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changeset 10:1e74ce7f9b2a draft

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Uploaded
author fabio
date Tue, 02 May 2017 17:55:30 -0400
parents 417b1cc9bd9d
children 3a56f8e72534
files ._ETn_example ._loadandplot.R ._loadandplot.xml ._plotwithscale.R ._plotwithscale.xml ._testandplot.R ._testandplot.xml ETn_example/._Control.bed ETn_example/._ETn_fixed.bed ETn_example/._README ETn_example/._Recombination_hotspots.txt ETn_example/._features.header ETn_example/._regions.header ETn_example/Control.bed ETn_example/ETn_fixed.bed ETn_example/README ETn_example/Recombination_hotspots.txt ETn_example/features.header ETn_example/regions.header example/._.DS_Store example/._Controls_regions.bed example/._Elements1_regions.bed example/._Elements2_regions.bed example/._Elements3_regions.bed example/._Feature1.bed example/._Feature2.bed example/._README example/._features.header.bed.txt example/._regions.header.txt example/Controls_regions.bed example/Elements1_regions.bed example/Elements2_regions.bed example/Elements3_regions.bed example/Feature1.bed example/Feature2.bed example/README example/features.header.bed.txt example/regions.header.txt 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/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/hard-withNAs/Feature2.bed examples/paper_example/regions.header.txt
diffstat 56 files changed, 15816 insertions(+), 21416 deletions(-) [+]
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Binary file ._ETn_example has changed
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
Binary file ETn_example/._Control.bed has changed
Binary file ETn_example/._ETn_fixed.bed has changed
Binary file ETn_example/._README has changed
Binary file ETn_example/._Recombination_hotspots.txt has changed
Binary file ETn_example/._features.header has changed
Binary file ETn_example/._regions.header has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Control.bed	Tue May 02 17:55:30 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+chr7	20897622	20969073
+chr7	24287742	24352061
+chr7	24375202	24439538
+chr7	24538044	24602106
+chr7	25005706	25070022
+chr7	25250353	25314413
+chr7	26322702	26392210
+chr7	26608730	26673037
+chr7	27159441	27228448
+chr7	27345642	27415142
+chr7	27463134	27528351
+chr7	28713332	28777662
+chr7	29601071	29665408
+chr7	30341005	30410554
+chr7	30498916	30569038
+chr7	31577745	31641984
+chr7	32243151	32307492
+chr7	32734762	32798823
+chr7	34200839	34272445
+chr7	34320840	34385175
+chr7	38989895	39054230
+chr7	49312352	49381773
+chr7	50020584	50090515
+chr7	50232501	50302452
+chr7	55744652	55812939
+chr7	60516833	60586286
+chr7	61108235	61177739
+chr7	61580838	61644899
+chr7	64864701	64929024
+chr7	86339549	86403885
+chr7	88089874	88153935
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+chr7	91330534	91394875
+chr7	92274579	92338897
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+chr7	96367166	96431487
+chr7	97101263	97165323
+chr7	97284514	97348575
+chr7	97529768	97599280
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+chr7	100396759	100461081
+chr7	102369758	102433820
+chr7	110115837	110185134
+chr7	110593609	110657942
+chr7	111828298	111892634
+chr7	113312731	113382215
+chr7	113768856	113840290
+chr7	115660728	115732171
+chr7	117629868	117694188
+chr7	120157418	120221754
+chr7	121024547	121088906
+chr7	125426839	125490900
+chr7	127489003	127553340
+chr7	130507539	130571878
+chr7	134261471	134325806
+chr7	138933955	138998277
+chr7	139084737	139149053
