+      id_features=featuresheader[featuresfilenames,1]
+      name_features=featuresheader[featuresfilenames,2]
+    }, error = function(err) {
+      quit(save="no", status=20) #error on header file
+      stop(err)
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
+    id_features=paste0('data_',featuresgalaxyids)
+    name_features=paste0('data_',featuresgalaxyids)
+  }
+  # read parameters (from smoothing on)
+  i_smoothing=which(args_names=='smoothing')
+  for(i in i_smoothing:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load data
+  tryCatch({
+    regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
+                                id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
+  }, error = function(err) {
+    if(grepl('invalid format',err$message)){
+      quit(save="no", status=31) # error, not enough columns in input file
+    }else if(grepl('duplicated regions',err$message)){
+      quit(save="no", status=32) # error, duplicated regions in region file
+    }else if(grepl('duplicated windows',err$message)){
+      quit(save="no", status=33) # error, duplicated windows in feature file
+    }else if(grepl('overlapping windows',err$message)){
+      quit(save="no", status=34) # error, overlapping windows in feature file
+    }else if(grepl('not all regions in datasets',err$message)){
+      quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
+    }else if(grepl('ifferent size windows',err$message)){
+      quit(save="no", status=36) # error, all windows in a feature files must have the same size
+    }
+    #error loading data
+
+    stop(err)
+
+    quit(save="no", status=30)
+    
+ })
+  
+  # smooth data
+  if(smoothing!='no'){
+    tryCatch({
+      if(smoothing=='locpoly'){
+        dist_knots=10
+      }else if(smoothing=='kernel'){
+        degree=3
+        dist_knots=10
+      }else if(smoothing=='splines'){
+        bandwidth=5
+      }
+      if(alignment=='scale'){
+        if(scale==0){
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+        }else{
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
+        }
+      }else{
+        regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                              bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+      }
+    }, error = function(err) {
+      quit(save="no", status=40) #error on smoothing
+      stop(err)
+    })
+  }
+  
+  # plot data
+  pdf(outpdf,width=10,height=8)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # create output
+  #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
+              #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
+              #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures,file=outrdata)
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.xml	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,321 @@
+<tool id="loadandplot" name="IWTomics Load" version="0.1.0">
+  <description>Smooth and Plot</description>
+  <command interpreter="Rscript">
+<![CDATA[
+    loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}" 
+      
+      #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
+      regionspaths="${region_paths}" 
+      #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
+      regionsgalaxyids="c(${region_galaxyids})" 
+      #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
+      regionsfilenames="${region_names}" 
+      #set region_header = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )
+      #if $region_header != "":
+        regionsheaderfile="${region_header}" 
+      #end if
+
+      #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
+      featurespaths="${feature_paths}" 
+      #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
+      featuresgalaxyids="c(${feature_galaxyids})" 
+      #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
+      featuresfilenames="${feature_names}" 
+      #set feature_header = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )
+      #if $feature_header != "":
+        featuresheaderfile="${feature_header}" 
+      #end if
+
+      smoothing="'${conditionaltype.smoothing}'" 
+      start.are.0based="${zerobased}" 
+      #if $conditionaltype.smoothing == 'no':
+        alignment="'${conditionaltype.alignment}'" 
+      #elif $conditionaltype.smoothing == 'locpoly':
+        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'" 
+        #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.locpolyconditionalscale.scalegrid}" 
+        #end if
+        bandwidth="${conditionaltype.locpolybandwidth}" 
+        degree="${conditionaltype.locpolydegree}" 
+        fill_gaps="${conditionaltype.fillgaps}" 
+      #elif $conditionaltype.smoothing == 'kernel':
+        alignment="'${conditionaltype.kernelconditionalscale.alignment}'" 
+        #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.kernelconditionalscale.scalegrid}" 
+        #end if
+        bandwidth="${conditionaltype.kernelbandwidth}" 
+        fill_gaps="${conditionaltype.fillgaps}" 
+      #elif $conditionaltype.smoothing == 'splines':
+        alignment="'${conditionaltype.splinesconditionalscale.alignment}'" 
+        #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.splinesconditionalscale.scalegrid}" 
+        #end if
+        degree="${conditionaltype.splinesdegree}" 
+        dist_knots="${conditionaltype.splinesdistknots}" 
+        fill_gaps="${conditionaltype.fillgaps}" 
+      #end if
+      
+      average="${plotres.average}" 
+      size="${plotres.size}" 
+      plottype="'${plotres.conditionalplottype.plottype}'" 
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})" 
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})" 
+        #end if
+      #end if
+
+      >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <inputs>
+    <!-- regions -->
+    <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
+    <repeat name="regionsheaderrepeat" title="Header file for regions (optional)" min="0" max="1" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
+      <param format="tabular" name="regionsheader" type="data" label="Select header file" />
+    </repeat>
+
+    <!-- features -->
+    <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
+    <repeat name="featuresheaderrepeat" title="Header file for features (optional)" min="0" max="1" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
+      <param format="tabular" name="featuresheader" type="data" label="Select header file" />
+    </repeat>
+
+    <!-- zero-base one-base -->
+    <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
+      <option value="TRUE">0-based</option>
