Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations
changeset 8:1d201e8378b3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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--- a/hicValidateLocations.xml Tue Jan 10 18:43:10 2023 +0000 +++ b/hicValidateLocations.xml Wed Oct 18 11:00:15 2023 +0000 @@ -8,19 +8,39 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ --data '$data' - --protein '$protein' - --method loops + --validationData '$validationData' + --validationType '$validationData.ext' + --method $method_selector --resolution '$resolution' - $addChrPrefixLoops - $addChrPrefixProtein + #if not $prefixLoop_selector == 'keep': + --chrPrefixLoops $prefixLoop_selector + #end if + #if not $prefixProtein_selector == 'keep': + --chrPrefixProtein $prefixProtein_selector + #end if + --outFileName outfile ]]> </command> <inputs> - <param argument="--data" type="data" format='bed' label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." /> - <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." /> - <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' /> - <param argument='--addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." help="Adding a 'chr'-prefix to chromosome name of the loops." /> - <param argument='--addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixProtein' falsevalue="" checked="false" label="Add chr prefix to protein." help="Adding a 'chr'-prefix to chromosome name of the protein." /> + <param argument="--data" type="data" format="bed" label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." /> + <param argument="--validationData" type="data" format="bed,cool" label="Validation data" help="The protein peak file or a cool file containing e.g. HiChIP information" /> + <param name="method_selector" type="select" label="Validate loop or TAD data"> + <option value="loops" selected="True">Loops</option> + <option value="tad">TADs</option> + </param> + <param argument="--resolution" type="integer" value="" label="Used resolution" help="The to be binned resolution." /> + <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data"> + <option value="keep" selected="True">Keep</option> + <option value="add">Add</option> + <option value="remove">Remove</option> + + </param> + + <param name="prefixProtein_selector" type="select" label="Add, remove, or keep the chr-prefix of the validation data"> + <option value="keep" selected="True">Keep</option> + <option value="add">Add</option> + <option value="remove">Remove</option> + </param> </inputs> <outputs> <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" /> @@ -28,10 +48,10 @@ </outputs> <tests> <test> - <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph" /> - <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" /> + <param name="data" ftype="bed" value="hicValidateLocations/loops_1.bedgraph" /> + <param name="validationData" ftype="bed" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" /> <param name="resolution" value="10000" /> - <param name="addChrPrefixLoops" value="True" /> + <param name="prefixLoop_selector" value="add" /> <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" /> <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" /> </test>
--- a/macros.xml Tue Jan 10 18:43:10 2023 +0000 +++ b/macros.xml Wed Oct 18 11:00:15 2023 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@TOOL_VERSION@">3.6</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.7.2</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $use_range.range_min:$use_range.range_max @@ -37,7 +37,8 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.1133705</citation> + <citation type="doi">10.1093/nar/gkaa220</citation> + <citation type="doi">10.1093/nar/gky504</citation> <yield /> </citations> </xml> @@ -348,6 +349,10 @@ <xml name='matrix_h5_cooler_multiple_macro'> <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" /> </xml> + + <xml name='matrix_cooler_multiple_macro'> + <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" /> + </xml> <xml name='convertFormat_single_macro'> <conditional name="inputFormat_conditional"> <param name="inputFormat_selector" type="select" label="Choose input file type"> @@ -356,6 +361,8 @@ <option value="optionHic">hic</option> <option value="optionHomer">Homer</option> <option value="optionHicpro">HiCPro</option> + <option value="option2Dtext">2D-text</option> + </param> <when value="optionCool"> <expand macro='matrix_h5_cooler_macro' /> @@ -377,9 +384,17 @@ <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> </when> <when value="optionHicpro"> - <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' /> + <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' /> <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> </when> + <when value="option2Dtext"> + <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' /> + + <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> + <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> + </param> + <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> + </when> </conditional> </xml> @@ -390,6 +405,9 @@ <option value="optionH5">h5</option> <option value="optionHomer">Homer</option> <option value="optionHicpro">HiCPro</option> + <option value="option2Dtext">2D-text</option> + + </param> <when value="optionCool"> <expand macro='matrix_h5_cooler_multiple_macro' /> @@ -408,6 +426,14 @@ <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' /> </when> + <when value="option2Dtext"> + <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' /> + + <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> + <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> + </param> + <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> + </when> </conditional> </xml> <xml name='convertFormat_single_output_macro'> @@ -418,6 +444,8 @@ <option value="h5">h5</option> <option value="homer">Homer</option> <option value="ginteractions">ginteractions</option> + <option value="hicpro">hicpro</option> + </param> <when value="cool"> <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> @@ -426,6 +454,7 @@ <when value='h5' /> <when value='homer' /> <when value='ginteractions' /> + <when value='hicpro' /> </conditional> </xml> <token name="@REFERENCES@">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 14274000 14278000 Eya1 673.000000000000 -23000 5.600000000000 +chr1 14295000 14298000 Eya1 673.000000000000 -3000 44.400000000000 +chr1 14314000 14319000 Eya1 673.000000000000 18000 24.200000000000 +chr1 14426000 14432000 Eya1 673.000000000000 131000 2.400000000000 +chr1 14447000 14455000 Eya1 673.000000000000 154000 4.400000000000 +chr1 14460000 14465000 Eya1 673.000000000000 164000 3.200000000000 +chr1 14480000 14488000 Eya1 673.000000000000 187000 7.600000000000 +chr1 14491000 14501000 Eya1 673.000000000000 200000 20.650000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 4481000 4488000 Sox17 810.000000000000 0 297.800000000000 +chr1 4499000 4502000 Sox17 810.000000000000 14000 20.400000000000 +chr1 4509000 4515000 Sox17 810.000000000000 27000 27.800000000000 +chr1 4561000 4567000 Sox17 810.000000000000 79000 11.600000000000 +chr1 4585000 4590000 Sox17 810.000000000000 102000 8.000000000000 +chr1 4652000 4658000 Sox17 810.000000000000 170000 6.000000000000 +chr1 4664000 4669000 Sox17 810.000000000000 181000 1.200000000000 +chr1 4674000 4679000 Sox17 810.000000000000 191000 1.600000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,10 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 19078000 19081000 Tfap2d 472.000000000000 -13000 0.000000000000 +chr1 19086000 19091000 Tfap2d 472.000000000000 -3000 32.800000000000 +chr1 19104000 19106000 Tfap2d 472.000000000000 12000 10.600000000000 +chr1 19109000 19114000 Tfap2d 472.000000000000 20000 18.600000000000 +chr1 19125000 19129000 Tfap2d 472.000000000000 35000 7.800000000000 +chr1 19133000 19139000 Tfap2d 472.000000000000 45000 10.000000000000 +chr1 19182000 19185000 Tfap2d 472.000000000000 91000 1.000000000000 +chr1 19189000 19238000 Tfap2d 472.000000000000 144000 25.800000000000 +chr1 19254000 19261000 Tfap2d 472.000000000000 167000 6.400000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 14274000 14278000 Eya1 832.000000000000 -23000 0.000000000000 +chr1 14295000 14298000 Eya1 832.000000000000 -3000 49.800000000000 +chr1 14314000 14319000 Eya1 832.000000000000 18000 23.400000000000 +chr1 14426000 14432000 Eya1 832.000000000000 131000 9.000000000000 +chr1 14447000 14455000 Eya1 832.000000000000 154000 12.400000000000 +chr1 14460000 14465000 Eya1 832.000000000000 164000 7.600000000000 +chr1 14480000 14488000 Eya1 832.000000000000 187000 3.200000000000 +chr1 14491000 14501000 Eya1 832.000000000000 200000 18.750000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 4481000 4488000 Sox17 978.000000000000 0 400.400000000000 +chr1 4499000 4502000 Sox17 978.000000000000 14000 21.000000000000 +chr1 4509000 4515000 Sox17 978.000000000000 27000 13.200000000000 +chr1 4561000 4567000 Sox17 978.000000000000 79000 12.400000000000 +chr1 4585000 4590000 Sox17 978.000000000000 102000 2.400000000000 +chr1 4652000 4658000 Sox17 978.000000000000 170000 5.000000000000 +chr1 4664000 4669000 Sox17 978.000000000000 181000 5.400000000000 +chr1 4674000 4679000 Sox17 978.000000000000 191000 5.200000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,10 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 19078000 19081000 Tfap2d 800.000000000000 -13000 9.000000000000 +chr1 19086000 19091000 Tfap2d 800.000000000000 -3000 88.600000000000 +chr1 19104000 19106000 Tfap2d 800.000000000000 12000 14.800000000000 +chr1 19109000 19114000 Tfap2d 800.000000000000 20000 22.200000000000 +chr1 19125000 19129000 Tfap2d 800.000000000000 35000 8.800000000000 +chr1 19133000 19139000 Tfap2d 800.000000000000 45000 12.800000000000 +chr1 19182000 19185000 Tfap2d 800.000000000000 91000 5.000000000000 +chr1 19189000 19238000 Tfap2d 800.000000000000 