+chr7	140067401	140131723
+chr7	140688526	140759900
+chr7	143399593	143469131
+chr7	145614147	145678208
+chr7	147730581	147794642
+chr7	149421578	149485895
+chr8	3801027	3865347
+chr8	4803179	4867504
+chr8	7824324	7888646
+chr8	15722072	15793287
+chr8	18251757	18315818
+chr8	18465381	18529442
+chr8	19045164	19112378
+chr8	22096250	22137512
+chr8	24678842	24743165
+chr8	25794478	25858799
+chr8	26014127	26078462
+chr8	26468922	26533260
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+chr8	30097851	30161911
+chr8	30460129	30524450
+chr8	30752787	30817107
+chr8	31563440	31627777
+chr8	36022443	36086504
+chr8	36959548	37023870
+chr8	39028207	39092267
+chr8	41087234	41151556
+chr8	41620051	41689555
+chr8	42004143	42068203
+chr8	43019118	43083438
+chr8	47722042	47786380
+chr8	59252906	59322400
+chr8	60789544	60853875
+chr8	61197366	61261703
+chr8	61532874	61596935
+chr8	63294270	63358605
+chr8	64185293	64253284
+chr8	64763207	64827530
+chr8	67113241	67177577
+chr8	69123511	69187572
+chr8	70169472	70233795
+chr8	72177196	72241533
+chr8	75436025	75500364
+chr8	76584577	76648638
+chr8	77497140	77561453
+chr8	77747147	77811482
+chr8	79352165	79416481
+chr8	80631654	80703131
+chr8	83678886	83743222
+chr8	87650996	87722809
+chr8	88349042	88413368
+chr8	94809868	94874201
+chr8	95383980	95448041
+chr8	102794796	102859131
+chr8	103935008	103999308
+chr8	109626938	109691000
+chr8	109709405	109773728
+chr8	116384465	116448815
+chr8	120505951	120570011
+chr8	121428979	121493588
+chr8	125683558	125747880
+chr8	128575325	128644983
+chr9	4047472	4116542
+chr9	4806803	4870864
+chr9	4884580	4954084
+chr9	6022806	6092325
+chr9	6275883	6339944
+chr9	7392890	7457209
+chr9	7462474	7526795
+chr9	7766967	7837187
+chr9	8271124	8335185
+chr9	8402204	8466265
+chr9	8764452	8828512
+chr9	11784168	11855632
+chr9	12170129	12234190
+chr9	12237687	12309084
+chr9	12318611	12382934
+chr9	12721775	12785836
+chr9	13835575	13899894
+chr9	15182924	15247260
+chr9	17955775	18020096
+chr9	18827860	18898433
+chr9	24340641	24404702
+chr9	24593904	24658240
+chr9	27266534	27330872
+chr9	30430874	30495213
+chr9	35587912	35657485
+chr9	35863647	35935120
+chr9	37845538	37909860
+chr9	38185239	38249385
+chr9	38896815	38961150
+chr9	41662492	41726552
+chr9	43638042	43702378
+chr9	45006098	45070433
+chr9	47047851	47112173
+chr9	49906212	49970548
+chr9	50402386	50472116
+chr9	52696613	52760674
+chr9	53981007	54045329
+chr9	55048978	55113313
+chr9	55639453	55703790
+chr9	57139057	57203396
+chr9	58372958	58437282
+chr9	59751834	59816157
+chr9	59828617	59892938
+chr9	67460563	67524885
+chr9	69791346	69855407
+chr9	72084500	72148804
+chr9	73306304	73370365
+chr9	75546159	75615764
+chr9	76067163	76131499
+chr9	78205560	78269895
+chr9	79863716	79932960
+chr9	83543186	83607520
+chr9	83961391	84025712
+chr9	84745537	84816469
+chr9	87287487	87351823
+chr9	88965683	89029744
+chr9	89914557	89978617
+chr9	95389913	95454249
+chr9	98540578	98604900
+chr9	104333243	104397304
+chr9	105712170	105776231
+chr9	105976408	106040743
+chr9	108139205	108203544
+chr9	111904500	111968818
+chr9	113768402	113832464
+chr9	120794546	120858880
+chr9	122321963	122386298
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/README	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,21 @@
+This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
+In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
+fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
+of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
+used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
+sites).
+Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
+particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
+hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
+fraction of the 1-kb window that is covered by recombination hotspots
+
+Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
+Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
+endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
+12(6): 1-41.
+Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
+Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
+active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
+Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
+B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
+genome. Genetics. 191: 757-764.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Recombination_hotspots.txt	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,2438 @@
+chr1	3079711	3144047	1	1	1	1	0.606	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.394	1	0.606	0	0	0	0	0	0	0.73	1	0.27	0.73	1	1	1	1	1	1	1	1	0.27	0	0	0	0	0	0	0	0.73	1	1	1	1	1	1
+chr1	3232230	3302517	1	1	1	0.211	0	0	0	0	0	0.789	1	1	1	0.211	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.789	1	1	1	1	1	1	0.924	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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+chr1	4589320	4653381	0	0	0	0	0	0	0	0	0	0	0	0.06	1	1	1	1	1	1	1	0.94	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.121	1	1	1	1	1	1	1	1	1	1	1	1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/features.header	Tue May 02 17:55:30 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/ETn_example/regions.header	Tue May 02 17:55:30 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 example/._.DS_Store has changed
Binary file example/._Controls_regions.bed has changed
Binary file example/._Elements1_regions.bed has changed
Binary file example/._Elements2_regions.bed has changed
Binary file example/._Elements3_regions.bed has changed
Binary file example/._Feature1.bed has changed
Binary file example/._Feature2.bed has changed
Binary file example/._README has changed
Binary file example/._features.header.bed.txt has changed
Binary file example/._regions.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Controls_regions.bed	Tue May 02 17:55:30 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements1_regions.bed	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,25 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements2_regions.bed	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,20 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements3_regions.bed	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,28 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Feature1.bed	Tue May 02 17:55:30 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Feature2.bed	Tue May 02 17:55:30 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/README	Tue May 02 17:55:30 2017 -0400
@@ -0,0 +1,2 @@
+This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", 
+corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/features.header.bed.txt	Tue May 02 17:55:30 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/example/regions.header.txt	Tue May 02 17:55:30 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
--- a/examples/ETn_example/Control.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/examples/ETn_example/ETn_fixed.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1296 +0,0 @@
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--- a/examples/ETn_example/Recombination_hotspots.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2438 +0,0 @@
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-chr9	105976408	106040743	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.913	0.087	1	1	1	1	1	1	0.913	0	0	0	0	0	0	0.422	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
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-chr1	136988763	137052763	0.973	0	0	0	0	0.027	1	1	1	1	1	0.973	0	0	0	0	0	0	0	0	0	0.027	1	1	1	1	1	1	0.973	0	0	0	0	0	0.027	1	1	1	1	1	1	1	0.973	0.027	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr1	137229123	137293123	1	1	1	1	1	1	1	1	1	1	1	0.613	0	0	0	0	0	0	0.387	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.613	0	0	0	0	0	0	0	0	0	0	0.387	1	1	1	1	1	1	1	1	0.613	0	0	0	0.387	1	1	1	0.613	0.387	1
-chr1	137689172	137753172	0.458	1	1	1	1	1	1	1	1	1	1	1	1	1	0.542	0	0	0.458	1	1	0.542	0.458	1	1	1	1	1	0.542	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	139995038	140059038	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	163888959	163952959	1	1	1	1	1	1	1	1	1	1	1	1	1	0.755	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.245	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.755	0	0	0	0	0
