| Previous changeset 9:417b1cc9bd9d (2017-05-02) Next changeset 11:3a56f8e72534 (2017-05-02) |
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Commit message:
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added:
._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 |
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removed:
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 |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a ETn_example/Control.bed --- /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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|
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a ETn_example/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/README Tue May 02 17:55:30 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a ETn_example/Recombination_hotspots.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/Recombination_hotspots.txt Tue May 02 17:55:30 2017 -0400 |
| b |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a ETn_example/features.header --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/features.header Tue May 02 17:55:30 2017 -0400 |
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| @@ -0,0 +1,1 @@ +Recombination_hotspots.txt Recomb_hot Recombination hotspots \ No newline at end of file |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a ETn_example/regions.header --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/regions.header Tue May 02 17:55:30 2017 -0400 |
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| @@ -0,0 +1,2 @@ +Control.bed Control Control +ETn_fixed.bed ETn_fixed ETn fixed \ No newline at end of file |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._.DS_Store |
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| Binary file example/._.DS_Store has changed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._Controls_regions.bed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._Elements1_regions.bed |
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| Binary file example/._Elements1_regions.bed has changed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._Elements2_regions.bed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._Feature1.bed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._Feature2.bed |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._README |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/._regions.header.txt |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Controls_regions.bed --- /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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| @@ -0,0 +1,35 @@ +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 |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Elements1_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements1_regions.bed Tue May 02 17:55:30 2017 -0400 |
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| @@ -0,0 +1,25 @@ +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 |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Elements2_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements2_regions.bed Tue May 02 17:55:30 2017 -0400 |
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| @@ -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 |
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| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Elements3_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements3_regions.bed Tue May 02 17:55:30 2017 -0400 |
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| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Feature1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Feature1.bed Tue May 02 17:55:30 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 @@\n+chr1\t91399892\t91401892\t0.914729028492568\n+chr1\t91401892\t91403892\t1.03788669317729\n+chr1\t91403892\t91405892\t1.15695078809331\n+chr1\t91405892\t91407892\t1.05433971377051\n+chr1\t91407892\t91409892\t1.05827244724317\n+chr1\t91409892\t91411892\t1.00216117481117\n+chr1\t91411892\t91413892\t0.873489001753337\n+chr1\t91413892\t91415892\t0.873100412116323\n+chr1\t91415892\t91417892\t0.928712683217515\n+chr1\t91417892\t91419892\t0.94132562114723\n+chr1\t91419892\t91421892\t1.06739894033636\n+chr1\t91421892\t91423892\t0.909275169317382\n+chr1\t91423892\t91425892\t1.10093887463398\n+chr1\t91425892\t91427892\t1.05342912580018\n+chr1\t91427892\t91429892\t0.970074712768588\n+chr1\t91429892\t91431892\t0.742552329847752\n+chr1\t91431892\t91433892\t1.09649292566553\n+chr1\t91433892\t91435892\t0.902578291528885\n+chr1\t91435892\t91437892\t0.821718064516058\n+chr1\t91437892\t91439892\t0.909063175846949\n+chr1\t91439892\t91441892\t1.12598647717153\n+chr1\t91441892\t91443892\t0.962991989888592\n+chr1\t91443892\t91445892\t0.886361985680751\n+chr1\t91445892\t91447892\t1.19735794895968\n+chr1\t91447892\t91449892\t1.1058589065373\n+chr1\t91449892\t91451892\t1.11830938343819\n+chr1\t91451892\t91453892\t0.891849450289035\n+chr1\t91453892\t91455892\t0.921613352575372\n+chr1\t91455892\t91457892\t0.961394603438276\n+chr1\t91457892\t91459892\t0.942120540462845\n+chr1\t91459892\t91461892\t1.04179227745858\n+chr1\t91461892\t91463892\t0.846036296260439\n+chr1\t91463892\t91465892\t0.903782108017989\n+chr1\t91465892\t91467892\t0.926324469715607\n+chr1\t91467892\t91469892\t1.01617788108211\n+chr1\t91469892\t91471892\t1.01871994841433\n+chr1\t91471892\t91473892\t0.86346600407464\n+chr1\t91473892\t91475892\t0.911534382002842\n+chr1\t91475892\t91477892\t0.909397860657818\n+chr1\t91477892\t91479892\t0.882437981483481\n+chr1\t91479892\t91481892\t1.20022730271