+      <option value="FALSE">1-based</option>
+    </param>
+
+    <!-- conditional smoothing -->
+    <conditional name="conditionaltype">
+      <!-- smoothing -->
+      <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
+        <option value="no">No</option>
+        <option value="locpoly">Local Polynomials</option>
+        <option value="kernel">Gaussian Kernel</option>
+        <option value="splines">B-Splines</option>
+      </param>
+      <!-- conditional choice: smoothing=no -->
+      <when value="no">
+        <param name="alignment" type="select" label="Region alignment" help="">
+          <option value="center">Center - Alignment on the central position</option>
+          <option value="left">Left - Alignment on the starting position</option>
+          <option value="right">Right - Alignment on the ending position</option>
+        </param>
+      </when>
+      <!-- conditional choice: smoothing=locpoly -->
+      <when value="locpoly">
+        <!-- conditional region alignment -->
+        <conditional name="locpolyconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=kernel -->
+      <when value="kernel">
+        <!-- conditional region alignment -->
+        <conditional name="kernelconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=splines -->
+      <when value="splines">
+        <!-- conditional region alignment -->
+        <conditional name="splinesconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
+        <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
+        
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+    </conditional>
+    
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot data" expanded="True">
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
+      <!-- sample size in each position -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type" help="">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
+    <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
+    <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
+    <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
+    <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
+  </outputs>
+
+  <help>
+This tool imports a collection of genomic region datasets, and associates to each region 
+multiple genomic feature measurements. It allows to align the regions in multiple ways
+(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
+measurements) and to create a graphical representation of the feature measurements in each
+region datasets (aligned curves or pointwise quantile curves).
+
+-----
+
+**Region datasets**
+
+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
+start end (extra columns present in the input file are ignored). Regions can be of different
+length::
+
+    chr2  49960150  50060150
+    chr2  55912445  56012445
+    ...
+
+-----
+
+**Feature measurements**
+
+Feature measurements corresponding to all the regions can be provided as a BED or Tabular
+file with tab delimited columns chr start end value::
+
+    chr2  49960150  49962150  0.9426
+    chr2  49962150  49964150  0.7816
+    ...
+
+Each feature must be measured in windows of a fixed size inside all the regions (missing
+values must be indicated as NA). Another way to import feature measurements is from a
+Tabular file with the first three columns chr start end corresponding to the different genomic
+regions, followed on the same row by all the measurements in fixed-size windows::
+
+    chr2  49960150  50060150  0.9426  0.7816  0.8921  ...  ...  1.2063
+    chr2  55912445  56012445  0.8719  0.9975  1.1619  ...  ...  0.9601
+    ...
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
+2. Region dataset identifiers;
+3. Feature identifiers;
+4. PDF file with the plotted data.
+
+1-3 can be used as input of the tool *IWTomics Test and Plot*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects. 
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {Pini, Alessia and Vantini, Simone},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+  <stdio>
+    <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
+    <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." />
+    <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
+    <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." />
+    <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." />
+    <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." />
+    <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." />
+    <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." />
+    <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." />
+    <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." />
+    <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." />
+    <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.R	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,117 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvalue=args_values$adjustedpvalue
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
+  feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
+  # read parameters (from test_subset on)
+  i_scale_subset=which(args_names=='scale_subset')
+  for(i in i_scale_subset:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(iwtomicsrdata)
+  # read testids and featureids and check them
+  unlisted=lapply(seq_along(test_subset),
+                   function(i){
+                     test_subset_i=eval(parse(text=test_subset[i]))
+                     feature_subset_i=eval(parse(text=feature_subset[i]))
+                     test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
+                     feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
+                     scale_subset_i=rep(scale_subset[i],length(test_subset_i))
+                     return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
+                   })
+  test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
+  feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
+  scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
+  testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  id_features_subset=featureids[feature_subset]
+  if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
+    quit(save="no", status=10)
+    stop('Wrong test ids')
+  }
+  if(sum(featureids!=idFeatures(regionsFeatures_test))){
+    quit(save="no", status=20)
+    stop('Wrong feature ids')
+  }
+  # retrieve test and features_subset ids
+  id_features_subset=featureids[feature_subset]
+  if(sum(duplicated(paste0(test_subset,id_features_subset)))){
+    quit(save="no", status=30)
+    stop('Two scale thresholds selected for the same test and feature.')