144000 126.600000000000 +chr1 19254000 19261000 Tfap2d 800.000000000000 167000 1.400000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,402 @@ +# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw +chr1 14100000 14101000 Eya1 673.000000000000 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14101000 14102000 Eya1 673.000000000000 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14102000 14103000 Eya1 673.000000000000 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14103000 14104000 Eya1 673.000000000000 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14104000 14105000 Eya1 673.000000000000 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14105000 14106000 Eya1 673.000000000000 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14106000 14107000 Eya1 673.000000000000 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14107000 14108000 Eya1 673.000000000000 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14108000 14109000 Eya1 673.000000000000 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14109000 14110000 Eya1 673.000000000000 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14110000 14111000 Eya1 673.000000000000 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14111000 14112000 Eya1 673.000000000000 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14112000 14113000 Eya1 673.000000000000 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14113000 14114000 Eya1 673.000000000000 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14114000 14115000 Eya1 673.000000000000 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14115000 14116000 Eya1 673.000000000000 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14116000 14117000 Eya1 673.000000000000 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14117000 14118000 Eya1 673.000000000000 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14118000 14119000 Eya1 673.000000000000 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14119000 14120000 Eya1 673.000000000000 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14120000 14121000 Eya1 673.000000000000 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14121000 14122000 Eya1 673.000000000000 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14122000 14123000 Eya1 673.000000000000 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14123000 14124000 Eya1 673.000000000000 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14124000 14125000 Eya1 673.000000000000 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14125000 14126000 Eya1 673.000000000000 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14126000 14127000 Eya1 673.000000000000 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14127000 14128000 Eya1 673.000000000000 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14128000 14129000 Eya1 673.000000000000 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14129000 14130000 Eya1 673.000000000000 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14130000 14131000 Eya1 673.000000000000 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14131000 14132000 Eya1 673.000000000000 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14132000 14133000 Eya1 673.000000000000 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14133000 14134000 Eya1 673.000000000000 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14134000 14135000 Eya1 673.000000000000 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14135000 14136000 Eya1 673.000000000000 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14136000 14137000 Eya1 673.000000000000 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14137000 14138000 Eya1 673.000000000000 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14138000 14139000 Eya1 673.000000000000 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14139000 14140000 Eya1 673.000000000000 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14140000 14141000 Eya1 673.000000000000 -160000 0.000891530461 0.012107544045 4.242405017910 0.600000000000 +chr1 14141000 14142000 Eya1 673.000000000000 -159000 0.000891530461 0.012107544045 4.789812097144 0.600000000000 +chr1 14142000 14143000 Eya1 673.000000000000 -158000 0.000891530461 0.012107544045 4.303889149198 0.600000000000 +chr1 14143000 14144000 Eya1 673.000000000000 -157000 0.000891530461 0.012107544045 4.367181637306 0.600000000000 +chr1 14144000 14145000 Eya1 673.000000000000 -156000 0.000891530461 0.012107544045 5.120143967809 0.600000000000 +chr1 14145000 14146000 Eya1 673.000000000000 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14146000 14147000 Eya1 673.000000000000 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14147000 14148000 Eya1 673.000000000000 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14148000 14149000 Eya1 673.000000000000 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14149000 14150000 Eya1 673.000000000000 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14150000 14151000 Eya1 673.000000000000 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14151000 14152000 Eya1 673.000000000000 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14152000 14153000 Eya1 673.000000000000 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14153000 14154000 Eya1 673.000000000000 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14154000 14155000 Eya1 673.000000000000 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14155000 14156000 Eya1 673.000000000000 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14156000 14157000 Eya1 673.000000000000 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14157000 14158000 Eya1 673.000000000000 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14158000 14159000 Eya1 673.000000000000 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14159000 14160000 Eya1 673.000000000000 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14160000 14161000 Eya1 673.000000000000 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14161000 14162000 Eya1 673.000000000000 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14162000 14163000 Eya1 673.000000000000 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14163000 14164000 Eya1 673.000000000000 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14164000 14165000 Eya1 673.000000000000 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14165000 14166000 Eya1 673.000000000000 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14166000 14167000 Eya1 673.000000000000 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14167000 14168000 Eya1 673.000000000000 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14168000 14169000 Eya1 673.000000000000 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14169000 14170000 Eya1 673.000000000000 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14170000 14171000 Eya1 673.000000000000 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14171000 14172000 Eya1 673.000000000000 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14172000 14173000 Eya1 673.000000000000 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14173000 14174000 Eya1 673.000000000000 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14174000 14175000 Eya1 673.000000000000 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14175000 14176000 Eya1 673.000000000000 -125000 0.000297176820 0.042850447268 0.916568982282 0.200000000000 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14371000 Eya1 673.000000000000 70000 0.000594353640 0.000000000000 0.479367797551 0.400000000000 +chr1 14371000 14372000 Eya1 673.000000000000 71000 0.000594353640 0.000000000000 0.463650820834 0.400000000000 +chr1 14372000 14373000 Eya1 673.000000000000 72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14373000 14374000 Eya1 673.000000000000 73000 0.000297176820 0.000000000000 0.245023391610 0.200000000000 +chr1 14374000 14375000 Eya1 673.000000000000 74000 0.000297176820 0.000000000000 0.235689167288 0.200000000000 +chr1 14375000 14376000 Eya1 673.000000000000 75000 0.001188707281 0.000000000000 0.918695593883 0.800000000000 +chr1 14376000 14377000 Eya1 673.000000000000 76000 0.001188707281 0.000000000000 0.912345163461 0.800000000000 +chr1 14377000 14378000 Eya1 673.000000000000 77000 0.001188707281 0.000000000000 0.883834376891 0.800000000000 +chr1 14378000 14379000 Eya1 673.000000000000 78000 0.000891530461 0.000000000000 0.729651967113 0.600000000000 +chr1 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1.394217609153 1.200000000000 +chr1 14397000 14398000 Eya1 673.000000000000 97000 0.001485884101 0.000000000000 1.204251218952 1.000000000000 +chr1 14398000 14399000 Eya1 673.000000000000 98000 0.001783060921 0.000000000000 1.410776013193 1.200000000000 +chr1 14399000 14400000 Eya1 673.000000000000 99000 0.002080237741 0.000000000000 1.767668754158 1.400000000000 +chr1 14400000 14401000 Eya1 673.000000000000 100000 0.001485884101 0.000000000000 1.410106128595 1.000000000000 +chr1 14401000 14402000 Eya1 673.000000000000 101000 0.000594353640 0.000000000000 0.603594208412 0.400000000000 +chr1 14402000 14403000 Eya1 673.000000000000 102000 0.000594353640 0.000000000000 0.587474482247 0.400000000000 +chr1 14403000 14404000 Eya1 673.000000000000 103000 0.000297176820 0.000000000000 0.324555574533 0.200000000000 +chr1 14404000 14405000 Eya1 673.000000000000 104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14405000 14406000 Eya1 673.000000000000 105000 0.000594353640 0.000000000000 0.592751199195 0.400000000000 +chr1 14406000 14407000 Eya1 673.000000000000 106000 0.000594353640 0.000000000000 0.578885673960 0.400000000000 +chr1 14407000 14408000 Eya1 673.000000000000 107000 0.000594353640 0.000000000000 0.556120506836 0.400000000000 +chr1 14408000 14409000 Eya1 673.000000000000 108000 0.000891530461 0.000000000000 0.813611919440 0.600000000000 +chr1 14409000 14410000 Eya1 673.000000000000 