379\n+chr1\t91481892\t91483892\t1.02286707465404\n+chr1\t91483892\t91485892\t1.00824959158441\n+chr1\t91485892\t91487892\t1.13387236604912\n+chr1\t91487892\t91489892\t0.917808428397605\n+chr1\t91489892\t91491892\t1.00980153326694\n+chr1\t91491892\t91493892\t1.0780078042687\n+chr1\t91493892\t91495892\t1.05789211157318\n+chr1\t91495892\t91497892\t0.983519376160091\n+chr1\t91497892\t91499892\t1.06301499098899\n+chr1\t116447079\t116449079\t0.909510507890661\n+chr1\t116449079\t116451079\t1.04923486926106\n+chr1\t116451079\t116453079\t0.972429435962863\n+chr1\t116453079\t116455079\t0.94348509718749\n+chr1\t116455079\t116457079\t0.877213727110183\n+chr1\t116457079\t116459079\t1.07609955711144\n+chr1\t116459079\t116461079\t1.05964706503259\n+chr1\t116461079\t116463079\t1.08048074104999\n+chr1\t116463079\t116465079\t1.10397643608295\n+chr1\t116465079\t116467079\t0.879172377236955\n+chr1\t116467079\t116469079\t0.952455624542298\n+chr1\t116469079\t116471079\t0.872450868701435\n+chr1\t116471079\t116473079\t0.734632500870684\n+chr1\t116473079\t116475079\t0.975852194327443\n+chr1\t116475079\t116477079\t1.15968481779916\n+chr1\t116477079\t116479079\t1.03479249038231\n+chr1\t116479079\t116481079\t0.958716780567544\n+chr1\t116481079\t116483079\t1.00882150410174\n+chr1\t116483079\t116485079\t0.894048456447358\n+chr1\t116485079\t116487079\t0.862250242465922\n+chr1\t116487079\t116489079\t1.08563273479841\n+chr1\t116489079\t116491079\t1.03570610668607\n+chr1\t116491079\t116493079\t1.282637134762\n+chr1\t116493079\t116495079\t1.05344881721884\n+chr1\t116495079\t116497079\t0.958843714832433\n+chr1\t116497079\t116499079\t0.907730747212707\n+chr1\t116499079\t116501079\t0.964823764805327\n+chr1\t116501079\t116503079\t0.972508803669119\n+chr1\t116503079\t116505079\t0.964761127498888\n+chr1\t116505079\t116507079\t1.21022463445566\n+chr1\t116507079\t116509079\t0.870817357520223\n+chr1\t116509079\t116511079\t0.970216007864307\n+chr1\t116511079\t116513079\t1.09860269791989\n+chr1\t116513079\t116515079\t1.01985884672516\n+chr1\t116515079\t116517079\t1.04151199469522\n+chr1\t116517079\t116519079\t1.10542491108645\n+chr1\t116519079\t116521079\t1.06697958402493\n+chr1\t116521079\t116523079\t0.972137682316022\n+chr1\t116523079\t116525079\t0.900068042346903\n+chr1\t116525079\t116527079\t1.00945179072767\n+chr1\t116527079\t116529079\t0.910760202377398\n+chr1\t116529079\t116531079\t0.960315923931081\n+chr1\t116531079\t116533079\t1.05558603806716\n+chr1\t116533079\t116535079\t0.92038544115'..b'1\t64656131\t0.97369678388939\n+chr18\t64656131\t64658131\t0.910087798040937\n+chr18\t64658131\t64660131\t0.946468289624316\n+chr18\t64660131\t64662131\t1.05842665628809\n+chr18\t64662131\t64664131\t0.927667349376235\n+chr18\t64664131\t64666131\t1.18742333150313\n+chr18\t64666131\t64668131\t1.22205250380213\n+chr18\t64668131\t64670131\t0.880563425486305\n+chr18\t64670131\t64672131\t0.914485239144026\n+chr18\t64672131\t64674131\t1.01034737175594\n+chr18\t64674131\t64676131\t1.62264521151304\n+chr18\t64676131\t64678131\t1.48296645852995\n+chr18\t64678131\t64680131\t1.28681962535927\n+chr18\t64680131\t64682131\t1.53492939742228\n+chr18\t64682131\t64684131\t1.58844790171606\n+chr18\t64684131\t64686131\t1.49033262314301\n+chr18\t64686131\t64688131\t1.31424965988202\n+chr18\t64688131\t64690131\t1.45337032575317\n+chr18\t64690131\t64692131\t1.35217898213701\n+chr18\t64692131\t64694131\t1.77532370910719\n+chr18\t64694131\t64696131\t1.60398303218395\n+chr18\t64696131\t64698131\t1.69307164801575\n+chr18\t64698131\t64700131\t1.54229556388787\n+chr18\t64700131\t64702131\t1.68106575665579\n+chr18\t64702131\t64704131\t1.48714225361666\n+chr18\t64704131\t64706131\t1.55224087444918\n+chr18\t64706131\t64708131\t1.3662045024589\n+chr18\t64708131\t64710131\t1.57624355139023\n+chr18\t64710131\t64712131\t1.44378437443185\n+chr18\t64712131\t64714131\t1.37811537520723\n+chr18\t64714131\t64716131\t1.06551636789331\n+chr18\t64716131\t64718131\t1.04029846172777\n+chr18\t64718131\t64720131\t1.1012560789095\n+chr18\t64720131\t64722131\t1.16248797408295\n+chr18\t64722131\t64724131\t1.10209650363972\n+chr18\t64724131\t64726131\t1.12702540883185\n+chr18\t64726131\t64728131\t1.06158233209566\n+chr18\t64728131\t64730131\t1.24500209867534\n+chr18\t64730131\t64732131\t0.834309455846338\n+chr18\t64732131\t64734131\t0.757289730474966\n+chr18\t64734131\t64736131\t1.10451816307643\n+chr18\t64736131\t64738131\t0.92262846294503\n+chr18\t64738131\t64740131\t0.804253155660302\n+chr18\t64740131\t64742131\t1.00162039935745\n+chr18\t64742131\t64744131\t0.956034285823398\n+chr21\t15966609\t15968609\t1.12440801594939\n+chr21\t15968609\t15970609\t0.958928874609379\n+chr21\t15970609\t15972609\t0.980859325447667\n+chr21\t15972609\t15974609\t0.985836855465142\n+chr21\t15974609\t15976609\t0.924304227149342\n+chr21\t15976609\t15978609\t0.981319441090073\n+chr21\t15978609\t15980609\t0.949853799394529\n+chr21\t15980609\t15982609\t0.858050928062694\n+chr21\t15982609\t15984609\t0.836178837413462\n+chr21\t15984609\t15986609\t1.20633196613812\n+chr21\t15986609\t15988609\t0.969230627046025\n+chr21\t15988609\t15990609\t1.06120061342825\n+chr21\t15990609\t15992609\t0.88573302960608\n+chr21\t15992609\t15994609\t0.987056692659576\n+chr21\t15994609\t15996609\t1.05266019775439\n+chr21\t15996609\t15998609\t1.29745136461899\n+chr21\t15998609\t16000609\t1.3631797211261\n+chr21\t16000609\t16002609\t1.58553521861437\n+chr21\t16002609\t16004609\t1.47800659441217\n+chr21\t16004609\t16006609\t1.75042011315262\n+chr21\t16006609\t16008609\t1.39329136735319\n+chr21\t16008609\t16010609\t1.57255744319984\n+chr21\t16010609\t16012609\t1.