--- a/ETn_example/Control.bed	Wed May 03 11:10:18 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1142 +0,0 @@
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--- a/ETn_example/DESCRIPTION.txt	Wed May 03 11:10:18 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-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

--- a/ETn_example/ETn_fixed.bed	Wed May 03 11:10:18 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-chr9	122321963	122386298

--- a/ETn_example/Recombination_hotspots.txt	Wed May 03 11:10:18 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2438 +0,0 @@
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-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
-chr1	3756792	3826331	0	0	0	0	0	0	0	0	0	0	0.11	1	1	1	1	1	0.89	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0.351	0	0	0	0	0	0	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	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
-chr1	5155380	5219717	1	0.061	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.939	1	1	1	1	1	1	1	0.724	0	0	0	0	0	0	0	0	0	0	0	0	0	0.276	1	1	1	1	1	1	1	1	0.724	0
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-chr9	107526650	107590650	0	0	0.82	1	1	1	1	1	1	0.18	0	0.82	1	1	1	1	1	1	0.18	0	0.82	1	1	1	1	0.18	0	0	0	0.82	1	1	0.18	0	0.82	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.18	0	0.82	1	0.18	0	0	0	0	0	0.82	1	1
-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
-chr9	107848560	107912560	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.73	1	0.27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	107941738	108005738	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.908	1	0.092	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	108683437	108747437	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	108962296	109026296	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.466	1	1	1	0.534	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	109947901	110011901	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	110485254	110549254	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	110616374	110680374	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.544	1	1	1	1	1	1	1	1	1	0.456	0.544	1	1	1	1	1	1	0.456	0.544	1	1	0.456	0.544	1	1	1
-chr9	111968818	112032818	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	113836504	113900504	0	0	0.457	1	1	1	1	0.543	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.457	1	1	1	1	1	1	1	1	0.543	0	0	0	0	0.457	1	1	1	1
-chr9	118910538	118974538	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.491	1	1	1	1	1	1	1	1	0.509	0	0	0	0	0	0	0	0	0	0
-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