109000 0.000891530461 0.000000000000 0.843660087147 0.600000000000 +chr1 14410000 14411000 Eya1 673.000000000000 110000 0.000297176820 0.000000000000 0.291145441917 0.200000000000 +chr1 14411000 14412000 Eya1 673.000000000000 111000 0.000297176820 0.000000000000 0.275736630113 0.200000000000 +chr1 14412000 14413000 Eya1 673.000000000000 112000 0.000297176820 0.000000000000 0.282827000656 0.200000000000 +chr1 14413000 14414000 Eya1 673.000000000000 113000 0.000297176820 0.000000000000 0.290291642960 0.200000000000 +chr1 14414000 14415000 Eya1 673.000000000000 114000 0.000297176820 0.000000000000 0.286096676989 0.200000000000 +chr1 14415000 14416000 Eya1 673.000000000000 115000 0.000297176820 0.000000000000 0.288598980306 0.200000000000 +chr1 14416000 14417000 Eya1 673.000000000000 116000 0.000594353640 0.000000000000 0.664358726512 0.400000000000 +chr1 14417000 14418000 Eya1 673.000000000000 117000 0.000891530461 0.000000000000 1.017014899996 0.600000000000 +chr1 14418000 14419000 Eya1 673.000000000000 118000 0.000594353640 0.000000000000 0.687426738036 0.400000000000 +chr1 14419000 14420000 Eya1 673.000000000000 119000 0.000594353640 0.000000000000 0.671114917005 0.400000000000 +chr1 14420000 14421000 Eya1 673.000000000000 120000 0.000594353640 0.000000000000 0.662136790955 0.400000000000 +chr1 14421000 14422000 Eya1 673.000000000000 121000 0.000297176820 0.000000000000 0.325623191563 0.200000000000 +chr1 14422000 14423000 Eya1 673.000000000000 122000 0.000594353640 0.000000000000 0.668847636862 0.400000000000 +chr1 14423000 14424000 Eya1 673.000000000000 123000 0.000594353640 0.000000000000 0.682685863943 0.400000000000 +chr1 14424000 14425000 Eya1 673.000000000000 124000 0.000594353640 0.000000000000 0.725197437366 0.400000000000 +chr1 14425000 14426000 Eya1 673.000000000000 125000 0.000594353640 0.000000000000 0.791915602137 0.400000000000 +chr1 14426000 14427000 Eya1 673.000000000000 126000 0.001188707281 0.000000000000 1.477454480806 0.800000000000 +chr1 14427000 14428000 Eya1 673.000000000000 127000 0.000594353640 0.000000000000 0.755644658251 0.400000000000 +chr1 14428000 14429000 Eya1 673.000000000000 128000 0.000594353640 0.000000000000 0.791915602137 0.400000000000 +chr1 14429000 14430000 Eya1 673.000000000000 129000 0.000594353640 0.000000000000 0.764397299148 0.400000000000 +chr1 14430000 14431000 Eya1 673.000000000000 130000 0.000594353640 0.000000000000 0.714725272130 0.400000000000 +chr1 14431000 14432000 Eya1 673.000000000000 131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14432000 14433000 Eya1 673.000000000000 132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14433000 14434000 Eya1 673.000000000000 133000 0.000297176820 0.000000000000 0.358657428234 0.200000000000 +chr1 14434000 14435000 Eya1 673.000000000000 134000 0.000297176820 0.000000000000 0.373545095179 0.200000000000 +chr1 14435000 14436000 Eya1 673.000000000000 135000 0.000297176820 0.000000000000 0.391262649240 0.200000000000 +chr1 14436000 14437000 Eya1 673.000000000000 136000 0.000297176820 0.000000000000 0.358657428234 0.200000000000 +chr1 14437000 14438000 Eya1 673.000000000000 137000 0.000297176820 0.000000000000 0.334423818431 0.200000000000 +chr1 14438000 14439000 Eya1 673.000000000000 138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14439000 14440000 Eya1 673.000000000000 139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14440000 14441000 Eya1 673.000000000000 140000 0.000000000000 1.000000000000 0.000000000000 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158000 0.001188707281 0.000000000000 1.583831204275 0.800000000000 +chr1 14459000 14460000 Eya1 673.000000000000 159000 0.000594353640 0.000000000000 0.770345916308 0.400000000000 +chr1 14460000 14461000 Eya1 673.000000000000 160000 0.001188707281 0.000000000000 1.517079697070 0.800000000000 +chr1 14461000 14462000 Eya1 673.000000000000 161000 0.001188707281 0.000000000000 1.429450544260 0.800000000000 +chr1 14462000 14463000 Eya1 673.000000000000 162000 0.001188707281 0.000000000000 1.616154290340 0.800000000000 +chr1 14463000 14464000 Eya1 673.000000000000 163000 0.000594353640 0.000000000000 0.821489212945 0.400000000000 +chr1 14464000 14465000 Eya1 673.000000000000 164000 0.000594353640 0.000000000000 0.857051516792 0.400000000000 +chr1 14465000 14466000 Eya1 673.000000000000 165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14466000 14467000 Eya1 673.000000000000 166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14467000 14468000 Eya1 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,402 @@ +# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw +chr1 14100000 14101000 Eya1 832.000000000000 -200000 0.000400641026 0.028365821799 2.426424093120 0.333333333333 +chr1 14101000 14102000 Eya1 832.000000000000 -199000 0.000300480769 0.036748857670 1.429857059822 0.250000000000 +chr1 14102000 14103000 Eya1 832.000000000000 -198000 0.000240384615 0.042850447268 0.931069711724 0.200000000000 +chr1 14103000 14104000 Eya1 832.000000000000 -197000 0.000240384615 0.042850447268 0.889688835341 0.200000000000 +chr1 14104000 14105000 Eya1 832.000000000000 -196000 0.000240384615 0.042850447268 0.976487746811 0.200000000000 +chr1 14105000 14106000 Eya1 832.000000000000 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14106000 14107000 Eya1 832.000000000000 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14107000 14108000 Eya1 832.000000000000 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14108000 14109000 Eya1 832.000000000000 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14109000 14110000 Eya1 832.000000000000 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14110000 14111000 Eya1 832.000000000000 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14111000 14112000 Eya1 832.000000000000 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14112000 14113000 Eya1 832.000000000000 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14113000 14114000 Eya1 832.000000000000 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14114000 14115000 Eya1 832.000000000000 -186000 0.000000000000 1.000000000000 0.000000000000 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Binary file test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig has changed
Binary file test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig has changed
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.6 +# Created with chicQualityControl version 3.7.2 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix. # Used Matrices 0_matrix.cool 1_matrix.cool # Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.6 +# Created with chicQualityControl version 3.7.2 # QC report for matrices: 0_matrix.cool 1_matrix.cool #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 has changed
Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/hg19.chrom.sizes Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,93 @@ +chr1 249250621 +chr2 243199373 +chr3 198022430 +chr4 191154276 +chr5 180915260 +chr6 171115067 +chr7 159138663 +chrX 155270560 +chr8 146364022 +chr9 141213431 +chr10 135534747 +chr11 135006516 +chr12 133851895 +chr13 115169878 +chr14 107349540 +chr15 102531392 +chr16 90354753 +chr17 81195210 +chr18 78077248 +chr20 63025520 +chrY 59373566 +chr19 59128983 +chr22 51304566 +chr21 48129895 +chr6_ssto_hap7 4928567 +chr6_mcf_hap5 4833398 +chr6_cox_hap2 4795371 +chr6_mann_hap4 4683263 +chr6_apd_hap1 4622290 +chr6_qbl_hap6 4611984 +chr6_dbb_hap3 4610396 +chr17_ctg5_hap1 1680828 +chr4_ctg9_hap1 590426 +chr1_gl000192_random 547496 +chrUn_gl000225 211173 +chr4_gl000194_random 191469 +chr4_gl000193_random 189789 +chr9_gl000200_random 187035 +chrUn_gl000222 186861 +chrUn_gl000212 186858 +chr7_gl000195_random 182896 +chrUn_gl000223 180455 +chrUn_gl000224 179693 +chrUn_gl000219 179198 +chr17_gl000205_random 174588 +chrUn_gl000215 172545 +chrUn_gl000216 172294 +chrUn_gl000217 172149 +chr9_gl000199_random 169874 +chrUn_gl000211 166566 +chrUn_gl000213 164239 +chrUn_gl000220 161802 +chrUn_gl000218 161147 +chr19_gl000209_random 159169 +chrUn_gl000221 155397 +chrUn_gl000214 137718 +chrUn_gl000228 129120 +chrUn_gl000227 128374 +chr1_gl000191_random 106433 +chr19_gl000208_random 92689 +chr9_gl000198_random 90085 +chr17_gl000204_random 81310 +chrUn_gl000233 45941 +chrUn_gl000237 45867 +chrUn_gl000230 43691 +chrUn_gl000242 43523 +chrUn_gl000243 43341 +chrUn_gl000241 42152 +chrUn_gl000236 41934 +chrUn_gl000240 41933 +chr17_gl000206_random 41001 +chrUn_gl000232 40652 +chrUn_gl000234 40531 +chr11_gl000202_random 40103 +chrUn_gl000238 39939 +chrUn_gl000244 39929 +chrUn_gl000248 39786 +chr8_gl000196_random 38914 +chrUn_gl000249 38502 +chrUn_gl000246 38154 +chr17_gl000203_random 37498 +chr8_gl000197_random 37175 +chrUn_gl000245 36651 +chrUn_gl000247 36422 +chr9_gl000201_random 36148 +chrUn_gl000235 34474 +chrUn_gl000239 33824 +chr21_gl000210_random 27682 +chrUn_gl000231 27386 +chrUn_gl000229 19913 +chrM 16571 +chrUn_gl000226 15008 +chr18_gl000207_random 4262
--- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,3 @@ chr1 4487435 4487435 Sox17 chr1 14300280 14300280 Eya1 -chr1 19093103 19093103 Tfap2d - +chr1 19093103 19093103 Tfap2d \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/target_list.bed Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,8 @@ +chr1 4480000 4549000 +chr1 4555000 4688000 +chr1 14274000 14279000 +chr1 14290000 14439000 +chr1 14444000 14467000 +chr1 14476000 14501000 +chr1 19077000 19118000 +chr1 19120000 19274000 \ No newline at end of file