20929102513908\n+chr21\t16012609\t16014609\t1.53853232166312\n+chr21\t16014609\t16016609\t1.64985481461386\n+chr21\t16016609\t16018609\t1.59575749789367\n+chr21\t16018609\t16020609\t1.42205668994404\n+chr21\t16020609\t16022609\t1.66053802113289\n+chr21\t16022609\t16024609\t1.70386086339594\n+chr21\t16024609\t16026609\t1.73541878893467\n+chr21\t16026609\t16028609\t1.39682491364686\n+chr21\t16028609\t16030609\t1.43336589770868\n+chr21\t16030609\t16032609\t1.63386317242737\n+chr21\t16032609\t16034609\t1.53233925104548\n+chr21\t16034609\t16036609\t1.53952241603109\n+chr21\t16036609\t16038609\t1.28074961173938\n+chr21\t16038609\t16040609\t1.27922409248079\n+chr21\t16040609\t16042609\t0.962647373836482\n+chr21\t16042609\t16044609\t0.950807449539781\n+chr21\t16044609\t16046609\t1.19549845149275\n+chr21\t16046609\t16048609\t1.03462200267827\n+chr21\t16048609\t16050609\t0.952643344080609\n+chr21\t16050609\t16052609\t1.20946321219477\n+chr21\t16052609\t16054609\t0.965927027586426\n+chr21\t16054609\t16056609\t0.976116334675594\n+chr21\t16056609\t16058609\t1.07756004404963\n+chr21\t16058609\t16060609\t0.987244607153093\n+chr21\t16060609\t16062609\t1.04620355385428\n+chr21\t16062609\t16064609\t1.02761240862396\n+chr21\t16064609\t16066609\t0.870263755617609\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/Feature2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Feature2.bed Tue May 02 17:55:30 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 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|
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/README Tue May 02 17:55:30 2017 -0400 |
| b |
| @@ -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". |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/features.header.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/features.header.bed.txt Tue May 02 17:55:30 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Feature1.bed ftr1 Feature 1 +Feature2.bed ftr2 Feature 2 \ No newline at end of file |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a example/regions.header.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/regions.header.txt Tue May 02 17:55:30 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/ETn_example/Control.bed --- a/examples/ETn_example/Control.bed Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1142 +0,0 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0810\t56584810\r\n-chr7\t56651195\t56715195\r\n-chr7\t77074960\t77138960\r\n-chr7\t77444459\t77508459\r\n-chr7\t79324748\t79388748\r\n-chr7\t80606988\t80670988\r\n-chr7\t85424277\t85488277\r\n-chr7\t86637488\t86701488\r\n-chr7\t87490216\t87554216\r\n-chr7\t94386826\t94450826\r\n-chr7\t94966452\t95030452\r\n-chr7\t98517363\t98581363\r\n-chr7\t99452639\t99516639\r\n-chr7\t100918461\t100982461\r\n-chr7\t102669140\t102733140\r\n-chr7\t103352710\t103416710\r\n-chr7\t103998756\t104062756\r\n-chr7\t105194424\t105258424\r\n-chr7\t105739791\t105803791\r\n-chr7\t107553010\t107617010\r\n-chr7\t110033354\t110097354\r\n-chr7\t110938758\t111002758\r\n-chr7\t122669176\t122733176\r\n-chr7\t122814547\t122878547\r\n-chr7\t122927103\t122991103\r\n-chr7\t123215332\t123279332\r\n-chr7\t127388603\t127452603\r\n-chr7\t133986042\t134050042\r\n-chr7\t134639723\t134703723\r\n-chr7\t134976215\t135040215\r\n-chr7\t139936722\t140000722\r\n-chr7\t144371823\t144435823\r\n-chr7\t144435823\t144499823\r\n-chr7\t146716018\t146780018\r\n-chr7\t149138752\t149202752\r\n-chr7\t149635306\t149699306\r\n-chr7\t149715608\t149779608\r\n-chr8\t6559442\t6623442\r\n-chr8\t6623442\t6687442\r\n-chr8\t7293954\t7357954\r\n-chr8\t11241630\t11305630\r\n-chr8\t11333377\t11397377\r\n-chr8\t12797793\t12861793\r\n-chr8\t17140927\t17204927\r\n-chr8\t17453277\t17517277\r\n-chr8\t18682008\t18746008\r\n-chr8\t24201916\t24265916\r\n-chr8\t26679408\t26743408\r\n-chr8\t32970842\t33034842\r\n-chr8\t33171781\t33235781\r\n-chr8\t34892948\t34956948\r\n-chr8\t35865387\t35929387\r\n-chr8\t39257582\t39321582\r\n-chr8\t39450262\t39514262\r\n-chr8\t49642107\t49706107\r\n-chr8\t49856227\t49920227\r\n-chr8\t50183963\t50247963\r\n-chr8\t50620889\t50684889\r\n-chr8\t51733915\t51797915\r\n-chr8\t59779596\t59843596\r\n-chr8\t64029519\t64093519\r\n-chr8\t72435881\t72499881\r\n-chr8\t72967674\t73031674\r\n-chr8\t73979868\t74043868\r\n-chr8\t74065191\t74129191\r\n-chr8\t80836252\t80900252\r\n-chr8\t83285181\t83349181\r\n-chr8\t86680889\t86744889\r\n-chr8\t87177477\t87241477\r\n-chr8\t87241477\t87305477\r\n-chr8\t87477935\t87541935\r\n-chr8\t90388211\t90452211\r\n-chr8\t90760313\t90824313\r\n-chr8\t92030994\t92094994\r\n-chr8\t93443787\t93507787\r\n-chr8\t96789585\t96853585\r\n-chr8\t97043262\t97107262\r\n-chr8\t97477230\t97541230\r\n-chr8\t111089991\t111153991\r\n-chr8\t111270619\t111334619\r\n-chr8\t111334619\t111398619\r\n-chr8\t111398619\t111462619\r\n-chr8\t117237918\t117301918\r\n-chr8\t125868555\t125932555\r\n-chr8\t126054477\t126118477\r\n-chr8\t127381524\t127445524\r\n-chr9\t7916325\t7980325\r\n-chr9\t10034653\t10098653\r\n-chr9\t21205558\t21269558\r\n-chr9\t27102323\t27166323\r\n-chr9\t28793755\t28857755\r\n-chr9\t28975979\t29039979\r\n-chr9\t29182458\t29246458\r\n-chr9\t29431925\t29495925\r\n-chr9\t30706012\t30770012\r\n-chr9\t32468538\t32532538\r\n-chr9\t36694615\t36758615\r\n-chr9\t36758615\t36822615\r\n-chr9\t41371667\t41435667\r\n-chr9\t42383364\t42447364\r\n-chr9\t43535422\t43599422\r\n-chr9\t44030826\t44094826\r\n-chr9\t44257286\t44321286\r\n-chr9\t44893563\t44957563\r\n-chr9\t45496156\t45560156\r\n-chr9\t45700064\t45764064\r\n-chr9\t47438414\t47502414\r\n-chr9\t47502414\t47566414\r\n-chr9\t47566414\t47630414\r\n-chr9\t47630