-chr1	164146377	164210377	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.317	1	1	0.683	0	0
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-chr1	170078935	170142935	0	0	0	0	0	0	0	0	0.875	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0.875	1	1	1	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.875	1	1	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	170185390	170249390	0	0	0	0	0	0	0	0	0	0	0.33	1	1	1	1	1	1	1	1	1	0.67	0	0	0	0.33	1	1	0.67	0	0	0	0.33	1	1	1	1	1	1	1	0.67	0	0.33	1	1	1	1	1	0.67	0	0	0	0	0	0	0	0	0.33	1	1	1	1	1	1	0.67
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-chr1	173284896	173348896	1	1	1	0.164	0	0	0	0.836	1	1	0.164	0	0	0.836	1	1	1	1	1	1	0.164	0	0	0	0	0	0	0.836	1	1	1	1	1	1	1	0.164	0.836	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.164	0	0	0	0	0	0	0	0	0	0	0.836
-chr1	174231860	174295860	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.2	0	0	0.8	1	1	1	1	1	1	1
-chr1	175209865	175273865	1	1	1	1	1	1	1	1	1	0.195	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.805	1	1	1	1	1	1	1	1	1	0.195	0	0	0.805	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr1	176812441	176876441	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.619	0	0	0	0	0	0.381	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.619	0	0	0	0
-chr1	179114819	179178819	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	183090720	183154720	0	0	0	0	0	0	0	0	0	0	0	0.66	1	1	0.34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.66	1	1	0.34	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	188499484	188563484	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	189774115	189838115	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.055	1	1	1	1	1	1	1	1	0.945	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	189902115	189966115	0	0.055	1	1	1	1	0.945	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	190477513	190541513	1	1	0.547	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.453	1	1	0.547	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	191934479	191998479	0.792	0	0.208	1	1	1	1	0.792	0.208	1	1	1	1	1	1	1	1	1	0.792	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.208	1	1	1	1	1	1	0.792	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	196512385	196576385	0	0	0	0	0	0.114	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.886	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr10	8440103	8504103	0	0	0	0.4	1	1	0.6	0	0	0	0	0	0	0	0	0	0	0.4	1	1	0.6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.4	1	1	0.6
-chr10	12363669	12427669	0	0	0	0	0	0	0.966	1	1	1	0.034	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr10	13778671	13842671	0	0	0	0	0	0	0	0	0	0	0.968	1	1	1	1	0.032	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.968	1	1	1	1	1	1	1	0.032	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr10	14108714	14172714	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.989	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.011	1	1	1	1	1	1	0.989	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr17	3481173	3545173	0	0	0	0	0	0	0.582	1	0.418	0.582	1	0.418	0	0.582	1	1	1	0.418	0	0	0	0.582	1	1	1	1	0.418	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.582	1	1	1	1	1	0.418	0	0	0	0	0	0	0	0	0	0	0
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-chr17	10584620	10648620	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.029	1	1	0.971	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr17	24231700	24295700	1	1	1	0.891	0	0	0	0	0	0	0	0	0	0	0.109	1	1	1	1	1	1	0.891	0.109	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.891	0	0	0	0	0	0	0	0	0	0.109
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-chr17	24605984	24669984	1	1	1	1	0.607	0	0	0	0.393	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.607	0.393	1	1	0.607	0	0	0	0	0.393	1	1	1	1	1	0.607	0	0	0	0.393	1	1	1	1	1	1	1	1	1	0.607	0	0
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-chr17	25012393	25076393	1	1	1	1	0.198	0	0	0	0	0	0	0.802	1	1	1	1	1	1	1	1	0.198	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.802	1	1	1	1	1	0.198	0	0	0	0	0.802	1	0.198	0.802
-chr17	25959539	26023539	0	0	0	0.948	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.052	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.948
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-chr17	27835926	27899926	0	0.335	1	1	1	1	1	1	0.665	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr9	69240049	69304049	0	0	0	0	0	0.767	1	1	1	1	0.233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.767	1	0.233	0	0	0	0	0	0	0	0	0	0	0
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-chr9	107590650	107654650	0.18	0.82	1	1	1	1	1	1	1	1	1	1	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0.82	1	1	1	1	1	1	1	1	1	1	0.18	0	0	0	0	0	0.82	1	1	1	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.82