--- a/test-data/distVsCounts.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,600 +1,600 @@ - Matrix Chromosome Distance Contacts -0 small_test_matrix_h5 all 0 0.09142620133910055 -1 small_test_matrix_h5 all 5000 0.07741782506891134 -2 small_test_matrix_h5 all 10000 0.04433044715929309 -3 small_test_matrix_h5 all 15000 0.03461983446557299 -4 small_test_matrix_h5 all 20000 0.027541995607526563 -5 small_test_matrix_h5 all 25000 0.023782660332541568 -6 small_test_matrix_h5 all 30000 0.02002019841977069 -7 small_test_matrix_h5 all 35000 0.01967193628907643 -8 small_test_matrix_h5 all 40000 0.017480230691479873 -9 small_test_matrix_h5 all 45000 0.015494884606233642 -10 small_test_matrix_h5 all 50000 0.014013686402856293 -11 small_test_matrix_h5 all 55000 0.012799142755089891 -12 small_test_matrix_h5 all 60000 0.011404919302007028 -13 small_test_matrix_h5 all 65000 0.011588417540514775 -14 small_test_matrix_h5 all 70000 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/small_test_matrix_chr4.hicpro Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,326 @@ +15 15 1 +15 38 1 +16 17 1 +17 17 2 +17 18 1 +17 38 1 +18 38 1 +18 151 1 +19 21 1 +19 52 1 +19 207 1 +20 57 1 +21 29 1 +22 23 2 +22 32 1 +22 41 1 +22 223 1 +23 26 1 +23 43 1 +25 39 1 +25 51 1 +26 36 1 +26 45 1 +26 67 1 +27 28 1 +27 31 1 +28 28 1 +28 30 1 +28 40 1 +29 31 1 +29 34 1 +30 30 1 +30 43 1 +31 31 1 +31 32 1 +31 35 2 +31 55 1 +31 78 1 +31 119 1 +31 188 1 +32 32 5 +32 36 1 +32 118 1 +33 45 1 +33 162 1 +35 38 1 +35 122 1 +36 36 1 +36 38 1 +36 41 1 +36 43 1 +36 57 1 +36 64 1 +37 53 1 +37 55 1 +37 130 1 +38 38 3 +38 129 1 +39 39 1 +40 42 1 +40 55 1 +40 192 1 +40 218 1 +41 52 1 +41 67 1 +41 79 1 +42 43 1 +42 49 1 +42 120 1 +43 45 1 +45 46 1 +45 71 1 +48 49 1 +48 51 1 +48 119 1 +50 84 1 +53 65 1 +54 54 1 +54 67 1 +55 55 1 +56 56 2 +56 57 1 +59 104 1 +61 64 1 +62 66 1 +62 89 1 +63 80 1 +65 68 1 +65 77 1 +65 118 1 +67 70 1 +68 68 1 +68 70 1 +70 142 1 +71 72 1 +71 74 1 +71 75 1 +75 80 1 +75 190 1 +77 168 1 +78 92 1 +80 83 1 +81 95 1 +82 103 1 +82 120 1 +87 126 1 +88 216 1 +89 89 1 +89 90 1 +90 113 1 +92 92 1 +93 96 1 +94 98 1 +95 97 1 +97 151 1 +104 104 1 +105 105 1 +106 198 1 +108 113 1 +109 109 1 +109 110 1 +109 119 1 +109 125 1 +109 159 1 +110 165 1 +110 189 1 +111 112 1 +111 128 1 +112 112 1 +112 194 1 +113 198 1 +114 114 1 +114 122 1 +114 123 1 +114 165 1 +114 196 1 +115 116 1 +116 121 1 +116 129 1 +116 155 1 +117 119 1 +117 128 1 +118 121 1 +118 189 1 +119 125 1 +119 132 1 +120 142 1 +120 149 1 +121 132 1 +121 236 1 +122 131 1 +122 138 1 +122 146 1 +124 125 1 +124 134 1 +125 125 1 +125 141 1 +127 174 1 +127 212 1 +128 130 1 +128 135 1 +129 129 1 +130 178 1 +130 191 1 +130 204 1 +130 213 1 +132 184 1 +132 208 1 +134 136 1 +134 190 1 +134 242 1 +135 177 1 +135 186 1 +136 180 1 +137 142 1 +137 147 1 +137 189 1 +138 143 1 +138 160 1 +141 142 1 +142 142 1 +142 143 1 +142 178 1 +143 143 1 +144 193 1 +145 145 1 +146 146 1 +146 155 1 +147 147 1 +148 149 1 +148 154 1 +149 149 1 +149 150 1 +149 153 1 +149 155 1 +149 169 1 +149 170 1 +149 176 1 +150 162 1 +151 153 1 +153 154 1 +153 186 1 +154 154 1 +154 199 1 +154 215 1 +155 155 1 +155 156 1 +155 159 1 +156 156 1 +160 161 1 +164 176 1 +165 171 1 +166 168 1 +168 168 1 +168 201 1 +169 178 1 +170 176 1 +170 195 1 +171 196 1 +174 178 2 +174 194 1 +175 232 1 +175 243 1 +176 176 1 +177 177 1 +177 209 1 +178 178 1 +179 231 1 +180 212 1 +182 198 1 +183 185 1 +183 186 1 +183 187 1 +188 188 2 +189 201 1 +190 201 1 +192 193 1 +192 242 1 +193 193 1 +193 196 1 +194 206 1 +194 220 1 +195 196 2 +195 221 1 +196 196 1 +196 215 1 +196 223 1 +197 199 1 +198 199 1 +198 201 1 +198 207 1 +198 210 1 +199 199 1 +199 200 1 +199 206 1 +199 212 1 +201 201 1 +201 222 1 +202 203 1 +202 205 1 +203 205 1 +203 209 1 +204 205 1 +204 206 1 +205 205 2 +205 206 2 +205 208 1 +205 217 1 +205 242 1 +207 208 4 +207 209 1 +207 213 1 +207 216 1 +208 224 1 +208 228 1 +208 235 1 +208 241 1 +211 232 1 +212 221 1 +212 222 1 +212 232 1 +213 213 2 +213 214 1 +213 240 1 +213 243 1 +215 218 1 +217 217 1 +217 220 1 +218 218 1 +218 241 1 +219 237 1 +219 238 1 +220 239 1 +221 221 1 +221 222 1 +222 225 1 +222 227 1 +223 229 1 +224 224 1 +226 227 1 +227 228 1 +227 236 1 +228 228 1 +228 231 2 +228 232 1 +228 237 1 +228 242 1 +229 230 1 +229 234 1 +229 237 1 +229 238 1 +230 233 2 +232 232 1 +234 234 3 +235 238 1 +235 243 1 +236 236 1 +236 239 1 +237 237 1 +238 241 1 +238 251 1 +239 243 1 +240 240 1 +241 242 1 +250 250 1 +250 251 1
--- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.6 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.2 # H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. # Accepted regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
--- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,1402 +1,1406 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.6 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.2 # H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr3L 165000 260000 ID_0.01_1 -0.10316675 . nan 1.0 1.0 -chr3L 260000 335000 ID_0.01_2 -0.026655 . 1.0 1.0 1.0 -chr3L 335000 360000 ID_0.01_3 -0.030848 . 1.0 1.0 1.0 -chr3L 360000 485000 ID_0.01_4 -0.0580815 . 1.0 1.0 1.0 -chr3L 485000 525000 ID_0.01_5 -0.07169775 . 1.0 1.0 1.0 -chr3L 525000 680000 ID_0.01_6 -0.1060405 . 1.0 1.0 1.0 -chr3L 680000 705000 ID_0.01_7 -0.0148855 . 1.0 1.0 1.0 -chr3L 705000 740000 ID_0.01_8 0.002784 . 1.0 1.0 1.0 -chr3L 740000 870000 ID_0.01_9 0.00949975 . 1.0 1.0 1.0 -chr3L 870000 1010000 ID_0.01_10 -0.09546975 . 1.0 1.0 1.0 -chr3L 1010000 1040000 ID_0.01_11 -0.05182175 . 1.0 1.0 1.0 -chr3L 1040000 1110000 ID_0.01_12 -0.05874875 . 1.0 1.0 1.0 -chr3L 1110000 1210000 ID_0.01_13 -0.048349 . 1.0 1.0 1.0 -chr3L 1210000 1245000 ID_0.01_14 -0.0567565 . 1.0 1.0 1.0 -chr3L 1245000 1300000 ID_0.01_15 -0.0641435 . 1.0 1.0 1.0 -chr3L 1300000 1465000 ID_0.01_16 -0.091379 . 1.0 1.0 1.0 -chr3L 1465000 1535000 ID_0.01_17 -0.01307225 . 1.0 1.0 1.0 -chr3L 1535000 1580000 ID_0.01_18 -0.08711525 . 1.0 1.0 1.0 -chr3L 1580000 1640000 ID_0.01_19 -0.08235875 . 1.0 1.0 1.0 -chr3L 1640000 1670000 ID_0.01_20 -0.0628755 . 1.0 1.0 1.0 -chr3L 1670000 1735000 ID_0.01_21 -0.037945 . 1.0 1.0 1.0 -chr3L 1735000 1815000 ID_0.01_22 -0.050313 . 1.0 1.0 1.0 -chr3L 1815000 1850000 ID_0.01_23 -0.01723525 . 1.0 1.0 1.0 -chr3L 1850000 1925000 ID_0.01_24 -0.0259975 . 1.0 1.0 1.0 -chr3L 1925000 2155000 ID_0.01_25 8.325e-05 . 1.0 1.0 1.0 -chr3L 2155000 2260000 ID_0.01_26 -0.0401965 . 1.0 1.0 1.0 -chr3L 2260000 2390000 ID_0.01_27 -0.07518575 . 1.0 1.0 1.0 -chr3L 2390000 2460000 ID_0.01_28 -0.072071 . 1.0 1.0 1.0 -chr3L 2460000 2560000 ID_0.01_29 -0.09132325 . 1.0 1.0 1.0 -chr3L 2560000 2600000 ID_0.01_30 -0.09179675 . 1.0 1.0 1.0 -chr3L 2600000 2740000 ID_0.01_31 -0.0934855 . 1.0 1.0 1.0 -chr3L 2740000 2885000 ID_0.01_32 -0.08927875 . 1.0 1.0 1.0 -chr3L 2885000 2945000 ID_0.01_33 -0.08972575 . 1.0 1.0 1.0 -chr3L 2945000 2960000 ID_0.01_34 0.029899 . 1.0 1.0 1.0 -chr3L 2960000 3045000 ID_0.01_35 0.0356865 . 1.0 1.0 1.0 -chr3L 3045000 3135000 ID_0.01_36 -0.00466875 . 1.0 1.0 1.0 -chr3L 3135000 3220000 ID_0.01_37 0.055702 . 1.0 1.0 1.0 -chr3L 3220000 3255000 ID_0.01_38 -0.059463 . 1.0 1.0 1.0 -chr3L 3255000 3315000 ID_0.01_39 -0.045796 . 1.0 1.0 1.0 -chr3L 3315000 3345000 ID_0.01_40 -0.05499875 . 1.0 1.0 1.0 -chr3L 3345000 3475000 ID_0.01_41 -0.04234075 . 1.0 1.0 1.0 -chr3L 3475000 3515000 ID_0.01_42 -0.05097675 . 1.0 1.0 1.0 -chr3L 3515000 3545000 ID_0.01_43 -0.012488 . 1.0 1.0 1.0 -chr3L 3545000 3615000 ID_0.01_44 0.02457925 . 1.0 1.0 1.0 -chr3L 3615000 3670000 ID_0.01_45 0.019683 . 1.0 1.0 1.0 -chr3L 3670000 3765000 ID_0.01_46 0.09945325 . 1.0 1.0 1.0 -chr3L 3765000 3785000 ID_0.01_47 -0.047454 . 1.0 1.0 1.0 -chr3L 3785000 3825000 ID_0.01_48 -0.041084 . 1.0 1.0 1.0 -chr3L 3825000 3900000 ID_0.01_49 -0.06101175 . 1.0 1.0 1.0 -chr3L 3900000 4000000 ID_0.01_50 -0.0684535 . 1.0 1.0 1.0 -chr3L 4000000 4120000 ID_0.01_51 -0.03007875 . 1.0 1.0 1.0 -chr3L 4120000 4165000 ID_0.01_52 -0.0807515 . 1.0 1.0 1.0 -chr3L 4165000 4200000 ID_0.01_53 -0.088488 . 1.0 1.0 1.0 -chr3L 4200000 4220000 ID_0.01_54 -0.098724 . 1.0 1.0 1.0 -chr3L 4220000 4270000 ID_0.01_55 -0.088911 . 1.0 1.0 1.0 -chr3L 4270000 4365000 ID_0.01_56 -0.11633575 . 1.0 1.0 1.0 -chr3L 4365000 4405000 ID_0.01_57 -0.0944955 . 1.0 1.0 1.0 -chr3L 4405000 4490000 ID_0.01_58 -0.07463925 . 1.0 1.0 1.0 -chr3L 4490000 4625000 ID_0.01_59 0.00287075 . 1.0 1.0 1.0 -chr3L 4625000 4650000 ID_0.01_60 0.04064075 . 1.0 1.0 1.0 -chr3L 4650000 4790000 ID_0.01_61 0.03764975 . 1.0 1.0 1.0 -chr3L 4790000 4895000 ID_0.01_62 -0.06999725 . 1.0 1.0 1.0 -chr3L 4895000 5000000 ID_0.01_63 -0.076914 . 1.0 1.0 1.0 -chr3L 5000000 5110000 ID_0.01_64 -0.0378805 . 1.0 1.0 1.0 -chr3L 5110000 5240000 ID_0.01_65 -0.061049 . 1.0 1.0 1.0 -chr3L 5240000 5280000 ID_0.01_66 0.07173475 . 1.0 1.0 1.0 -chr3L 5280000 5360000 ID_0.01_67 0.02598475 . 1.0 1.0 1.0 -chr3L 5360000 5465000 ID_0.01_68 -0.06976425 . 1.0 1.0 1.0 -chr3L 5465000 5555000 ID_0.01_69 0.0082995 . 1.0 1.0 1.0 -chr3L 5555000 5575000 ID_0.01_70 -0.03433 . 1.0 1.0 1.0 -chr3L 5575000 5745000 ID_0.01_71 0.00900825 . 1.0 1.0 1.0 -chr3L 5745000 5815000 ID_0.01_72 -0.09901225 . 1.0 1.0 1.0 -chr3L 5815000 5875000 ID_0.01_73 -0.08504275 . 1.0 1.0 1.0 -chr3L 5875000 5960000 ID_0.01_74 -0.107036 . 1.0 1.0 1.0 -chr3L 5960000 5990000 ID_0.01_75 -0.0645035 . 1.0 1.0 1.0 -chr3L 5990000 6120000 ID_0.01_76 -0.06534175 . 1.0 1.0 1.0 -chr3L 6120000 6195000 ID_0.01_77 -0.06653425 . 1.0 1.0 1.0 -chr3L 6195000 6230000 ID_0.01_78 -0.08219225 . 1.0 1.0 1.0 -chr3L 6230000 6255000 ID_0.01_79 -0.07949925 . 1.0 1.0 1.0 -chr3L 6255000 6370000 ID_0.01_80 -0.0959415 . 1.0 1.0 1.0 -chr3L 6370000 6445000 ID_0.01_81 -0.0155925 . 1.0 1.0 1.0 -chr3L 6445000 6490000 ID_0.01_82 -0.0843135 . 1.0 1.0 1.0 -chr3L 6490000 6560000 ID_0.01_83 -0.07350925 . 1.0 1.0 1.0 -chr3L 6560000 6585000 ID_0.01_84 0.050254 . 1.0 1.0 1.0 -chr3L 6585000 6730000 ID_0.01_85 0.05181025 . 1.0 1.0 1.0 -chr3L 6730000 6875000 ID_0.01_86 -0.08674075 . 1.0 1.0 1.0 -chr3L 6875000 6960000 ID_0.01_87 0.015592 . 1.0 1.0 1.0 -chr3L 6960000 7075000 ID_0.01_88 -0.06386025 . 1.0 1.0 1.0 -chr3L 7075000 7120000 ID_0.01_89 -0.05008325 . 1.0 1.0 1.0 -chr3L 7120000 7145000 ID_0.01_90 -0.04982075 . 1.0 1.0 1.0 -chr3L 7145000 7305000 ID_0.01_91 -0.049721 . 1.0 1.0 1.0 -chr3L 7305000 7370000 ID_0.01_92 -0.10379175 . 