414\t47694414\r\n-chr9\t48557242\t48621242\r\n-chr9\t56295240\t56359240\r\n-chr9\t56707178\t56771178\r\n-chr9\t57431374\t57495374\r\n-chr9\t59569429\t59633429\r\n-chr9\t62718979\t62782979\r\n-chr9\t63147522\t63211522\r\n-chr9\t63788832\t63852832\r\n-chr9\t69050403\t69114403\r\n-chr9\t69176049\t69240049\r\n-chr9\t69240049\t69304049\r\n-chr9\t71796844\t71860844\r\n-chr9\t74791622\t74855622\r\n-chr9\t79491629\t79555629\r\n-chr9\t79932960\t79996960\r\n-chr9\t84626957\t84690957\r\n-chr9\t96193779\t96257779\r\n-chr9\t107312141\t107376141\r\n-chr9\t107376141\t107440141\r\n-chr9\t107462650\t107526650\r\n-chr9\t107526650\t107590650\r\n-chr9\t107590650\t107654650\r\n-chr9\t107848560\t107912560\r\n-chr9\t107941738\t108005738\r\n-chr9\t108683437\t108747437\r\n-chr9\t108962296\t109026296\r\n-chr9\t109947901\t110011901\r\n-chr9\t110485254\t110549254\r\n-chr9\t110616374\t110680374\r\n-chr9\t111968818\t112032818\r\n-chr9\t113836504\t113900504\r\n-chr9\t118910538\t118974538\r\n-chr9\t121627136\t121691136\r\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/ETn_example/ETn_fixed.bed --- 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 |
| b |
| b'@@ -1,1296 +0,0 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69758\t102433820\r\n-chr7\t110115837\t110185134\r\n-chr7\t110593609\t110657942\r\n-chr7\t111828298\t111892634\r\n-chr7\t113312731\t113382215\r\n-chr7\t113768856\t113840290\r\n-chr7\t115660728\t115732171\r\n-chr7\t117629868\t117694188\r\n-chr7\t120157418\t120221754\r\n-chr7\t121024547\t121088906\r\n-chr7\t125426839\t125490900\r\n-chr7\t127489003\t127553340\r\n-chr7\t130507539\t130571878\r\n-chr7\t134261471\t134325806\r\n-chr7\t138933955\t138998277\r\n-chr7\t139084737\t139149053\r\n-chr7\t140067401\t140131723\r\n-chr7\t140688526\t140759900\r\n-chr7\t143399593\t143469131\r\n-chr7\t145614147\t145678208\r\n-chr7\t147730581\t147794642\r\n-chr7\t149421578\t149485895\r\n-chr8\t3801027\t3865347\r\n-chr8\t4803179\t4867504\r\n-chr8\t7824324\t7888646\r\n-chr8\t15722072\t15793287\r\n-chr8\t18251757\t18315818\r\n-chr8\t18465381\t18529442\r\n-chr8\t19045164\t19112378\r\n-chr8\t22096250\t22137512\r\n-chr8\t24678842\t24743165\r\n-chr8\t25794478\t25858799\r\n-chr8\t26014127\t26078462\r\n-chr8\t26468922\t26533260\r\n-chr8\t28479149\t28543469\r\n-chr8\t30097851\t30161911\r\n-chr8\t30460129\t30524450\r\n-chr8\t30752787\t30817107\r\n-chr8\t31563440\t31627777\r\n-chr8\t36022443\t36086504\r\n-chr8\t36959548\t37023870\r\n-chr8\t39028207\t39092267\r\n-chr8\t41087234\t41151556\r\n-chr8\t41620051\t41689555\r\n-chr8\t42004143\t42068203\r\n-chr8\t43019118\t43083438\r\n-chr8\t47722042\t47786380\r\n-chr8\t59252906\t59322400\r\n-chr8\t60789544\t60853875\r\n-chr8\t61197366\t61261703\r\n-chr8\t61532874\t61596935\r\n-chr8\t63294270\t63358605\r\n-chr8\t64185293\t64253284\r\n-chr8\t64763207\t64827530\r\n-chr8\t67113241\t67177577\r\n-chr8\t69123511\t69187572\r\n-chr8\t70169472\t70233795\r\n-chr8\t72177196\t72241533\r\n-chr8\t75436025\t75500364\r\n-chr8\t76584577\t76648638\r\n-chr8\t77497140\t77561453\r\n-chr8\t77747147\t77811482\r\n-chr8\t79352165\t79416481\r\n-chr8\t80631654\t80703131\r\n-chr8\t83678886\t83743222\r\n-chr8\t87650996\t87722809\r\n-chr8\t88349042\t88413368\r\n-chr8\t94809868\t94874201\r\n-chr8\t95383980\t95448041\r\n-chr8\t102794796\t102859131\r\n-chr8\t103935008\t103999308\r\n-chr8\t109626938\t109691000\r\n-chr8\t109709405\t109773728\r\n-chr8\t116384465\t116448815\r\n-chr8\t120505951\t120570011\r\n-chr8\t121428979\t121493588\r\n-chr8\t125683558\t125747880\r\n-chr8\t128575325\t128644983\r\n-chr9\t4047472\t4116542\r\n-chr9\t4806803\t4870864\r\n-chr9\t4884580\t4954084\r\n-chr9\t6022806\t6092325\r\n-chr9\t6275883\t6339944\r\n-chr9\t7392890\t7457209\r\n-chr9\t7462474\t7526795\r\n-chr9\t7766967\t7837187\r\n-chr9\t8271124\t8335185\r\n-chr9\t8402204\t8466265\r\n-chr9\t8764452\t8828512\r\n-chr9\t11784168\t11855632\r\n-chr9\t12170129\t12234190\r\n-chr9\t12237687\t12309084\r\n-chr9\t12318611\t12382934\r\n-chr9\t12721775\t12785836\r\n-chr9\t13835575\t13899894\r\n-chr9\t15182924\t15247260\r\n-chr9\t17955775\t18020096\r\n-chr9\t18827860\t18898433\r\n-chr9\t24340641\t24404702\r\n-chr9\t24593904\t24658240\r\n-chr9\t27266534\t27330872\r\n-chr9\t30430874\t30495213\r\n-chr9\t35587912\t35657485\r\n-chr9\t35863647\t35935120\r\n-chr9\t37845538\t37909860\r\n-chr9\t38185239\t38249385\r\n-chr9\t38896815\t38961150\r\n-chr9\t41662492\t41726552\r\n-chr9\t43638042\t43702378\r\n-chr9\t45006098\t45070433\r\n-chr9\t47047851\t47112173\r\n-chr9\t49906212\t49970548\r\n-chr9\t50402386\t50472116\r\n-chr9\t52696613\t52760674\r\n-chr9\t53981007\t54045329\r\n-chr9\t55048978\t55113313\r\n-chr9\t55639453\t55703790\r\n-chr9\t57139057\t57203396\r\n-chr9\t58372958\t58437282\r\n-chr9\t59751834\t59816157\r\n-chr9\t59828617\t59892938\r\n-chr9\t67460563\t67524885\r\n-chr9\t69791346\t69855407\r\n-chr9\t72084500\t72148804\r\n-chr9\t73306304\t73370365\r\n-chr9\t75546159\t75615764\r\n-chr9\t76067163\t76131499\r\n-chr9\t78205560\t78269895\r\n-chr9\t79863716\t79932960\r\n-chr9\t83543186\t83607520\r\n-chr9\t83961391\t84025712\r\n-chr9\t84745537\t84816469\r\n-chr9\t87287487\t87351823\r\n-chr9\t88965683\t89029744\r\n-chr9\t89914557\t89978617\r\n-chr9\t95389913\t95454249\r\n-chr9\t98540578\t98604900\r\n-chr9\t104333243\t104397304\r\n-chr9\t105712170\t105776231\r\n-chr9\t105976408\t106040743\r\n-chr9\t108139205\t108203544\r\n-chr9\t111904500\t111968818\r\n-chr9\t113768402\t113832464\r\n-chr9\t120794546\t120858880\r\n-chr9\t122321963\t122386298\r\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/ETn_example/Recombination_hotspots.txt --- 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 |