+  }
+  # If scale_subset=0, do not change the threshold
+  default=(scale_subset==0)
+  scale_subset=scale_subset[!default]
+  test_subset=test_subset[!default]
+  id_features_subset=id_features_subset[!default]
+  
+  # get scale threshold
+  scale_threshold=lapply(regionsFeatures_test@test$result,
+                         function(result) unlist(lapply(result,function(feature) feature$max_scale)))
+  for(i in seq_along(test_subset)){
+    if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
+      quit(save="no", status=40)
+      stop('Scale threshold too high.')
+    }
+    scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
+  }
+  
+  # create adjustedvalue output
+  pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
+  for(test in seq_along(pval)){
+    for(id_feature in idFeatures(regionsFeatures_test)){
+      write(paste0('Test: ',testids[test],', on feature ',id_feature),
+              file=adjustedpvalue,append=TRUE,sep='\t')
+        pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
+        row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
+        write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvalue,append=TRUE,sep='\t')
+      }
+    }
+  
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    tryCatch({
+      pdf(iwtomicssumpdf,width=15,height=10)
+      plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
+      dev.off()
+    }, error = function(err) {
+      if (grepl('selected features with different resolution',err$message)) {
+        quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
+        stop(err)
+      }
+      quit(save="no", status=60) #error 
+      stop(err)
+    })
+  }
+  
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.xml	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,197 @@
+<tool id="plotwithscale" name="IWTomics Plot with Threshold" version="0.1.0">
+  <description>on Test Scale</description>
+  <command interpreter="Rscript">
+<![CDATA[
+    plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" 
+      iwtomicsrdata="${rdata}"
+      iwtomicstests="${testids}" 
+      iwtomicsselectedfeatures="${featureids}" 
+
+      #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
+      test_subset="${test_subset}"
+      #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
+      feature_subset="${feature_subset}"
+      #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
+      scale_subset="c(${scale_subset})"
+
+      testalpha="${plotres.alpha}"
+      average="${plotres.average}" 
+      size="${plotres.size}" 
+      plottype="'${plotres.conditionalplottype.plottype}'" 
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})" 
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})" 
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'" 
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
+        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
+        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+      #end if
+
+      >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"    
+    -->
+  </command>
+
+  <inputs>
+    <help>
+    ...
+    </help>
+
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
+    <!-- test IDs -->
+    <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
+
+    <!-- repeat threshold on test scale -->
+    <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
+      <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
+        <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
+        <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
+        <param name="scale" type="integer" value="0" min="0" label="Scale" />
+      </repeat>
+    </section>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
+      <!-- average -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+
+    <!-- summary plot -->
+    <section name="plotsum" title="Summary plot" expanded="True">
+      <!-- conditional group by -->
+      <conditional name="conditionalgroupby">
+        <!-- group by -->
+        <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
+          <option value="none">No plot</option>
+          <option value="test">Group by test</option>
+          <option value="feature">Group by feature</option>
+        </param>
+        <when value="test">
+          <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+        <when value="feature">
+          <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
+    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+  </outputs>
+
+  <help>
+This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves 
+for the different tests performed at the selected scale, and it creates a graphical representation of the 
+Interval-Wise Testing results and a summary plot (optional) at the selected scale.  
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs. 
+These files are created by the tool *IWTomics Test and Plot*. 
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects. 
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {A Pini and S. Vantini},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+  <stdio>
+    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="Wrong test ids." />
+    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" source="both" level="fatal" description="Two scale thresholds selected for the same test and feature." />
+    <exit_code range="40" source="both" level="fatal" description="Scale threshold too high." />
+    <exit_code range="50" source="both" level="fatal" description="Group by 'test' but selected features with different resolution." />
+    <exit_code range="60" source="both" level="fatal" description="Summary plot error. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.R	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,99 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvaluematrix=args_values$adjustedpvaluematrix
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  regionids=args_values$regionids
+  featureids=args_values$featureids
+  rdatafile=args_values$rdatafile
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  # read parameters (from region1 on)
+  i_region1=which(args_names=='region1')
+  for(i in i_region1:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(rdatafile)
+  # read regionids and featureids
+  regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  # retrieve region1, region2 and features_subset ids and check they are in the RData
+  id_region1=regionids[region1]
+  id_region2=regionids[region2]
+  id_features_subset=featureids[features_subset]
+  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
+    quit(save="no", status=10)
+    stop('Wrong region ids')
+  }
+  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
+    quit(save="no", status=20)
+    stop('Wrong feature ids')
+  }
+  if(sum(duplicated(paste0(id_region1,id_region2)))){
+    quit(save="no", status=30)
+    stop('Same test repeated multiple times.')