1.0 1.0 1.0 -chr3L 7370000 7525000 ID_0.01_93 -0.0351445 . 1.0 1.0 1.0 -chr3L 7525000 7605000 ID_0.01_94 -0.05807975 . 1.0 1.0 1.0 -chr3L 7605000 7630000 ID_0.01_95 -0.02439625 . 1.0 1.0 1.0 -chr3L 7630000 7700000 ID_0.01_96 -0.0078695 . 1.0 1.0 1.0 -chr3L 7700000 7760000 ID_0.01_97 -0.05487375 . 1.0 1.0 1.0 -chr3L 7760000 7805000 ID_0.01_98 -0.0722705 . 1.0 1.0 1.0 -chr3L 7805000 7900000 ID_0.01_99 -0.048435 . 1.0 1.0 1.0 -chr3L 7900000 7950000 ID_0.01_100 -0.04267725 . 1.0 1.0 1.0 -chr3L 7950000 8010000 ID_0.01_101 -0.02681575 . 1.0 1.0 1.0 -chr3L 8010000 8055000 ID_0.01_102 -0.049908 . 1.0 1.0 1.0 -chr3L 8055000 8200000 ID_0.01_103 -0.077315 . 1.0 1.0 1.0 -chr3L 8200000 8305000 ID_0.01_104 -0.03326775 . 1.0 1.0 1.0 -chr3L 8305000 8340000 ID_0.01_105 -0.07717275 . 1.0 1.0 1.0 -chr3L 8340000 8410000 ID_0.01_106 -0.07715575 . 1.0 1.0 1.0 -chr3L 8410000 8435000 ID_0.01_107 -0.088482 . 1.0 1.0 1.0 -chr3L 8435000 8465000 ID_0.01_108 -0.098101 . 1.0 1.0 1.0 -chr3L 8465000 8505000 ID_0.01_109 -0.09699025 . 1.0 1.0 1.0 -chr3L 8505000 8645000 ID_0.01_110 -0.09547525 . 1.0 1.0 1.0 -chr3L 8645000 8670000 ID_0.01_111 0.015577 . 1.0 1.0 1.0 -chr3L 8670000 8710000 ID_0.01_112 0.00026425 . 1.0 1.0 1.0 -chr3L 8710000 8770000 ID_0.01_113 0.03299475 . 1.0 1.0 1.0 -chr3L 8770000 8855000 ID_0.01_114 0.05842025 . 1.0 1.0 1.0 -chr3L 8855000 8875000 ID_0.01_115 -0.04306275 . 1.0 1.0 1.0 -chr3L 8875000 8970000 ID_0.01_116 -0.042365 . 1.0 1.0 1.0 -chr3L 8970000 9120000 ID_0.01_117 -0.09925675 . 1.0 1.0 1.0 -chr3L 9120000 9225000 ID_0.01_118 -0.07110225 . 1.0 1.0 1.0 -chr3L 9225000 9355000 ID_0.01_119 -0.0200285 . 1.0 1.0 1.0 -chr3L 9355000 9395000 ID_0.01_120 -0.10868725 . 1.0 1.0 1.0 -chr3L 9395000 9485000 ID_0.01_121 -0.10117225 . 1.0 1.0 1.0 -chr3L 9485000 9605000 ID_0.01_122 -0.10105 . 1.0 1.0 1.0 -chr3L 9605000 9720000 ID_0.01_123 -0.0327885 . 1.0 1.0 1.0 -chr3L 9720000 9820000 ID_0.01_124 -0.10868725 . 1.0 1.0 1.0 -chr3L 9820000 9895000 ID_0.01_125 -0.0672575 . 1.0 1.0 1.0 -chr3L 9895000 9965000 ID_0.01_126 -0.1071045 . 1.0 1.0 1.0 -chr3L 9965000 10120000 ID_0.01_127 -0.10162625 . 1.0 1.0 1.0 -chr3L 10120000 10205000 ID_0.01_128 -0.02085 . 1.0 1.0 1.0 -chr3L 10205000 10320000 ID_0.01_129 -0.08171475 . 1.0 1.0 1.0 -chr3L 10320000 10445000 ID_0.01_130 -0.038513 . 1.0 1.0 1.0 -chr3L 10445000 10535000 ID_0.01_131 -0.04705425 . 1.0 1.0 1.0 -chr3L 10535000 10585000 ID_0.01_132 0.00456875 . 1.0 1.0 1.0 -chr3L 10585000 10685000 ID_0.01_133 -0.02505125 . 1.0 1.0 1.0 -chr3L 10685000 10740000 ID_0.01_134 0.08679725 . 1.0 1.0 1.0 -chr3L 10740000 10780000 ID_0.01_135 0.065835 . 1.0 1.0 1.0 -chr3L 10780000 10840000 ID_0.01_136 0.060989 . 1.0 1.0 1.0 -chr3L 10840000 10885000 ID_0.01_137 -0.03974775 . 1.0 1.0 1.0 -chr3L 10885000 10960000 ID_0.01_138 -0.04725125 . 1.0 1.0 1.0 -chr3L 10960000 11070000 ID_0.01_139 0.03732375 . 1.0 1.0 1.0 -chr3L 11070000 11195000 ID_0.01_140 -0.088851 . 1.0 1.0 1.0 -chr3L 11195000 11230000 ID_0.01_141 -0.1098975 . 1.0 1.0 1.0 -chr3L 11230000 11295000 ID_0.01_142 -0.0901485 . 1.0 1.0 1.0 -chr3L 11295000 11380000 ID_0.01_143 -0.05611625 . 1.0 1.0 1.0 -chr3L 11380000 11515000 ID_0.01_144 -0.02769625 . 1.0 1.0 1.0 -chr3L 11515000 11625000 ID_0.01_145 -0.1065995 . 1.0 1.0 1.0 -chr3L 11625000 11715000 ID_0.01_146 -0.090991 . 1.0 1.0 1.0 -chr3L 11715000 11785000 ID_0.01_147 -0.0141535 . 1.0 1.0 1.0 -chr3L 11785000 11825000 ID_0.01_148 -0.062442 . 1.0 1.0 1.0 -chr3L 11825000 11930000 ID_0.01_149 -0.0614325 . 1.0 1.0 1.0 -chr3L 11930000 11945000 ID_0.01_150 -0.041385 . 1.0 1.0 1.0 -chr3L 11945000 11980000 ID_0.01_151 -0.023826 . 1.0 1.0 1.0 -chr3L 11980000 12075000 ID_0.01_152 -0.0250355 . 1.0 1.0 1.0 -chr3L 12075000 12135000 ID_0.01_153 -0.0904175 . 1.0 1.0 1.0 -chr3L 12135000 12200000 ID_0.01_154 -0.10699525 . 1.0 1.0 1.0 -chr3L 12200000 12285000 ID_0.01_155 -0.0274905 . 1.0 1.0 1.0 -chr3L 12285000 12415000 ID_0.01_156 -0.039511 . 1.0 1.0 1.0 -chr3L 12415000 12490000 ID_0.01_157 -0.00526025 . 1.0 1.0 1.0 -chr3L 12490000 12520000 ID_0.01_158 -0.029715 . 1.0 1.0 1.0 -chr3L 12520000 12700000 ID_0.01_159 -0.039666 . 1.0 1.0 1.0 -chr3L 12700000 12725000 ID_0.01_160 -0.03720925 . 1.0 1.0 1.0 -chr3L 12725000 12780000 ID_0.01_161 -0.0410715 . 1.0 1.0 1.0 -chr3L 12780000 12870000 ID_0.01_162 -0.0651715 . 1.0 1.0 1.0 -chr3L 12870000 12925000 ID_0.01_163 -0.066515 . 1.0 1.0 1.0 -chr3L 12925000 13015000 ID_0.01_164 -0.08273825 . 1.0 1.0 1.0 -chr3L 13015000 13050000 ID_0.01_165 -0.09834475 . 1.0 1.0 1.0 -chr3L 13050000 13160000 ID_0.01_166 -0.10480475 . 1.0 1.0 1.0 -chr3L 13160000 13265000 ID_0.01_167 -0.038191 . 1.0 1.0 1.0 -chr3L 13265000 13390000 ID_0.01_168 -0.031713 . 1.0 1.0 1.0 -chr3L 13390000 13520000 ID_0.01_169 -0.08558725 . 1.0 1.0 1.0 -chr3L 13520000 13585000 ID_0.01_170 -0.07756375 . 1.0 1.0 1.0 -chr3L 13585000 13665000 ID_0.01_171 -0.06155175 . 1.0 1.0 1.0 -chr3L 13665000 13695000 ID_0.01_172 -0.01819075 . 1.0 1.0 1.0 -chr3L 13695000 13835000 ID_0.01_173 -0.00876475 . 1.0 1.0 1.0 -chr3L 13835000 13985000 ID_0.01_174 -0.09447725 . 1.0 1.0 1.0 -chr3L 13985000 14065000 ID_0.01_175 -0.07893625 . 1.0 1.0 1.0 -chr3L 14065000 14110000 ID_0.01_176 -0.08770825 . 1.0 1.0 1.0 -chr3L 14110000 14215000 ID_0.01_177 -0.03526875 . 1.0 1.0 1.0 -chr3L 14215000 14285000 ID_0.01_178 -0.03334825 . 1.0 1.0 1.0 -chr3L 14285000 14390000 ID_0.01_179 -0.0179095 . 1.0 1.0 1.0 -chr3L 14390000 14425000 ID_0.01_180 0.05096825 . 1.0 1.0 1.0 -chr3L 14425000 14460000 ID_0.01_181 0.02575375 . 1.0 1.0 1.0 -chr3L 14460000 14535000 ID_0.01_182 0.02146575 . 1.0 1.0 1.0 -chr3L 14535000 14605000 ID_0.01_183 -0.0406925 . 1.0 1.0 1.0 -chr3L 14605000 14650000 ID_0.01_184 -0.048831 . 1.0 1.0 1.0 -chr3L 14650000 14735000 ID_0.01_185 -0.0406465 . 1.0 1.0 1.0 -chr3L 14735000 14890000 ID_0.01_186 -0.11298775 . 1.0 1.0 1.0 -chr3L 14890000 14965000 ID_0.01_187 -0.007654 . 1.0 1.0 1.0 -chr3L 14965000 15005000 ID_0.01_188 -0.043583 . 1.0 1.0 1.0 -chr3L 15005000 15135000 ID_0.01_189 -0.085687 . 1.0 1.0 1.0 -chr3L 15135000 15245000 ID_0.01_190 -0.06121325 . 1.0 1.0 1.0 -chr3L 15245000 15355000 ID_0.01_191 -0.036634 . 1.0 1.0 1.0 -chr3L 15355000 15450000 ID_0.01_192 0.0581035 . 1.0 1.0 1.0 -chr3L 15450000 15515000 ID_0.01_193 0.0045765 . 1.0 1.0 1.0 -chr3L 15515000 15530000 ID_0.01_194 -0.07869125 . 1.0 1.0 1.0 -chr3L 15530000 15580000 ID_0.01_195 -0.06834375 . 1.0 1.0 1.0 -chr3L 15580000 15685000 ID_0.01_196 -0.050761 . 1.0 1.0 1.0 -chr3L 15685000 15795000 ID_0.01_197 0.039769 . 1.0 1.0 1.0 -chr3L 15795000 15820000 ID_0.01_198 -0.049537 . 1.0 1.0 1.0 -chr3L 15820000 15950000 ID_0.01_199 -0.0439065 . 1.0 1.0 1.0 -chr3L 15950000 16000000 ID_0.01_200 -0.0345245 . 1.0 1.0 1.0 -chr3L 16000000 16120000 ID_0.01_201 0.07653425 . 1.0 1.0 1.0 -chr3L 16120000 16175000 ID_0.01_202 -0.0516855 . 1.0 1.0 1.0 -chr3L 16175000 16405000 ID_0.01_203 -0.0698515 . 1.0 1.0 1.0 -chr3L 16405000 16575000 ID_0.01_204 -0.0615085 . 1.0 1.0 1.0 -chr3L 16575000 16720000 ID_0.01_205 -0.11633575 . 1.0 1.0 1.0 -chr3L 16720000 16845000 ID_0.01_206 -0.07164275 . 1.0 1.0 1.0 -chr3L 16845000 16925000 ID_0.01_207 -0.06520975 . 1.0 1.0 1.0 -chr3L 16925000 17025000 ID_0.01_208 -0.08319 . 1.0 1.0 1.0 -chr3L 17025000 17100000 ID_0.01_209 -0.0640675 . 1.0 1.0 1.0 -chr3L 17100000 17135000 ID_0.01_210 -0.026472 . 1.0 1.0 1.0 -chr3L 17135000 17215000 ID_0.01_211 -0.0018855 . 1.0 1.0 1.0 -chr3L 17215000 17270000 ID_0.01_212 -0.0158685 . 1.0 1.0 1.0 -chr3L 17270000 17350000 ID_0.01_213 0.03657775 . 1.0 1.0 1.0 -chr3L 17350000 17425000 ID_0.01_214 0.062336 . 1.0 1.0 1.0 -chr3L 17425000 17480000 ID_0.01_215 0.00865775 . 1.0 1.0 1.0 -chr3L 17480000 17550000 ID_0.01_216 -0.097315 . 1.0 1.0 1.0 -chr3L 17550000 17630000 ID_0.01_217 -0.10612275 . 1.0 1.0 1.0 -chr3L 17630000 17770000 ID_0.01_218 -0.07611675 . 1.0 1.0 1.0 -chr3L 17770000 17855000 ID_0.01_219 -0.0506175 . 1.0 1.0 1.0 -chr3L 17855000 17885000 ID_0.01_220 -0.06025075 . 1.0 1.0 1.0 -chr3L 17885000 17965000 ID_0.01_221 -0.01261725 . 1.0 1.0 1.0 -chr3L 17965000 18040000 ID_0.01_222 -0.0328375 . 1.0 1.0 1.0 -chr3L 18040000 18125000 ID_0.01_223 -0.0043705 . 1.0 1.0 1.0 -chr3L 18125000 18250000 ID_0.01_224 -0.044299 . 1.0 1.0 1.0 -chr3L 18250000 18300000 ID_0.01_225 -0.0754875 . 1.0 1.0 1.0 -chr3L 18300000 18330000 ID_0.01_226 -0.03245175 . 1.0 1.0 1.0 -chr3L 18330000 18405000 ID_0.01_227 -0.02034625 . 1.0 1.0 1.0 -chr3L 18405000 18450000 ID_0.01_228 0.082286 . 1.0 1.0 1.0 -chr3L 18450000 18575000 ID_0.01_229 0.052447 . 1.0 1.0 1.0 -chr3L 18575000 18670000 ID_0.01_230 -0.07423625 . 1.0 1.0 1.0 -chr3L 18670000 18720000 ID_0.01_231 -0.03959775 . 1.0 1.0 1.0 -chr3L 18720000 18745000 ID_0.01_232 -0.038368 . 1.0 1.0 1.0 -chr3L 18745000 18820000 ID_0.01_233 -0.04427875 . 1.0 1.0 1.0 -chr3L 18820000 18890000 ID_0.01_234 -0.0727695 . 1.0 1.0 1.0 -chr3L 18890000 19060000 ID_0.01_235 -0.046292 . 1.0 1.0 1.0 -chr3L 19060000 19090000 ID_0.01_236 -0.033827 . 1.0 1.0 1.0 -chr3L 19090000 19115000 ID_0.01_237 -0.035873 . 1.0 1.0 1.0 -chr3L 19115000 19140000 ID_0.01_238 -0.044785 . 1.0 1.0 1.0 -chr3L 19140000 19200000 ID_0.01_239 -0.034991 . 1.0 1.0 1.0 -chr3L 19200000 19265000 ID_0.01_240 -0.0179575 . 1.0 1.0 1.0 -chr3L 19265000 19280000 ID_0.01_241 0.00234625 . 1.0 1.0 1.0 -chr3L 19280000 19345000 ID_0.01_242 0.03160025 . 1.0 1.0 1.0 -chr3L 19345000 19415000 ID_0.01_243 -0.0136645 . 1.0 1.0 1.0 -chr3L 19415000 19505000 ID_0.01_244 0.01178775 . 1.0 1.0 1.0 -chr3L 19505000 19580000 ID_0.01_245 -0.0743135 . 1.0 1.0 1.0 -chr3L 19580000 19620000 ID_0.01_246 -0.036058 . 1.0 1.0 1.0 -chr3L 19620000 19680000 ID_0.01_247 -0.02795225 . 1.0 1.0 1.0 -chr3L 19680000 19795000 ID_0.01_248 -0.02994275 . 1.0 1.0 1.0 -chr3L 19795000 19865000 ID_0.01_249 -0.11633575 . 1.0 1.0 1.0 -chr3L 19865000 19890000 ID_0.01_250 -0.06805475 . 1.0 1.0 1.0 -chr3L 19890000 20045000 ID_0.01_251 -0.068095 . 1.0 1.0 1.0 -chr3L 20045000 20105000 ID_0.01_252 0.007372 . 