| b |
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|
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/ETn_example/features.header --- a/examples/ETn_example/features.header Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -Recombination_hotspots.txt Recomb_hot Recombination hotspots \ No newline at end of file |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/ETn_example/regions.header --- a/examples/ETn_example/regions.header Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Control.bed Control Control -ETn_fixed.bed ETn_fixed ETn fixed \ No newline at end of file |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/Feature1.bed --- a/examples/easy/features/Feature1.bed Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 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hr18\t64682131\t64684131\t1.58844790171606\n-chr18\t64684131\t64686131\t1.49033262314301\n-chr18\t64686131\t64688131\t1.31424965988202\n-chr18\t64688131\t64690131\t1.45337032575317\n-chr18\t64690131\t64692131\t1.35217898213701\n-chr18\t64692131\t64694131\t1.77532370910719\n-chr18\t64694131\t64696131\t1.60398303218395\n-chr18\t64696131\t64698131\t1.69307164801575\n-chr18\t64698131\t64700131\t1.54229556388787\n-chr18\t64700131\t64702131\t1.68106575665579\n-chr18\t64702131\t64704131\t1.48714225361666\n-chr18\t64704131\t64706131\t1.55224087444918\n-chr18\t64706131\t64708131\t1.3662045024589\n-chr18\t64708131\t64710131\t1.57624355139023\n-chr18\t64710131\t64712131\t1.44378437443185\n-chr18\t64712131\t64714131\t1.37811537520723\n-chr18\t64714131\t64716131\t1.06551636789331\n-chr18\t64716131\t64718131\t1.04029846172777\n-chr18\t64718131\t64720131\t1.1012560789095\n-chr18\t64720131\t64722131\t1.16248797408295\n-chr18\t64722131\t64724131\t1.10209650363972\n-chr18\t64724131\t64726131\t1.12702540883185\n-chr18\t64726131\t64728131\t1.06158233209566\n-chr18\t64728131\t64730131\t1.24500209867534\n-chr18\t64730131\t64732131\t0.834309455846338\n-chr18\t64732131\t64734131\t0.757289730474966\n-chr18\t64734131\t64736131\t1.10451816307643\n-chr18\t64736131\t64738131\t0.92262846294503\n-chr18\t64738131\t64740131\t0.804253155660302\n-chr18\t64740131\t64742131\t1.00162039935745\n-chr18\t64742131\t64744131\t0.956034285823398\n-chr21\t15966609\t15968609\t1.12440801594939\n-chr21\t15968609\t15970609\t0.958928874609379\n-chr21\t15970609\t15972609\t0.980859325447667\n-chr21\t15972609\t15974609\t0.985836855465142\n-chr21\t15974609\t15976609\t0.924304227149342\n-chr21\t15976609\t15978609\t0.981319441090073\n-chr21\t15978609\t15980609\t0.949853799394529\n-chr21\t15980609\t15982609\t0.858050928062694\n-chr21\t15982609\t15984609\t0.836178837413462\n-chr21\t15984609\t15986609\t1.20633196613812\n-chr21\t15986609\t15988609\t0.969230627046025\n-chr21\t15988609\t15990609\t1.06120061342825\n-chr21\t15990609\t15992609\t0.88573302960608\n-chr21\t15992609\t15994609\t0.987056692659576\n-chr21\t15994609\t15996609\t1.05266019775439\n-chr21\t15996609\t15998609\t1.29745136461899\n-chr21\t15998609\t16000609\t1.3631797211261\n-chr21\t16000609\t16002609\t1.58553521861437\n-chr21\t16002609\t16004609\t1.47800659441217\n-chr21\t16004609\t16006609\t1.75042011315262\n-chr21\t16006609\t16008609\t1.39329136735319\n-chr21\t16008609\t16010609\t1.57255744319984\n-chr21\t16010609\t16012609\t1.20929102513908\n-chr21\t16012609\t16014609\t1.53853232166312\n-chr21\t16014609\t16016609\t1.64985481461386\n-chr21\t16016609\t16018609\t1.59575749789367\n-chr21\t16018609\t16020609\t1.42205668994404\n-chr21\t16020609\t16022609\t1.66053802113289\n-chr21\t16022609\t16024609\t1.70386086339594\n-chr21\t16024609\t16026609\t1.73541878893467\n-chr21\t16026609\t16028609\t1.39682491364686\n-chr21\t16028609\t16030609\t1.43336589770868\n-chr21\t16030609\t16032609\t1.63386317242737\n-chr21\t16032609\t16034609\t1.53233925104548\n-chr21\t16034609\t16036609\t1.53952241603109\n-chr21\t16036609\t16038609\t1.28074961173938\n-chr21\t16038609\t16040609\t1.27922409248079\n-chr21\t16040609\t16042609\t0.962647373836482\n-chr21\t16042609\t16044609\t0.950807449539781\n-chr21\t16044609\t16046609\t1.19549845149275\n-chr21\t16046609\t16048609\t1.03462200267827\n-chr21\t16048609\t16050609\t0.952643344080609\n-chr21\t16050609\t16052609\t1.20946321219477\n-chr21\t16052609\t16054609\t0.965927027586426\n-chr21\t16054609\t16056609\t0.976116334675594\n-chr21\t16056609\t16058609\t1.07756004404963\n-chr21\t16058609\t16060609\t0.987244607153093\n-chr21\t16060609\t16062609\t1.04620355385428\n-chr21\t16062609\t16064609\t1.02761240862396\n-chr21\t16064609\t16066609\t0.870263755617609\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/Feature1.txt --- a/examples/easy/features/Feature1.txt Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,108 +0,0 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1.36511676391135\t1.76042989892118\t1.53636384405283\t1.36400537184779\t1.43911636642378\t1.56924511048934\t1.70469378764198\t1.34572901005354\t1.36332916924972\t1.52198483612669\t1.47050373408664\t1.58811465522032\t1.4083288518989\t1.73908358029847\t1.45114875687858\t1.73076778372283\t1.52487597018861\t1.62714709398344\t1.78537740444483\t1.48638174687684\t0.862437907103511\t0.987084013514053\t1.41699500098639\t0.659590450328438\t1.12615102560033\t0.806229989636672\t1.00226441827563\t0.666941898632686\t0.920857732285355\t0.947249379646065\t0.754814280534639\t0.995567494860033\t0.935044081124308\t0.781716110672392\t1.2357532037144\n-chr16\t66789863\t66889863\t1.23931263393505\t1.09817782961762\t1.12096344268416\t0.952887777446966\t0.983098388086139\t1.18391078396702\t0.888674995547935\t0.917506162739365\t0.844134861525