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-chr9	121627136	121691136	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- a/examples/ETn_example/features.header	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Recombination_hotspots.txt	Recomb_hot	Recombination hotspots
\ No newline at end of file
--- a/examples/ETn_example/regions.header	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Control.bed	Control	Control
-ETn_fixed.bed	ETn_fixed	ETn fixed
\ No newline at end of file
--- a/examples/easy/features/Feature1.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5400 +0,0 @@
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-chr21	16062609	16064609	1.02761240862396
-chr21	16064609	16066609	0.870263755617609
--- a/examples/easy/features/Feature1.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
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--- a/examples/easy/features/Feature2.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/examples/easy/features/Feature2.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
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-chr5	91277761	91377761	6.16112741185719	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	6.1233155206185
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-chr21	15966609	16066609	3.61661096782077	4.73386208722406	5.8015549021153	4.96167153907388	3.95102647749112	3.97020922833049	5.33786080501161	4.36434578068312	5.80198476623914	5.35739211903602	6.08746983525949	4.34773396054126	5.13949591522979	3.73402272260864	5.39450798275315	5.55466043086729	5.28998031818056	6.19329925730006	2.67150074437477	5.16423939358034	4.69609507505699	5.44942073640721	6.03847400860453	5.97649168698122	5.36013704359642	7.92817462773764	7.69377454814871	8.80647396276848	8.52452119781362	7.89462789559928	6.13805198380259	4.64531272265593	6.29826676008479	7.79487866360525	7.31994055340419	8.8004479775322	8.25854856063076	5.04576860851306	7.30730130969012	7.83870783306589	7.63074529828173	6.43100021814285	7.27551387601485	6.26545170591659	7.12562466213381	6.26895239202312	7.3992370168724	7.97487587946482	6.76355670816454	6.11742019669001
--- a/examples/easy/features/features.header.bed.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Feature1.bed	ftr1	Feature 1
-Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- a/examples/easy/features/features.header.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Feature1.txt	ftr1	Feature 1
-Feature2.txt	ftr2	Feature 2
\ No newline at end of file
--- a/examples/easy/regions/Controls_regions.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-chr1	91399892	91499892
-chr1	116447079	116547079
-chr2	231381109	231481109
-chr3	47386633	47486633
-chr3	99195712	99295712
-chr3	116765114	116865114
-chr3	134345017	134445017
-chr4	68064019	68164019
-chr4	137465811	137565811
-chr4	173293016	173393016
-chr5	59044110	59144110
-chr5	94592763	94692763
-chr5	108436006	108536006
-chr5	110836898	110936898
-chr5	146661073	146761073
-chr6	99727306	99827306
-chr7	88291325	88391325
-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	98959030	99059030
-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
--- a/examples/easy/regions/Elements1_regions.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-chr2	49960150	50060150
-chr2	55912445	56012445
-chr3	140326750	140426750
-chr4	41772201	41872201
-chr4	70629719	70729719
-chr4	109340735	109440735
-chr5	15025389	15125389
-chr5	43028888	43128888
-chr5	58231354	58331354
-chr5	91277761	91377761
-chr5	119464508	119564508
-chr6	85309170	85409170
-chr6	85762072	85862072
-chr6	134621363	134721363
-chr6	147470164	147570164
-chr7	77195798	77295798
-chr7	77880914	77980914
-chr7	114805399	114905399
-chr10	46350885	46450885
-chr10	67833078	67933078
-chr12	27722692	27822692
-chr12	95518506	95618506
-chr12	117863466	117963466
-chr14	100464166	100564166
-chrX	29266748	29366748
--- a/examples/easy/regions/Elements2_regions.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-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
--- a/examples/easy/regions/Elements3_regions.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-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
--- a/examples/easy/regions/regions.header.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-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
--- a/examples/hard-withNAs/Feature2.bed	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5401 +0,0 @@
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-
--- a/examples/paper_example/regions.header.txt	Tue May 02 17:37:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-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