1.0 1.0 1.0 -chr3L 20105000 20195000 ID_0.01_253 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0.06558875 . 1.0 1.0 1.0 -chr3L 21825000 21895000 ID_0.01_270 -0.012039 . 1.0 1.0 1.0 -chr3L 21895000 21930000 ID_0.01_271 -0.01766375 . 1.0 1.0 1.0 -chr3L 21930000 22015000 ID_0.01_272 -0.00711075 . 1.0 1.0 1.0 -chr3L 22015000 22070000 ID_0.01_273 0.083152 . 1.0 1.0 1.0 -chr3L 22070000 22100000 ID_0.01_274 0.0638995 . 1.0 1.0 1.0 -chr3L 22100000 22250000 ID_0.01_275 0.00261925 . 1.0 1.0 1.0 -chr3L 22250000 22355000 ID_0.01_276 -0.07011075 . 1.0 1.0 1.0 -chr3L 22355000 22420000 ID_0.01_277 -0.045749 . 1.0 1.0 1.0 -chr3L 22420000 22495000 ID_0.01_278 -0.03755225 . 1.0 1.0 1.0 -chr3L 22495000 22595000 ID_0.01_279 -0.015081 . 1.0 1.0 1.0 -chr3L 22595000 22690000 ID_0.01_280 0.05889875 . 1.0 1.0 1.0 -chr3L 22690000 22815000 ID_0.01_281 -0.07253425 . 1.0 1.0 1.0 -chr3L 22815000 22880000 ID_0.01_282 -0.0899575 . 1.0 1.0 1.0 -chr3L 22880000 22990000 ID_0.01_283 -0.049646 . 1.0 1.0 1.0 -chr3L 22990000 23035000 ID_0.01_284 0.051599 . 1.0 1.0 1.0 -chr3L 23035000 23120000 ID_0.01_285 0.0162535 . 1.0 1.0 1.0 -chr3L 23120000 23200000 ID_0.01_286 -0.08982175 . 1.0 1.0 1.0 -chr3L 23200000 23265000 ID_0.01_287 -0.088425 . 1.0 1.0 1.0 -chr3L 23265000 23320000 ID_0.01_288 -0.05795675 . 1.0 1.0 1.0 -chr3L 23320000 23435000 ID_0.01_289 -0.06270725 . 1.0 1.0 1.0 -chr3L 23435000 23530000 ID_0.01_290 -0.11318675 . 1.0 1.0 1.0 -chr3L 23530000 23645000 ID_0.01_291 -0.11633575 . 1.0 1.0 1.0 -chr3L 23645000 23660000 ID_0.01_292 -0.11100775 . 1.0 1.0 1.0 -chr3L 23660000 23770000 ID_0.01_293 -0.10274175 . 1.0 1.0 1.0 -chr3L 23770000 23840000 ID_0.01_294 -0.10392225 . 1.0 1.0 1.0 -chr3L 23840000 23975000 ID_0.01_295 -0.08260325 . 1.0 1.0 1.0 -chr3L 23975000 24135000 ID_0.01_296 -0.11633575 . 1.0 1.0 1.0 -chr3L 24135000 24190000 ID_0.01_297 -0.094302 . 1.0 nan 1.0 -chr2L 210000 250000 ID_0.01_299 -0.05569675 . nan 1.0 1.0 -chr2L 250000 280000 ID_0.01_300 -0.06548675 . 1.0 1.0 1.0 -chr2L 280000 400000 ID_0.01_301 -0.0860065 . 1.0 1.0 1.0 -chr2L 400000 455000 ID_0.01_302 -0.0502635 . 1.0 1.0 1.0 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ID_0.01_631 -0.0184595 . 1.0 1.0 1.0 -chrX 3860000 3930000 ID_0.01_632 -0.02515225 . 1.0 1.0 1.0 -chrX 3930000 4125000 ID_0.01_633 -0.06873975 . 1.0 1.0 1.0 -chrX 4125000 4225000 ID_0.01_634 0.03353825 . 1.0 1.0 1.0 -chrX 4225000 4320000 ID_0.01_635 -0.0470475 . 1.0 1.0 1.0 -chrX 4320000 4470000 ID_0.01_636 -0.04577875 . 1.0 1.0 1.0 -chrX 4470000 4535000 ID_0.01_637 0.03129775 . 1.0 1.0 1.0 -chrX 4535000 4615000 ID_0.01_638 -0.06873975 . 1.0 1.0 1.0 -chrX 4615000 4700000 ID_0.01_639 -0.03641575 . 1.0 1.0 1.0 -chrX 4700000 4775000 ID_0.01_640 0.002193 . 1.0 1.0 1.0 -chrX 4775000 4830000 ID_0.01_641 -0.02999 . 1.0 1.0 1.0 -chrX 4830000 4940000 ID_0.01_642 0.004205 . 1.0 1.0 1.0 -chrX 4940000 5165000 ID_0.01_643 -0.06873975 . 1.0 1.0 1.0 -chrX 5165000 5270000 ID_0.01_644 -0.032438 . 1.0 1.0 1.0 -chrX 5270000 5310000 ID_0.01_645 -0.0500965 . 1.0 1.0 1.0 -chrX 5310000 5330000 ID_0.01_646 -0.04867725 . 1.0 1.0 1.0 -chrX 5330000 5370000 ID_0.01_647 -0.0438415 . 1.0 1.0 1.0 -chrX 5370000 5470000 ID_0.01_648 -0.01440425 . 1.0 1.0 1.0 -chrX 5470000 5725000 ID_0.01_649 -0.06873975 . 1.0 1.0 1.0 -chrX 5725000 5805000 ID_0.01_650 -0.0559375 . 1.0 1.0 1.0 -chrX 5805000 5835000 ID_0.01_651 -0.06873975 . 1.0 1.0 1.0 -chrX 5835000 5890000 ID_0.01_652 -0.06873975 . 1.0 1.0 1.0 -chrX 5890000 5955000 ID_0.01_653 -0.0510205 . 1.0 1.0 1.0 -chrX 5955000 6020000 ID_0.01_654 -0.042279 . 1.0 1.0 1.0 -chrX 6020000 6100000 ID_0.01_655 -0.029748 . 1.0 1.0 1.0 -chrX 6100000 6200000 ID_0.01_656 -0.06431075 . 1.0 1.0 1.0 -chrX 6200000 6270000 ID_0.01_657 -0.06873975 . 1.0 1.0 1.0 -chrX 6270000 6420000 ID_0.01_658 -0.06873975 . 1.0 1.0 1.0 -chrX 6420000 6495000 ID_0.01_659 -0.055952 . 1.0 1.0 1.0 -chrX 6495000 6565000 ID_0.01_660 -0.032883 . 1.0 1.0 1.0 -chrX 6565000 6620000 ID_0.01_661 -0.06873975 . 1.0 1.0 1.0 -chrX 6620000 6765000 ID_0.01_662 -0.06873975 . 1.0 1.0 1.0 -chrX 6765000 6840000 ID_0.01_663 -0.05764525 . 1.0 1.0 1.0 -chrX 6840000 6865000 ID_0.01_664 -0.0403345 . 1.0 1.0 1.0 -chrX 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1.0 1.0 -chrX 9000000 9045000 ID_0.01_682 -0.06188775 . 1.0 1.0 1.0 -chrX 9045000 9125000 ID_0.01_683 -0.06873975 . 1.0 1.0 1.0 -chrX 9125000 9195000 ID_0.01_684 -0.05880325 . 1.0 1.0 1.0 -chrX 9195000 9280000 ID_0.01_685 -0.05880325 . 1.0 1.0 1.0 -chrX 9280000 9305000 ID_0.01_686 -0.00807375 . 1.0 1.0 1.0 -chrX 9305000 9350000 ID_0.01_687 -0.025808 . 1.0 1.0 1.0 -chrX 9350000 9450000 ID_0.01_688 -0.04654875 . 1.0 1.0 1.0 -chrX 9450000 9615000 ID_0.01_689 -0.06873975 . 1.0 1.0 1.0 -chrX 9615000 9720000 ID_0.01_690 -0.03547875 . 1.0 1.0 1.0 -chrX 9720000 9845000 ID_0.01_691 -0.06873975 . 1.0 1.0 1.0 -chrX 9845000 9975000 ID_0.01_692 -0.0527935 . 1.0 1.0 1.0 -chrX 9975000 10050000 ID_0.01_693 -0.02916575 . 1.0 1.0 1.0 -chrX 10050000 10085000 ID_0.01_694 -0.018568 . 1.0 1.0 1.0 -chrX 10085000 10110000 ID_0.01_695 -0.0322145 . 1.0 1.0 1.0 -chrX 10110000 10205000 ID_0.01_696 -0.023041 . 1.0 1.0 1.0 -chrX 10205000 10360000 ID_0.01_697 -0.05810275 . 1.0 1.0 1.0 -chrX 10360000 10390000 ID_0.01_698 -0.04351825 . 1.0 1.0 1.0 -chrX 10390000 10425000 ID_0.01_699 -0.03859725 . 1.0 1.0 1.0 -chrX 10425000 10540000 ID_0.01_700 -0.03685 . 1.0 1.0 1.0 -chrX 10540000 10570000 ID_0.01_701 0.00410225 . 1.0 1.0 1.0 -chrX 10570000 10605000 ID_0.01_702 -0.02050525 . 1.0 1.0 1.0 -chrX 10605000 10685000 ID_0.01_703 -0.06873975 . 1.0 1.0 1.0 -chrX 10685000 10740000 ID_0.01_704 -0.06873975 . 1.0 1.0 1.0 -chrX 10740000 10875000 ID_0.01_705 -0.06873975 . 1.0 1.0 1.0 -chrX 10875000 10970000 ID_0.01_706 0.11662475 . 1.0 1.0 1.0 -chrX 10970000 11005000 ID_0.01_707 -0.0460075 . 1.0 1.0 1.0 -chrX 11005000 11045000 ID_0.01_708 -0.0559375 . 1.0 1.0 1.0 -chrX 11045000 11130000 ID_0.01_709 -0.05131975 . 1.0 1.0 1.0 -chrX 11130000 11230000 ID_0.01_710 0.01917425 . 1.0 1.0 1.0 -chrX 11230000 11400000 ID_0.01_711 -0.06873975 . 1.0 1.0 1.0 -chrX 11400000 11445000 ID_0.01_712 -0.06873975 . 1.0 1.0 1.0 -chrX 11445000 11500000 ID_0.01_713 -0.064487 . 1.0 1.0 1.0 -chrX 11500000 11605000 ID_0.01_714 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1.0 -chrX 12810000 12880000 ID_0.01_731 -0.042259 . 1.0 1.0 1.0 -chrX 12880000 12965000 ID_0.01_732 0.08867225 . 1.0 1.0 1.0 -chrX 12965000 13290000 ID_0.01_733 0.0322335 . 1.0 1.0 1.0 -chrX 13290000 13470000 ID_0.01_734 -0.0590395 . 1.0 1.0 1.0 -chrX 13470000 13565000 ID_0.01_735 -0.044019 . 1.0 1.0 1.0 -chrX 13565000 13615000 ID_0.01_736 -0.03122825 . 1.0 1.0 1.0 -chrX 13615000 13675000 ID_0.01_737 -0.0307365 . 1.0 1.0 1.0 -chrX 13675000 13745000 ID_0.01_738 -0.06389025 . 1.0 1.0 1.0 -chrX 13745000 13955000 ID_0.01_739 -0.06873975 . 1.0 1.0 1.0 -chrX 13955000 14025000 ID_0.01_740 -0.06873975 . 1.0 1.0 1.0 -chrX 14025000 14080000 ID_0.01_741 -0.00795425 . 1.0 1.0 1.0 -chrX 14080000 14155000 ID_0.01_742 -0.06873975 . 1.0 1.0 1.0 -chrX 14155000 14270000 ID_0.01_743 -0.06873975 . 1.0 1.0 1.0 -chrX 14270000 14330000 ID_0.01_744 -0.0394785 . 1.0 1.0 1.0 -chrX 14330000 14445000 ID_0.01_745 0.0111925 . 1.0 1.0 1.0 -chrX 14445000 14470000 ID_0.01_746 -0.04285925 . 1.0 1.0 1.0 -chrX 14470000 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1.0 1.0 -chrX 17395000 17430000 ID_0.01_780 0.026895 . 1.0 1.0 1.0 -chrX 17430000 17525000 ID_0.01_781 -0.01271725 . 1.0 1.0 1.0 -chrX 17525000 17635000 ID_0.01_782 -0.06388975 . 1.0 1.0 1.0 -chrX 17635000 17715000 ID_0.01_783 -0.001567 . 1.0 1.0 1.0 -chrX 17715000 17805000 ID_0.01_784 -0.06295675 . 1.0 1.0 1.0 -chrX 17805000 17855000 ID_0.01_785 0.0374145 . 1.0 1.0 1.0 -chrX 17855000 17895000 ID_0.01_786 0.036681 . 1.0 1.0 1.0 -chrX 17895000 17945000 ID_0.01_787 0.02818375 . 1.0 1.0 1.0 -chrX 17945000 18055000 ID_0.01_788 0.02332775 . 1.0 1.0 1.0 -chrX 18055000 18210000 ID_0.01_789 -0.04913325 . 1.0 1.0 1.0 -chrX 18210000 18270000 ID_0.01_790 -0.015514 . 1.0 1.0 1.0 -chrX 18270000 18390000 ID_0.01_791 -0.059908 . 1.0 1.0 1.0 -chrX 18390000 18535000 ID_0.01_792 -0.06873975 . 1.0 1.0 1.0 -chrX 18535000 18635000 ID_0.01_793 -0.06873975 . 1.0 1.0 1.0 -chrX 18635000 18690000 ID_0.01_794 -0.04284475 . 1.0 1.0 1.0 -chrX 18690000 18750000 ID_0.01_795 -0.05764275 . 1.0 1.0 1.0 -chrX 18750000 18915000 ID_0.01_796 -0.063632 . 1.0 1.0 1.0 -chrX 18915000 19025000 ID_0.01_797 -0.01725275 . 1.0 1.0 1.0 -chrX 19025000 19075000 ID_0.01_798 -0.0192025 . 1.0 1.0 1.0 -chrX 19075000 19175000 ID_0.01_799 -0.036954 . 1.0 1.0 1.0 -chrX 19175000 19370000 ID_0.01_800 -0.06873975 . 1.0 1.0 1.0 -chrX 19370000 19480000 ID_0.01_801 -0.06873975 . 1.0 1.0 1.0 -chrX 19480000 19565000 ID_0.01_802 -0.05727125 . 1.0 1.0 1.0 -chrX 19565000 19680000 ID_0.01_803 -0.06873975 . 1.0 1.0 1.0 -chrX 19680000 19850000 ID_0.01_804 -0.0568755 . 1.0 1.0 1.0 -chrX 19850000 19910000 ID_0.01_805 -0.05478675 . 1.0 1.0 1.0 -chrX 19910000 19945000 ID_0.01_806 -0.06873975 . 1.0 1.0 1.0 -chrX 19945000 20025000 ID_0.01_807 -0.06873975 . 1.0 1.0 1.0 -chrX 20025000 20070000 ID_0.01_808 -0.01962325 . 1.0 1.0 1.0 -chrX 20070000 20220000 ID_0.01_809 -0.05764525 . 1.0 1.0 1.0 -chrX 20220000 20390000 ID_0.01_810 -0.06873975 . 1.0 1.0 1.0 -chrX 20390000 20455000 ID_0.01_811 -0.04103925 . 1.0 1.0 1.0 -chrX 20455000 20490000 ID_0.01_812 0.03779075 . 1.0 1.0 1.0 -chrX 20490000 20570000 ID_0.01_813 0.04029475 . 1.0 1.0 1.0 -chrX 20570000 20675000 ID_0.01_814 0.01527775 . 1.0 1.0 1.0 -chrX 20675000 20705000 ID_0.01_815 -0.02371025 . 1.0 1.0 1.0 -chrX 20705000 20765000 ID_0.01_816 -0.0014335 . 1.0 1.0 1.0 -chrX 20765000 20820000 ID_0.01_817 -0.026365 . 1.0 1.0 1.0 -chrX 20820000 20850000 ID_0.01_818 -0.03530925 . 1.0 1.0 1.0 -chrX 20850000 20900000 ID_0.01_819 -0.0243455 . 1.0 1.0 1.0 -chrX 20900000 20930000 ID_0.01_820 -0.06873975 . 1.0 1.0 1.0 -chrX 20930000 20985000 ID_0.01_821 -0.064119 . 1.0 1.0 1.0 -chrX 20985000 21190000 ID_0.01_822 -0.03381725 . 