003\t1.16657268125931\t1.08304613247569\t0.94598652343715\t0.714263829988687\t0.827219158083302\t0.94672627836798\t1.38237000367024\t1.59746513476797\t1.29302322983991\t1.26276071700752\t1.48530537683203\t1.48276649689778\t1.58726712167964\t1.51736021607023\t1.89197352510795\t1.64847301405742\t1.58063738424899\t1.36575043459335\t1.59974418777365\t1.45345351536548\t1.32227741167541\t1.65931202249993\t1.78854481764008\t1.82260010075797\t1.4660990689996\t1.52359943278828\t0.972959486608333\t0.813890831745644\t1.18591966074082\t0.841418502712299\t0.926559191878404\t1.10742664757625\t1.01227164329923\t1.3693323112704\t0.734353101016267\t1.14728857866619\t0.664215195905833\t0.845493702757984\t0.882147184498605\t0.809127231389519\t0.81628923965675\n-chr18\t64644131\t64744131\t0.76920442503801\t0.966910211157223\t0.809264366882404\t0.702989429562877\t1.14723876951643\t0.97369678388939\t0.910087798040937\t0.946468289624316\t1.05842665628809\t0.927667349376235\t1.18742333150313\t1.22205250380213\t0.880563425486305\t0.914485239144026\t1.01034737175594\t1.62264521151304\t1.48296645852995\t1.28681962535927\t1.53492939742228\t1.58844790171606\t1.49033262314301\t1.31424965988202\t1.45337032575317\t1.35217898213701\t1.77532370910719\t1.60398303218395\t1.69307164801575\t1.54229556388787\t1.68106575665579\t1.48714225361666\t1.55224087444918\t1.3662045024589\t1.57624355139023\t1.44378437443185\t1.37811537520723\t1.06551636789331\t1.04029846172777\t1.1012560789095\t1.16248797408295\t1.10209650363972\t1.12702540883185\t1.06158233209566\t1.24500209867534\t0.834309455846338\t0.757289730474966\t1.10451816307643\t0.92262846294503\t0.804253155660302\t1.00162039935745\t0.956034285823398\n-chr21\t15966609\t16066609\t1.12440801594939\t0.958928874609379\t0.980859325447667\t0.985836855465142\t0.924304227149342\t0.981319441090073\t0.949853799394529\t0.858050928062694\t0.836178837413462\t1.20633196613812\t0.969230627046025\t1.06120061342825\t0.88573302960608\t0.987056692659576\t1.05266019775439\t1.29745136461899\t1.3631797211261\t1.58553521861437\t1.47800659441217\t1.75042011315262\t1.39329136735319\t1.57255744319984\t1.20929102513908\t1.53853232166312\t1.64985481461386\t1.59575749789367\t1.42205668994404\t1.66053802113289\t1.70386086339594\t1.73541878893467\t1.39682491364686\t1.43336589770868\t1.63386317242737\t1.53233925104548\t1.53952241603109\t1.28074961173938\t1.27922409248079\t0.962647373836482\t0.950807449539781\t1.19549845149275\t1.03462200267827\t0.952643344080609\t1.20946321219477\t0.965927027586426\t0.976116334675594\t1.07756004404963\t0.987244607153093\t1.04620355385428\t1.02761240862396\t0.870263755617609\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/Feature2.bed --- a/examples/easy/features/Feature2.bed Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 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|
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/Feature2.txt --- a/examples/easy/features/Feature2.txt Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,108 +0,0 @@\n-chr1\t91399892\t91499892\t4.52457845989749\t4.69885317507985\t3.62988338998133\t4.45623107548837\t4.59364249841659\t5.70905494693032\t2.42812136492091\t3.21325702299381\t5.83146415223743\t4.145234941891\t5.61198015818556\t3.64586797215646\t6.20636700257446\t6.24535453369189\t5.45642255152577\t2.25812560771762\t4.85449016203815\t3.90115956418853\t4.73358990127742\t5.10493877711061\t6.26626452775677\t4.50874633533701\t5.70230938739608\t5.94455591845681\t4.52518856675072\t4.63848705114735\t4.34603429138827\t3.03830118655551\t6.03275619780653\t5.68223277080844\t5.50525041823675\t4.5213830572052\t5.50133572404842\t4.91055078504098\t4.05752990001426\t5.10897499920239\t5.43128593940068\t4.86148316107809\t4.48947054967865\t4.04898383490831\t5.68808370629557\t3.38402935045047\t4.55469509198871\t5.54674749210028\t6.80643757003305\t4.36576921982342\t4.78762392440088\t4.7968645329394\t5.2766452300238\t4.11389723526811\n-chr1\t116447079\t116547079\t3.50479481019937\t5.80805807123363\t4.84431415016648\t3.05704665156576\t4.08848780835827\t5.09637693701485\t5.69818646616106\t4.19878801898032\t4.5516661398769\t4.2453176706507\t4.67523653585105\t3.95251471557774\t4.96923766290807\t4.96920479716357\t5.02676539089313\t5.00052315566\t4.16809348391652\t4.59306360967521\t3.53563628215594\t4.50469161954188\t5.56857122702899\t4.58351619746089\t4.25823600023412\t5.90593508834324\t4.75083460476364\t2.771628447275\t3.55096260651244\t6.17656545119289\t4.36022614599567\t3.07947070495695\t6.00325415448973\t4.75152529713703\t4.63430887067622\t6.20396270678022\t4.10708349972204\t6.37204838467736\t4.20892327541064\t5.26217726205883\t4.98426282331262\t4.54088329611304\t6.19908300654713\t4.13307018130982\t4.81616315789755\t4.45075212625821\t5.3278384644649\t4.94456667744961\t5.50278785965628\t5.8872187869518\t4.21048517958463\t5.89303173115761\n-chr2\t231381109\t231481109\t3.65002443734394\t4.47874599073521\t4.88116399860845\t5.24892216831522\t5.57750386069008\t4.69045789308631\t4.856254872219\t4.76937409633355\t3.88332694429089\t4.7832595968199\t6.27320412810246\t5.52912684698304\t5.55698205840569\t6.82309944835591\t4.32144630570487\t5.09123393836864\t3.8114520831504\t4.33905869134521\t5.73772866313889\t4.75547354956085\t5.26564551683356\t6.08956652702895\t4.10272890424613\t3.91111960206344\t4.0667531114092\t5.61155110205229\t6.07809813384265\t4.95887081709017\t2.74883664355264\t5.34666739034634\t5.08448528571052\t4.56036382706695\t6.56980209831026\t6.6109625717574\t4.49783474436294\t5.7740241064298\t6.07305711202637\t4.2103285961496\t3.76220540829883\t4.46462097097549\t4