+  }
+  
+  # perform test
+  tryCatch({
+    # fix repeated probs
+    if(statistics=='quantile'){
+      # fix repeated probs
+      testprobs=sort(unique(testprobs))
+    }else{
+      testprobs=0.5
+    }
+    regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
+                                      statistics=statistics,probs=testprobs,B=B)
+    # create adjustedvaluematrix output
+    for(test in seq_along(id_region1)){
+      for(id_feature in id_features_subset){
+        write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
+              file=adjustedpvaluematrix,append=TRUE,sep='\t')
+        pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
+        row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
+        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
+      }
+    }
+  }, error = function(err) {
+    quit(save="no", status=40) #error testing
+    stop(err)
+  })
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    pdf(iwtomicssumpdf,width=15,height=10)
+    plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
+    dev.off()
+  }
+  
+  # create output
+  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures_test,file=iwtomicsrdata)
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.xml	Tue May 02 11:05:18 2017 -0400
@@ -0,0 +1,235 @@
+<tool id="testandplot" name="IWTomics Test" version="0.1.0">
+  <description>and Plot</description>
+  <command interpreter="Rscript">
+<![CDATA[
+    testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}" 
+      regionids="${regionids}" 
+      featureids="${featureids}" 
+      rdatafile="${rdata}"
+
+      #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
+      #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
+      region1="c(${region1})"
+      region2="c(${region2})"
+
+      features_subset="c(${featureslist})"
+      
+      statistics="'${conditionalstatistics.statistics}'"
+      #if $conditionalstatistics.statistics == "quantile":
+        #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
+        testprobs="c(${probabilities})" 
+      #end if
+
+      B="${permutations}"
+
+      testalpha="${plotres.alpha}"
+      average="${plotres.average}" 
+      size="${plotres.size}" 
+      plottype="'${plotres.conditionalplottype.plottype}'" 
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})" 
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})" 
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'" 
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
+        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
+        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+      #end if
+
+     >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <inputs>
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- region IDs -->
+    <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+
+    <!-- repeat region ids -->
+    <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
+      <repeat name="regions" title="Two-sample test" min="1">
+        <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
+        <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
+      </repeat>
+    </section>
+
+    <!-- feature ids list -->
+    <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
+
+    <!-- conditional statistics -->
+    <conditional name="conditionalstatistics">
+      <!-- statistics -->
+      <param name="statistics" type="select" label="Test statistics">
+        <option value="mean">Mean difference</option>
+        <option value="median">Median difference</option>
+        <option value="variance">Variance ratio</option>
+        <option value="quantile">Quantile difference(s)</option>
+      </param>
+      <!-- conditional choice: statistics=quantile -->
+      <when value="quantile">
+        <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
+          <repeat name="qprobabilities" title="Probabilities" min="1">
+            <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+          </repeat>
+        </section>
+      </when>
+    </conditional>
+
+    <!-- permutations -->
+    <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
+      <!-- average -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+
+    <!-- summary plot -->
+    <section name="plotsum" title="Summary plot" expanded="True">
+      <!-- conditional group by -->
+      <conditional name="conditionalgroupby">
+        <!-- group by -->
+        <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
+          <option value="none">No plot</option>
+          <option value="test">Group by test</option>
+          <option value="feature">Group by feature</option>
+        </param>
+        <when value="test">
+          <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+        <when value="feature">
+          <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
+    <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+    <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
+    <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
+    <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
+  </outputs>
+
+  <help>
+This tool statistically evaluates differences in genomic features between groups of regions along the genome. 
+In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise 
+Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation 
+tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
+and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results 
+and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale* 
+permits to select the scale to be used in the plots.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs. 
+These files are created by the tool *IWTomics Load Smooth and Plot*. 
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot;
+4. RData with the IWTomicsData object with the test results;
+5. Test identifiers;
+6. Feature identifiers.
+
+4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects. 
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {A Pini and S. Vantini},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+  <stdio>
+    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />
+    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />
+    <exit_code range="40" source="both" level="fatal" description="Testing error." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+</tool>