1.0 1.0 1.0 -chrX 21190000 21265000 ID_0.01_823 -0.022185 . 1.0 1.0 1.0 -chrX 21265000 21390000 ID_0.01_824 -0.06873975 . 1.0 1.0 1.0 -chrX 21390000 21510000 ID_0.01_825 -0.063632 . 1.0 1.0 1.0 -chrX 21510000 21930000 ID_0.01_826 -0.06873975 . 1.0 1.0 1.0 -chrX 21930000 22020000 ID_0.01_827 -0.05764525 . 1.0 1.0 1.0 -chrX 22020000 22115000 ID_0.01_828 -0.0279065 . 1.0 nan 1.0 -chrX 22115000 22275000 ID_0.01_829 -0.00088375 . 1.0 nan 1.0 -chr2R 160000 205000 ID_0.01_831 -0.09549125 . nan 1.0 1.0 -chr2R 205000 295000 ID_0.01_832 -0.09544475 . 1.0 1.0 1.0 -chr2R 295000 495000 ID_0.01_833 -0.10955875 . 1.0 1.0 1.0 -chr2R 495000 580000 ID_0.01_834 -0.06407475 . 1.0 1.0 1.0 -chr2R 580000 620000 ID_0.01_835 -0.09939775 . 1.0 1.0 1.0 -chr2R 620000 730000 ID_0.01_836 -0.105582 . 1.0 1.0 1.0 -chr2R 730000 840000 ID_0.01_837 -0.083229 . 1.0 1.0 1.0 -chr2R 840000 880000 ID_0.01_838 -0.068971 . 1.0 1.0 1.0 -chr2R 880000 980000 ID_0.01_839 -0.07297475 . 1.0 1.0 1.0 -chr2R 980000 1065000 ID_0.01_840 -0.0917465 . 1.0 1.0 1.0 -chr2R 1065000 1115000 ID_0.01_841 -0.0921445 . 1.0 1.0 1.0 -chr2R 1115000 1225000 ID_0.01_842 -0.09623225 . 1.0 1.0 1.0 -chr2R 1225000 1315000 ID_0.01_843 -0.0945825 . 1.0 1.0 1.0 -chr2R 1315000 1440000 ID_0.01_844 -0.106689 . 1.0 1.0 1.0 -chr2R 1440000 1510000 ID_0.01_845 -0.03268775 . 1.0 1.0 1.0 -chr2R 1510000 1665000 ID_0.01_846 -0.088113 . 1.0 1.0 1.0 -chr2R 1665000 1710000 ID_0.01_847 -0.01964725 . 1.0 1.0 1.0 -chr2R 1710000 1740000 ID_0.01_848 0.0019615 . 1.0 1.0 1.0 -chr2R 1740000 1880000 ID_0.01_849 0.03608825 . 1.0 1.0 1.0 -chr2R 1880000 1985000 ID_0.01_850 -0.05367375 . 1.0 1.0 1.0 -chr2R 1985000 2040000 ID_0.01_851 -0.02962375 . 1.0 1.0 1.0 -chr2R 2040000 2105000 ID_0.01_852 -0.0417505 . 1.0 1.0 1.0 -chr2R 2105000 2380000 ID_0.01_853 -0.0951475 . 1.0 1.0 1.0 -chr2R 2380000 2460000 ID_0.01_854 -0.08858475 . 1.0 1.0 1.0 -chr2R 2460000 2530000 ID_0.01_855 -0.05676875 . 1.0 1.0 1.0 -chr2R 2530000 2580000 ID_0.01_856 -0.0802925 . 1.0 1.0 1.0 -chr2R 2580000 2650000 ID_0.01_857 -0.05817075 . 1.0 1.0 1.0 -chr2R 2650000 2765000 ID_0.01_858 0.0085065 . 1.0 1.0 1.0 -chr2R 2765000 2860000 ID_0.01_859 0.03997525 . 1.0 1.0 1.0 -chr2R 2860000 2880000 ID_0.01_860 -0.03639025 . 1.0 1.0 1.0 -chr2R 2880000 2950000 ID_0.01_861 0.0069545 . 1.0 1.0 1.0 -chr2R 2950000 3085000 ID_0.01_862 -0.02647325 . 1.0 1.0 1.0 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12580000 12670000 ID_0.01_978 0.055233 . 1.0 1.0 1.0 -chr2R 12670000 12760000 ID_0.01_979 -0.06795725 . 1.0 1.0 1.0 -chr2R 12760000 12905000 ID_0.01_980 -0.01657725 . 1.0 1.0 1.0 -chr2R 12905000 12990000 ID_0.01_981 -0.09266575 . 1.0 1.0 1.0 -chr2R 12990000 13185000 ID_0.01_982 -0.06561475 . 1.0 1.0 1.0 -chr2R 13185000 13295000 ID_0.01_983 0.008407 . 1.0 1.0 1.0 -chr2R 13295000 13315000 ID_0.01_984 -0.0677165 . 1.0 1.0 1.0 -chr2R 13315000 13340000 ID_0.01_985 -0.0643875 . 1.0 1.0 1.0 -chr2R 13340000 13425000 ID_0.01_986 -0.058182 . 1.0 1.0 1.0 -chr2R 13425000 13475000 ID_0.01_987 -0.09635975 . 1.0 1.0 1.0 -chr2R 13475000 13560000 ID_0.01_988 -0.0909975 . 1.0 1.0 1.0 -chr2R 13560000 13610000 ID_0.01_989 -0.0814595 . 1.0 1.0 1.0 -chr2R 13610000 13700000 ID_0.01_990 -0.09870575 . 1.0 1.0 1.0 -chr2R 13700000 13735000 ID_0.01_991 -0.06323075 . 1.0 1.0 1.0 -chr2R 13735000 13800000 ID_0.01_992 -0.05482225 . 1.0 1.0 1.0 -chr2R 13800000 13820000 ID_0.01_993 -0.011235 . 1.0 1.0 1.0 -chr2R 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1.0 1.0 1.0 -chr2R 16715000 16750000 ID_0.01_1026 -0.017405 . 1.0 1.0 1.0 -chr2R 16750000 16845000 ID_0.01_1027 -0.0596635 . 1.0 1.0 1.0 -chr2R 16845000 16915000 ID_0.01_1028 -0.0392095 . 1.0 1.0 1.0 -chr2R 16915000 16975000 ID_0.01_1029 -0.04303925 . 1.0 1.0 1.0 -chr2R 16975000 17050000 ID_0.01_1030 -0.0984415 . 1.0 1.0 1.0 -chr2R 17050000 17145000 ID_0.01_1031 -0.08768675 . 1.0 1.0 1.0 -chr2R 17145000 17175000 ID_0.01_1032 -0.06926 . 1.0 1.0 1.0 -chr2R 17175000 17270000 ID_0.01_1033 -0.0896475 . 1.0 1.0 1.0 -chr2R 17270000 17295000 ID_0.01_1034 -0.033435 . 1.0 1.0 1.0 -chr2R 17295000 17370000 ID_0.01_1035 0.00201275 . 1.0 1.0 1.0 -chr2R 17370000 17420000 ID_0.01_1036 -0.0170355 . 1.0 1.0 1.0 -chr2R 17420000 17545000 ID_0.01_1037 -0.0013115 . 1.0 1.0 1.0 -chr2R 17545000 17575000 ID_0.01_1038 -0.10955875 . 1.0 1.0 1.0 -chr2R 17575000 17600000 ID_0.01_1039 -0.10955875 . 1.0 1.0 1.0 -chr2R 17600000 17680000 ID_0.01_1040 -0.10419925 . 1.0 1.0 1.0 -chr2R 17680000 17775000 ID_0.01_1041 -0.010073 . 1.0 1.0 1.0 -chr2R 17775000 17830000 ID_0.01_1042 0.03911875 . 1.0 1.0 1.0 -chr2R 17830000 17960000 ID_0.01_1043 0.11165925 . 1.0 1.0 1.0 -chr2R 17960000 18120000 ID_0.01_1044 -0.095325 . 1.0 1.0 1.0 -chr2R 18120000 18155000 ID_0.01_1045 -0.02804525 . 1.0 1.0 1.0 -chr2R 18155000 18195000 ID_0.01_1046 -0.0307365 . 1.0 1.0 1.0 -chr2R 18195000 18300000 ID_0.01_1047 -0.01803875 . 1.0 1.0 1.0 -chr2R 18300000 18390000 ID_0.01_1048 0.04134725 . 1.0 1.0 1.0 -chr2R 18390000 18430000 ID_0.01_1049 -0.04366925 . 1.0 1.0 1.0 -chr2R 18430000 18485000 ID_0.01_1050 -0.0664675 . 1.0 1.0 1.0 -chr2R 18485000 18585000 ID_0.01_1051 -0.05165725 . 1.0 1.0 1.0 -chr2R 18585000 18690000 ID_0.01_1052 -0.053443 . 1.0 1.0 1.0 -chr2R 18690000 18815000 ID_0.01_1053 -0.0469615 . 1.0 1.0 1.0 -chr2R 18815000 18845000 ID_0.01_1054 -0.075967 . 1.0 1.0 1.0 -chr2R 18845000 18950000 ID_0.01_1055 -0.09439325 . 1.0 1.0 1.0 -chr2R 18950000 19015000 ID_0.01_1056 -0.0463415 . 1.0 1.0 1.0 -chr2R 19015000 19150000 ID_0.01_1057 0.000571 . 1.0 1.0 1.0 -chr2R 19150000 19250000 ID_0.01_1058 -0.02951825 . 1.0 1.0 1.0 -chr2R 19250000 19275000 ID_0.01_1059 -0.02837425 . 1.0 1.0 1.0 -chr2R 19275000 19320000 ID_0.01_1060 -0.04698875 . 1.0 1.0 1.0 -chr2R 19320000 19435000 ID_0.01_1061 -0.0316155 . 1.0 1.0 1.0 -chr2R 19435000 19580000 ID_0.01_1062 -0.0901405 . 1.0 1.0 1.0 -chr2R 19580000 19745000 ID_0.01_1063 -0.10713375 . 1.0 1.0 1.0 -chr2R 19745000 19785000 ID_0.01_1064 -0.06872475 . 1.0 1.0 1.0 -chr2R 19785000 19925000 ID_0.01_1065 -0.10457925 . 1.0 1.0 1.0 -chr2R 19925000 20015000 ID_0.01_1066 -0.06192675 . 1.0 1.0 1.0 -chr2R 20015000 20065000 ID_0.01_1067 -0.0657535 . 1.0 1.0 1.0 -chr2R 20065000 20160000 ID_0.01_1068 -0.08050375 . 1.0 1.0 1.0 -chr2R 20160000 20295000 ID_0.01_1069 -0.04011575 . 1.0 1.0 1.0 -chr2R 20295000 20315000 ID_0.01_1070 0.01231975 . 1.0 1.0 1.0 -chr2R 20315000 20410000 ID_0.01_1071 0.025472 . 1.0 1.0 1.0 -chr2R 20410000 20560000 ID_0.01_1072 -0.10180525 . 1.0 1.0 1.0 -chr2R 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ID_0.01_1123 -0.023661 . 1.0 1.0 1.0 -chr3R 3650000 3710000 ID_0.01_1124 -0.02165875 . 1.0 1.0 1.0 -chr3R 3710000 3740000 ID_0.01_1125 -0.01603825 . 1.0 1.0 1.0 -chr3R 3740000 3830000 ID_0.01_1126 -0.05471 . 1.0 1.0 1.0 -chr3R 3830000 3925000 ID_0.01_1127 -0.072962 . 1.0 1.0 1.0 -chr3R 3925000 4045000 ID_0.01_1128 -0.08821075 . 1.0 1.0 1.0 -chr3R 4045000 4115000 ID_0.01_1129 -0.01555925 . 1.0 1.0 1.0 -chr3R 4115000 4165000 ID_0.01_1130 -0.1055805 . 1.0 1.0 1.0 -chr3R 4165000 4260000 ID_0.01_1131 -0.11179375 . 1.0 1.0 1.0 -chr3R 4260000 4425000 ID_0.01_1132 -0.0487275 . 1.0 1.0 1.0 -chr3R 4425000 4495000 ID_0.01_1133 -0.03174575 . 1.0 1.0 1.0 -chr3R 4495000 4595000 ID_0.01_1134 -0.04505925 . 1.0 1.0 1.0 -chr3R 4595000 4685000 ID_0.01_1135 -0.085168 . 1.0 1.0 1.0 -chr3R 4685000 4820000 ID_0.01_1136 -0.081637 . 1.0 1.0 1.0 -chr3R 4820000 4875000 ID_0.01_1137 -0.0984675 . 1.0 1.0 1.0 -chr3R 4875000 4985000 ID_0.01_1138 -0.094817 . 1.0 1.0 1.0 -chr3R 4985000 5055000 ID_0.01_1139 0.01289125 . 1.0 1.0 1.0 -chr3R 5055000 5215000 ID_0.01_1140 0.03692225 . 1.0 1.0 1.0 -chr3R 5215000 5280000 ID_0.01_1141 -0.04637 . 1.0 1.0 1.0 -chr3R 5280000 5360000 ID_0.01_1142 -0.060544 . 1.0 1.0 1.0 -chr3R 5360000 5430000 ID_0.01_1143 -0.08234025 . 1.0 1.0 1.0 -chr3R 5430000 5455000 ID_0.01_1144 -0.08224525 . 1.0 1.0 1.0 -chr3R 5455000 5585000 ID_0.01_1145 -0.06995975 . 1.0 1.0 1.0 -chr3R 5585000 5710000 ID_0.01_1146 -0.11469275 . 1.0 1.0 1.0 -chr3R 5710000 5830000 ID_0.01_1147 -0.044996 . 1.0 1.0 1.0 -chr3R 5830000 5960000 ID_0.01_1148 -0.00554225 . 1.0 1.0 1.0 -chr3R 5960000 6070000 ID_0.01_1149 -0.08993 . 1.0 1.0 1.0 -chr3R 6070000 6165000 ID_0.01_1150 -0.0810555 . 1.0 1.0 1.0 -chr3R 6165000 6275000 ID_0.01_1151 -0.10241275 . 1.0 1.0 1.0 -chr3R 6275000 6385000 ID_0.01_1152 -0.06761875 . 1.0 1.0 1.0 -chr3R 6385000 6450000 ID_0.01_1153 0.056357 . 1.0 1.0 1.0 -chr3R 6450000 6480000 ID_0.01_1154 -0.01331625 . 1.0 1.0 1.0 -chr3R 6480000 6595000 ID_0.01_1155 -0.002913 . 1.0 1.0 1.0 -chr3R 6595000 6690000 ID_0.01_1156 0.027459 . 1.0 1.0 1.0 -chr3R 6690000 6730000 ID_0.01_1157 -0.06199125 . 1.0 1.0 1.0 -chr3R 6730000 6875000 ID_0.01_1158 -0.0913745 . 1.0 1.0 1.0 -chr3R 6875000 7040000 ID_0.01_1159 -0.0332115 . 1.0 1.0 1.0 -chr3R 7040000 7100000 ID_0.01_1160 -0.11112375 . 1.0 1.0 1.0 -chr3R 7100000 7175000 ID_0.01_1161 -0.0924375 . 1.0 1.0 1.0 -chr3R 7175000 7240000 ID_0.01_1162 -0.0967015 . 1.0 1.0 1.0 -chr3R 7240000 7410000 ID_0.01_1163 -0.07084025 . 1.0 1.0 1.0 -chr3R 7410000 7460000 ID_0.01_1164 -0.0765645 . 1.0 1.0 1.0 -chr3R 7460000 7575000 ID_0.01_1165 -0.08356775 . 1.0 1.0 1.0 -chr3R 7575000 7625000 ID_0.01_1166 -0.06955825 . 1.0 1.0 1.0 -chr3R 7625000 7740000 ID_0.01_1167 -0.0166525 . 1.0 1.0 1.0 -chr3R 7740000 7805000 ID_0.01_1168 -0.09952275 . 1.0 1.0 1.0 -chr3R 7805000 7945000 ID_0.01_1169 -0.100695 . 1.0 1.0 1.0 -chr3R 7945000 8060000 ID_0.01_1170 0.079666 . 1.0 1.0 1.0 -chr3R 8060000 8085000 ID_0.01_1171 0.0213175 . 1.0 1.0 1.0 -chr3R 8085000 8175000 ID_0.01_1172 0.0235365 . 1.0 1.0 1.0 -chr3R 8175000 8330000 ID_0.01_1173 -0.0252505 . 1.0 1.0 1.0 -chr3R 8330000 8445000 ID_0.01_1174 -0.11469275 . 1.0 1.0 1.0 -chr3R 8445000 8555000 ID_0.01_1175 -0.0869855 . 1.0 1.0 1.0 -chr3R 8555000 8600000 ID_0.01_1176 -0.07822175 . 1.0 1.0 1.0 -chr3R 8600000 8695000 ID_0.01_1177 -0.043304 . 1.0 1.0 1.0 -chr3R 8695000 8770000 ID_0.01_1178 0.0405805 . 1.0 1.0 1.0 -chr3R 8770000 8790000 ID_0.01_1179 -0.069562 . 