.08404426236734\t6.16846596175892\t4.22448280007424\t5.1552686002743\t4.5779372521734\t5.10547091573954\t4.96853283895841\t4.86822848135078\t5.31459420951145\t6.24101720801896\n-chr3\t47386633\t47486633\t4.09596033449515\t4.07230746010421\t4.65197240747189\t7.70463090935265\t4.73912495872321\t5.60964876739082\t6.11177708056056\t4.89980327152514\t4.94905612156509\t4.21935432231768\t6.27100659960316\t4.3450351881932\t3.82786751768814\t6.43323336460165\t6.33841131952014\t5.24696587341606\t4.26541142112186\t5.59951189289468\t5.05801476554245\t3.99601175353724\t5.63678859075887\t3.58096017150362\t5.68043798959572\t4.55899712898582\t4.37086533466305\t4.50905260991771\t5.03809389855175\t3.6945883594127\t6.19399174564743\t5.23449824601615\t6.1676479514996\t5.86676007002734\t6.53680001481286\t4.73482668061333\t3.35240452774924\t4.99407139122312\t5.47675553543773\t5.30194342226811\t5.09825215231807\t3.77077905728502\t6.68382264765928\t5.82434460034624\t4.18717806817281\t6.18998154264233\t5.28164650431212\t5.98345756376929\t4.67369708864151\t4.52195958012368\t5.43532172251744\t5.13608361020296\n-chr3\t99195712\t99295712\t2.98541588679884\t4.64004314795036\t5.33548172541399\t2.36188304575616\t4.45412879832543\t4.35923863066936\t4.08870840191095\t4.99380403004534\t6.65788405891536\t5.22320984544592\t5.38869819125743\t4.41458442470435\t3.26764741439462\t4.8457712147328\t5.23644396042348\t5.68200893268156\t3.70630689944258\t4.32402493152407\t5.84856363762841\t5.33624649953953\t6.45575642385979\t5.02916767207099\t4.63608134821275\t5.06794153913366\t4.58570064365636\t6.3865325877188\t4.50889853451662\t5.84073939684362\t6.79205901'..b'09457952744\t4.31369212217363\t4.95973363989703\t4.53664554948649\t5.12646368013998\t5.71726199522551\t7.36995172835196\t7.08112119059345\t5.43714055484003\t6.12904664316528\t7.93800853584246\t8.94085529563152\t8.14124492011379\t6.22427415616342\t7.10860559216707\t8.9567863029512\t7.82203858664542\t6.30569827604839\t7.02881545402183\t5.62723662863744\t4.42038428787984\t9.65042809176235\t6.19378870376292\t5.65420146622265\t7.95279060421279\t7.15314624259123\t6.70867437716412\t6.46816033648073\t7.20326782939778\t6.66322376334915\t9.50996256911588\n-chr16\t1875335\t1975335\t5.23050632969674\t5.77390743811245\t3.70838711060465\t4.07834032620523\t4.54284717228119\t6.17801158447106\t4.36590188076073\t5.5397033463123\t4.80686478776706\t6.41848616407323\t4.87429733270304\t6.81755485580385\t5.72646449782228\t4.72130959890093\t3.11602847845617\t3.14902713014032\t6.138334980776\t5.9261267392592\t6.44142723513162\t5.66997411716342\t4.54907065852107\t6.00177710097404\t5.33344781407657\t4.98210078814615\t5.24872433496883\t7.36696657783225\t7.27048671425272\t6.61409437299061\t5.60064393341905\t6.91169252807607\t7.88416422704186\t4.35597237725345\t6.20539660896072\t5.49042026822412\t5.84018583807527\t6.69954604637854\t6.26727562565873\t6.44667012773155\t5.52782663702238\t7.44972514793523\t7.51071852309635\t7.4403075741738\t6.89749871784936\t6.00259154885881\t8.12764100917452\t7.79632273592047\t7.52900512394721\t8.17824031076193\t8.39694007515061\t7.6578638429657\n-chr16\t66789863\t66889863\t4.20219136844637\t4.96057268471407\t7.13065962374515\t3.13585770953668\t4.71383131126227\t5.11181211129019\t6.06368200366066\t6.07780764922902\t5.80196933617308\t5.02969827619796\t5.84568938204219\t5.53844981237557\t4.81009028700636\t4.78377799299102\t5.94854080598072\t3.6112222202023\t5.04840922816053\t4.70369564089873\t4.5445895783609\t8.4111436452991\t6.1737953718075\t4.89055291508244\t4.37215130030829\t5.88029196127544\t4.99471773490328\t7.77060207600064\t5.64475863027809\t6.96894711302944\t6.94363103940403\t6.88934760570583\t5.51348126998068\t5.20026071507928\t5.29868133479264\t7.66942824372164\t8.34041314538861\t5.19302682732285\t6.41553754793579\t5.98745148435748\t7.11243736677169\t6.31280680428733\t7.37364171960973\t6.41240347060552\t7.30615595443907\t7.55045210305389\t8.10653868283062\t6.26604674936984\t7.49553937554043\t8.19887130588279\t5.98758340739978\t7.78681536964228\n-chr18\t64644131\t64744131\t7.23163212395252\t4.11213111022161\t5.37716181941055\t5.77143553770517\t3.7169759268732\t5.25442380932218\t7.45772820471094\t5.48095406750538\t3.62733589187025\t4.55331693366933\t6.8774312824165\t5.2001203442027\t4.95990659880495\t4.02077893319017\t4.05668535153819\t4.23509896158418\t4.23418796991892\t5.45699681002164\t5.19535591598228\t6.0555950876448\t3.54284284855037\t5.0657204197487\t4.61156619971275\t4.66622025797826\t5.34521271919367\t9.87597953863361\t7.05091406041253\t8.00182216055189\t7.91390780851007\t6.60478767008177\t8.42205253797048\t8.4092636416611\t7.33893411142367\t6.44977234209029\t6.14212509408095\t7.33470365201403\t6.14466300830508\t6.28759018496124\t6.13121264285508\t6.25464222302313\t6.22857474092805\t6.7164061474755\t7.71694797882967\t6.47134532938063\t5.44078856911433\t6.72171185147245\t7.45623695140267\t6.66053173863693\t7.26582262622926\t7.26639325298473\n-chr21\t15966609\t16066609\t3.61661096782077\t4.73386208722406\t5.8015549021153\t4.96167153907388\t3.95102647749112\t3.97020922833049\t5.33786080501161\t4.36434578068312\t5.80198476623914\t5.35739211903602\t6.08746983525949\t4.34773396054126\t5.13949591522979\t3.73402272260864\t5.39450798275315\t5.55466043086729\t5.28998031818056\t6.19329925730006\t2.67150074437477\t5.16423939358034\t4.69609507505699\t5.44942073640721\t6.03847400860453\t5.97649168698122\t5.36013704359642\t7.92817462773764\t7.69377454814871\t8.80647396276848\t8.52452119781362\t7.89462789559928\t6.13805198380259\t4.64531272265593\t6.29826676008479\t7.79487866360525\t7.31994055340419\t8.8004479775322\t8.25854856063076\t5.04576860851306\t7.30730130969012\t7.83870783306589\t7.63074529828173\t6.43100021814285\t7.27551387601485\t6.26545170591659\t7.12562466213381\t6.26895239202312\t7.3992370168724\t7.97487587946482\t6.76355670816454\t6.11742019669001\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/features.header.bed.txt --- 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 |
| b |
| @@ -1,2 +0,0 @@ -Feature1.bed ftr1 Feature 1 -Feature2.bed ftr2 Feature 2 \ No newline at end of file |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/features/features.header.txt --- 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 |
| b |
| @@ -1,2 +0,0 @@ -Feature1.txt ftr1 Feature 1 -Feature2.txt ftr2 Feature 2 \ No newline at end of file |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/regions/Controls_regions.bed --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/regions/Elements1_regions.bed --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/regions/Elements2_regions.bed --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/regions/Elements3_regions.bed --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/easy/regions/regions.header.txt --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/hard-withNAs/Feature2.bed --- a/examples/hard-withNAs/Feature2.bed Tue May 02 17:37:40 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5401 +0,0 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7585\t4.58894113645188\r\n-chrX\t37067585\t37069585\t3.71717685239281\r\n-chrX\t37069585\t37071585\t4.58796696740988\r\n-chrX\t37071585\t37073585\t5.59947138638049\r\n-chrX\t37073585\t37075585\t6.05734650462578\r\n-chrX\t37075585\t37077585\t4.48158179401952\r\n-chrX\t37077585\t37079585\t3.84606980112288\r\n-chrX\t37079585\t37081585\t5.60036515077628\r\n-chrX\t37081585\t37083585\t4.7988860011278\r\n-chrX\t37083585\t37085585\t5.72216107507848\r\n-chrX\t37085585\t37087585\t4.86913891902086\r\n-chrX\t37087585\t37089585\t5.82455803778606\r\n-chrX\t37089585\t37091585\t4.16446009380301\r\n-chrX\t37091585\t37093585\t4.63404391451533\r\n-chrX\t37093585\t37095585\t4.79357306408379\r\n-chrX\t37095585\t37097585\t5.14434162104312\r\n-chrX\t37097585\t37099585\t4.26547789878118\r\n-chrX\t37099585\t37101585\t3.40216484594991\r\n-chrX\t37101585\t37103585\t4.74371184978272\r\n-chrX\t37103585\t37105585\t5.2129067039706\r\n-chrX\t37105585\t37107585\t4.32151841433918\r\n-chrX\t37107585\t37109585\t4.90636437901617\r\n-chrX\t37109585\t37111585\t5.63036609909793\r\n-chrX\t37111585\t37113585\t6.74871839286766\r\n-chrX\t37113585\t37115585\t5.86869049479244\r\n-chrX\t37115585\t37117585\t4.61355674591477\r\n-chrX\t37117585\t37119585\t4.86401145328662\r\n-chrX\t37119585\t37121585\t5.86712733709456\r\n-chrX\t37121585\t37123585\t5.28490137892296\r\n-chrX\t37123585\t37125585\t4.2972056277626\r\n-chrX\t37125585\t37127585\t6.12987499929255\r\n-chrX\t37127585\t37129585\t3.6075236114256\r\n-chrX\t103593349\t103595349\t6.37340190485477\r\n-chrX\t103595349\t103597349\t4.10474288351457\r\n-chrX\t103597349\t103599349\t6.02078692162347\r\n-chrX\t103599349\t103601349\t6.59348452737096\r\n-chrX\t103601349\t103603349\t5.11365716238428\r\n-chrX\t103603349\t103605349\t3.62971024923456\r\n-chrX\t103605349\t103607349\t5.42856007221458\r\n-chrX\t103607349\t103609349\t4.3279027245615\r\n-chrX\t103609349\t103611349\t5.07950379344802\r\n-chrX\t103611349\t103613349\t5.6907476922242\r\n-chrX\t103613349\t103615349\t4.90776693084081\r\n-chrX\t103615349\t103617349\t6.23128939684067\r\n-chrX\t103617349\t103619349\t3.76134500557007\r\n-chrX\t103619349\t103621349\t5.31089684191184\r\n-chrX\t103621349\t103623349\t3.27099290965503\r\n-chrX\t103623349\t103625349\t4.09777047720062\r\n-chrX\t103625349\t103627349\t5.52286959370605\r\n-chrX\t103627349\t103629349\t4.21440588097924\r\n-chrX\t103629349\t103631349\t6.09499556724381\r\n-chrX\t103631349\t103633349\t3.79112962123879\r\n-chrX\t103633349\t103635349\t4.2640571911545\r\n-chrX\t103635349\t103637349\t4.28724904018904\r\n-chrX\t103637349\t103639349\t3.37347033628808\r\n-chrX\t103639349\t103641349\t3.61482331330979\r\n-chrX\t103641349\t103643349\t4.35575752957776\r\n-chrX\t103643349\t103645349\t5.11289775334567\r\n-chrX\t103645349\t103647349\t4.17082227412053\r\n-chrX\t103647349\t103649349\t4.32059434655099\r\n-chrX\t103649349\t103651349\t6.58340150820527\r\n-chrX\t103651349\t103653349\t4.09769472659799\r\n-chrX\t103653349\t103655349\t5.66833924151096\r\n-chrX\t103655349\t103657349\t4.64441521765574\r\n-chrX\t103657349\t103659349\t6.03588217585307\r\n-chrX\t103659349\t103661349\t4.65670812807146\r\n-chrX\t103661349\t103663349\t5.17171577253924\r\n-chrX\t103663349\t103665349\t4.37221612406053\r\n-chrX\t103665349\t103667349\t6.04105348527609\r\n-chrX\t103667349\t103669349\t6.56026680863041\r\n-chrX\t103669349\t103671349\t5.12457673118236\r\n-chrX\t103671349\t103673349\t4.60592949236729\r\n-chrX\t103673349\t103675349\t4.18768432297649\r\n-chrX\t103675349\t103677349\t4.34805676009423\r\n-chrX\t103677349\t103679349\t7.32776790008722\r\n-chrX\t103679349\t103681349\t4.45831876954239\r\n-chrX\t103681349\t103683349\t5.414270828553\r\n-chrX\t103683349\t103685349\t5.19188276315724\r\n-chrX\t103685349\t103687349\t5.78869637333301\r\n-chrX\t103687349\t103689349\t4.94708954456459\r\n-chrX\t103689349\t103691349\t3.16857310121393\r\n-chrX\t103691349\t103693349\t4.28592378866411\r\n-\r\n' |
| b |
| diff -r 417b1cc9bd9d -r 1e74ce7f9b2a examples/paper_example/regions.header.txt --- 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 |
| b |
| @@ -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 |