1.0 1.0 1.0 -chr3R 8790000 8855000 ID_0.01_1180 -0.03371425 . 1.0 1.0 1.0 -chr3R 8855000 8950000 ID_0.01_1181 -0.0521565 . 1.0 1.0 1.0 -chr3R 8950000 9025000 ID_0.01_1182 -0.01163375 . 1.0 1.0 1.0 -chr3R 9025000 9155000 ID_0.01_1183 0.02988525 . 1.0 1.0 1.0 -chr3R 9155000 9190000 ID_0.01_1184 -0.065617 . 1.0 1.0 1.0 -chr3R 9190000 9445000 ID_0.01_1185 -0.10440325 . 1.0 1.0 1.0 -chr3R 9445000 9555000 ID_0.01_1186 -0.0888795 . 1.0 1.0 1.0 -chr3R 9555000 9650000 ID_0.01_1187 -0.052408 . 1.0 1.0 1.0 -chr3R 9650000 9800000 ID_0.01_1188 -0.07661675 . 1.0 1.0 1.0 -chr3R 9800000 9915000 ID_0.01_1189 -0.06576625 . 1.0 1.0 1.0 -chr3R 9915000 10065000 ID_0.01_1190 -0.098744 . 1.0 1.0 1.0 -chr3R 10065000 10140000 ID_0.01_1191 -0.01751525 . 1.0 1.0 1.0 -chr3R 10140000 10285000 ID_0.01_1192 -0.073234 . 1.0 1.0 1.0 -chr3R 10285000 10440000 ID_0.01_1193 0.01077775 . 1.0 1.0 1.0 -chr3R 10440000 10480000 ID_0.01_1194 -0.060105 . 1.0 1.0 1.0 -chr3R 10480000 10515000 ID_0.01_1195 -0.0770145 . 1.0 1.0 1.0 -chr3R 10515000 10655000 ID_0.01_1196 -0.08507825 . 1.0 1.0 1.0 -chr3R 10655000 10725000 ID_0.01_1197 0.0767165 . 1.0 1.0 1.0 -chr3R 10725000 10755000 ID_0.01_1198 0.008892 . 1.0 1.0 1.0 -chr3R 10755000 10920000 ID_0.01_1199 0.02667225 . 1.0 1.0 1.0 -chr3R 10920000 10955000 ID_0.01_1200 -0.0296155 . 1.0 1.0 1.0 -chr3R 10955000 11030000 ID_0.01_1201 -0.075882 . 1.0 1.0 1.0 -chr3R 11030000 11155000 ID_0.01_1202 -0.06293775 . 1.0 1.0 1.0 -chr3R 11155000 11295000 ID_0.01_1203 -0.109499 . 1.0 1.0 1.0 -chr3R 11295000 11320000 ID_0.01_1204 0.021681 . 1.0 1.0 1.0 -chr3R 11320000 11375000 ID_0.01_1205 0.02274025 . 1.0 1.0 1.0 -chr3R 11375000 11400000 ID_0.01_1206 0.01457775 . 1.0 1.0 1.0 -chr3R 11400000 11510000 ID_0.01_1207 -0.02120475 . 1.0 1.0 1.0 -chr3R 11510000 11615000 ID_0.01_1208 0.027476 . 1.0 1.0 1.0 -chr3R 11615000 11705000 ID_0.01_1209 -0.0042395 . 1.0 1.0 1.0 -chr3R 11705000 11755000 ID_0.01_1210 0.0618155 . 1.0 1.0 1.0 -chr3R 11755000 11795000 ID_0.01_1211 -0.045442 . 1.0 1.0 1.0 -chr3R 11795000 11810000 ID_0.01_1212 -0.05860825 . 1.0 1.0 1.0 -chr3R 11810000 11915000 ID_0.01_1213 -0.0550275 . 1.0 1.0 1.0 -chr3R 11915000 12020000 ID_0.01_1214 0.06476725 . 1.0 1.0 1.0 -chr3R 12020000 12095000 ID_0.01_1215 -0.07062675 . 1.0 1.0 1.0 -chr3R 12095000 12165000 ID_0.01_1216 -0.09505675 . 1.0 1.0 1.0 -chr3R 12165000 12200000 ID_0.01_1217 -0.069725 . 1.0 1.0 1.0 -chr3R 12200000 12260000 ID_0.01_1218 -0.055654 . 1.0 1.0 1.0 -chr3R 12260000 12295000 ID_0.01_1219 -0.10428725 . 1.0 1.0 1.0 -chr3R 12295000 12475000 ID_0.01_1220 -0.11145675 . 1.0 1.0 1.0 -chr3R 12475000 12505000 ID_0.01_1221 -0.01250275 . 1.0 1.0 1.0 -chr3R 12505000 12575000 ID_0.01_1222 -0.009183 . 1.0 1.0 1.0 -chr3R 12575000 12670000 ID_0.01_1223 -0.026389 . 1.0 1.0 1.0 -chr3R 12670000 12740000 ID_0.01_1224 -0.04390025 . 1.0 1.0 1.0 -chr3R 12740000 12775000 ID_0.01_1225 -0.009504 . 1.0 1.0 1.0 -chr3R 12775000 12805000 ID_0.01_1226 -0.009823 . 1.0 1.0 1.0 -chr3R 12805000 12875000 ID_0.01_1227 -0.0176885 . 1.0 1.0 1.0 -chr3R 12875000 12920000 ID_0.01_1228 -0.085944 . 1.0 1.0 1.0 -chr3R 12920000 13055000 ID_0.01_1229 -0.088056 . 1.0 1.0 1.0 -chr3R 13055000 13065000 ID_0.01_1230 0.02551975 . 1.0 1.0 1.0 -chr3R 13065000 13165000 ID_0.01_1231 0.04950025 . 1.0 1.0 1.0 -chr3R 13165000 13200000 ID_0.01_1232 0.04378675 . 1.0 1.0 1.0 -chr3R 13200000 13225000 ID_0.01_1233 0.0424255 . 1.0 1.0 1.0 -chr3R 13225000 13315000 ID_0.01_1234 0.0544345 . 1.0 1.0 1.0 -chr3R 13315000 13360000 ID_0.01_1235 0.11092275 . 1.0 1.0 1.0 -chr3R 13360000 13440000 ID_0.01_1236 0.01667425 . 1.0 1.0 1.0 -chr3R 13440000 13495000 ID_0.01_1237 -0.06125525 . 1.0 1.0 1.0 -chr3R 13495000 13545000 ID_0.01_1238 -0.08284775 . 1.0 1.0 1.0 -chr3R 13545000 13590000 ID_0.01_1239 -0.06110725 . 1.0 1.0 1.0 -chr3R 13590000 13725000 ID_0.01_1240 -0.03928725 . 1.0 1.0 1.0 -chr3R 13725000 13830000 ID_0.01_1241 0.023938 . 1.0 1.0 1.0 -chr3R 13830000 13905000 ID_0.01_1242 0.00793875 . 1.0 1.0 1.0 -chr3R 13905000 13965000 ID_0.01_1243 -0.01205075 . 1.0 1.0 1.0 -chr3R 13965000 14070000 ID_0.01_1244 -0.02961175 . 1.0 1.0 1.0 -chr3R 14070000 14120000 ID_0.01_1245 -0.06893525 . 1.0 1.0 1.0 -chr3R 14120000 14240000 ID_0.01_1246 -0.03839675 . 1.0 1.0 1.0 -chr3R 14240000 14380000 ID_0.01_1247 -0.0522915 . 1.0 1.0 1.0 -chr3R 14380000 14480000 ID_0.01_1248 -0.032096 . 1.0 1.0 1.0 -chr3R 14480000 14565000 ID_0.01_1249 -0.0983995 . 1.0 1.0 1.0 -chr3R 14565000 14735000 ID_0.01_1250 -0.09574025 . 1.0 1.0 1.0 -chr3R 14735000 14775000 ID_0.01_1251 -0.086167 . 1.0 1.0 1.0 -chr3R 14775000 14875000 ID_0.01_1252 -0.0837245 . 1.0 1.0 1.0 -chr3R 14875000 14985000 ID_0.01_1253 -0.09261925 . 1.0 1.0 1.0 -chr3R 14985000 15060000 ID_0.01_1254 -0.0672105 . 1.0 1.0 1.0 -chr3R 15060000 15155000 ID_0.01_1255 -0.0598935 . 1.0 1.0 1.0 -chr3R 15155000 15315000 ID_0.01_1256 0.06270025 . 1.0 1.0 1.0 -chr3R 15315000 15370000 ID_0.01_1257 0.035499 . 1.0 1.0 1.0 -chr3R 15370000 15490000 ID_0.01_1258 0.00496875 . 1.0 1.0 1.0 -chr3R 15490000 15515000 ID_0.01_1259 -0.04944075 . 1.0 1.0 1.0 -chr3R 15515000 15560000 ID_0.01_1260 -0.0455655 . 1.0 1.0 1.0 -chr3R 15560000 15595000 ID_0.01_1261 -0.0591275 . 1.0 1.0 1.0 -chr3R 15595000 15645000 ID_0.01_1262 -0.075517 . 1.0 1.0 1.0 -chr3R 15645000 15745000 ID_0.01_1263 -0.03652625 . 1.0 1.0 1.0 -chr3R 15745000 15830000 ID_0.01_1264 -0.0121245 . 1.0 1.0 1.0 -chr3R 15830000 15865000 ID_0.01_1265 0.01194425 . 1.0 1.0 1.0 -chr3R 15865000 15915000 ID_0.01_1266 0.03510975 . 1.0 1.0 1.0 -chr3R 15915000 15935000 ID_0.01_1267 0.0658725 . 1.0 1.0 1.0 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1.0 1.0 -chr3R 17490000 17520000 ID_0.01_1284 -0.04999425 . 1.0 1.0 1.0 -chr3R 17520000 17600000 ID_0.01_1285 -0.02900275 . 1.0 1.0 1.0 -chr3R 17600000 17630000 ID_0.01_1286 -0.018032 . 1.0 1.0 1.0 -chr3R 17630000 17670000 ID_0.01_1287 0.00256125 . 1.0 1.0 1.0 -chr3R 17670000 17700000 ID_0.01_1288 -0.00398125 . 1.0 1.0 1.0 -chr3R 17700000 17715000 ID_0.01_1289 -0.02050575 . 1.0 1.0 1.0 -chr3R 17715000 17745000 ID_0.01_1290 -0.016624 . 1.0 1.0 1.0 -chr3R 17745000 17835000 ID_0.01_1291 -0.03185675 . 1.0 1.0 1.0 -chr3R 17835000 17880000 ID_0.01_1292 -0.02028125 . 1.0 1.0 1.0 -chr3R 17880000 17915000 ID_0.01_1293 -0.042281 . 1.0 1.0 1.0 -chr3R 17915000 17935000 ID_0.01_1294 -0.05210225 . 1.0 1.0 1.0 -chr3R 17935000 18030000 ID_0.01_1295 -0.04894525 . 1.0 1.0 1.0 -chr3R 18030000 18120000 ID_0.01_1296 -0.07584425 . 1.0 1.0 1.0 -chr3R 18120000 18180000 ID_0.01_1297 -0.0833235 . 1.0 1.0 1.0 -chr3R 18180000 18310000 ID_0.01_1298 -0.09684475 . 1.0 1.0 1.0 -chr3R 18310000 18395000 ID_0.01_1299 -0.069608 . 1.0 1.0 1.0 -chr3R 18395000 18445000 ID_0.01_1300 -0.06729775 . 1.0 1.0 1.0 -chr3R 18445000 18485000 ID_0.01_1301 -0.04397025 . 1.0 1.0 1.0 -chr3R 18485000 18525000 ID_0.01_1302 -0.0533955 . 1.0 1.0 1.0 -chr3R 18525000 18690000 ID_0.01_1303 -0.11469275 . 1.0 1.0 1.0 -chr3R 18690000 18735000 ID_0.01_1304 -0.075545 . 1.0 1.0 1.0 -chr3R 18735000 18885000 ID_0.01_1305 -0.0485985 . 1.0 1.0 1.0 -chr3R 18885000 19005000 ID_0.01_1306 -0.09972425 . 1.0 1.0 1.0 -chr3R 19005000 19100000 ID_0.01_1307 -0.1054935 . 1.0 1.0 1.0 -chr3R 19100000 19185000 ID_0.01_1308 -0.080215 . 1.0 1.0 1.0 -chr3R 19185000 19255000 ID_0.01_1309 -0.1117525 . 1.0 1.0 1.0 -chr3R 19255000 19285000 ID_0.01_1310 -0.07804225 . 1.0 1.0 1.0 -chr3R 19285000 19380000 ID_0.01_1311 -0.069411 . 1.0 1.0 1.0 -chr3R 19380000 19460000 ID_0.01_1312 -0.05580225 . 1.0 1.0 1.0 -chr3R 19460000 19565000 ID_0.01_1313 -0.01161525 . 1.0 1.0 1.0 -chr3R 19565000 19695000 ID_0.01_1314 -0.08905275 . 1.0 1.0 1.0 -chr3R 19695000 19740000 ID_0.01_1315 -0.10521125 . 1.0 1.0 1.0 -chr3R 19740000 19935000 ID_0.01_1316 -0.1117525 . 1.0 1.0 1.0 -chr3R 19935000 20020000 ID_0.01_1317 -0.10631075 . 1.0 1.0 1.0 -chr3R 20020000 20050000 ID_0.01_1318 -0.083403 . 1.0 1.0 1.0 -chr3R 20050000 20150000 ID_0.01_1319 -0.0909175 . 1.0 1.0 1.0 -chr3R 20150000 20220000 ID_0.01_1320 -0.0227935 . 1.0 1.0 1.0 -chr3R 20220000 20335000 ID_0.01_1321 -0.034021 . 1.0 1.0 1.0 -chr3R 20335000 20375000 ID_0.01_1322 -0.10360825 . 1.0 1.0 1.0 -chr3R 20375000 20455000 ID_0.01_1323 -0.11469275 . 1.0 1.0 1.0 -chr3R 20455000 20615000 ID_0.01_1324 -0.10752325 . 1.0 1.0 1.0 -chr3R 20615000 20710000 ID_0.01_1325 -0.099168 . 1.0 1.0 1.0 -chr3R 20710000 20720000 ID_0.01_1326 -0.07351875 . 1.0 1.0 1.0 -chr3R 20720000 20765000 ID_0.01_1327 -0.0705095 . 1.0 1.0 1.0 -chr3R 20765000 20860000 ID_0.01_1328 -0.0862985 . 1.0 1.0 1.0 -chr3R 20860000 20900000 ID_0.01_1329 -0.01276525 . 1.0 1.0 1.0 -chr3R 20900000 20935000 ID_0.01_1330 -0.02185325 . 1.0 1.0 1.0 -chr3R 20935000 20965000 ID_0.01_1331 -0.05891975 . 1.0 1.0 1.0 -chr3R 20965000 21085000 ID_0.01_1332 -0.0613935 . 1.0 1.0 1.0 -chr3R 21085000 21175000 ID_0.01_1333 -0.094928 . 1.0 1.0 1.0 -chr3R 21175000 21220000 ID_0.01_1334 -0.0413955 . 1.0 1.0 1.0 -chr3R 21220000 21320000 ID_0.01_1335 -0.05028725 . 1.0 1.0 1.0 -chr3R 21320000 21335000 ID_0.01_1336 -0.086029 . 1.0 1.0 1.0 -chr3R 21335000 21390000 ID_0.01_1337 -0.06100175 . 1.0 1.0 1.0 -chr3R 21390000 21475000 ID_0.01_1338 -0.0656765 . 1.0 1.0 1.0 -chr3R 21475000 21615000 ID_0.01_1339 -0.0932985 . 1.0 1.0 1.0 -chr3R 21615000 21730000 ID_0.01_1340 -0.081974 . 1.0 1.0 1.0 -chr3R 21730000 21820000 ID_0.01_1341 0.07025075 . 1.0 1.0 1.0 -chr3R 21820000 21845000 ID_0.01_1342 -0.00145975 . 1.0 1.0 1.0 -chr3R 21845000 21950000 ID_0.01_1343 0.0360515 . 1.0 1.0 1.0 -chr3R 21950000 21990000 ID_0.01_1344 0.002742 . 1.0 1.0 1.0 -chr3R 21990000 22075000 ID_0.01_1345 0.00713375 . 1.0 1.0 1.0 -chr3R 22075000 22220000 ID_0.01_1346 -0.087915 . 1.0 1.0 1.0 -chr3R 22220000 22270000 ID_0.01_1347 0.0614505 . 1.0 1.0 1.0 -chr3R 22270000 22310000 ID_0.01_1348 -0.02575325 . 1.0 1.0 1.0 -chr3R 22310000 22380000 ID_0.01_1349 -0.04946475 . 1.0 1.0 1.0 -chr3R 22380000 22500000 ID_0.01_1350 -0.055847 . 1.0 1.0 1.0 -chr3R 22500000 22520000 ID_0.01_1351 -0.0631105 . 1.0 1.0 1.0 -chr3R 22520000 22605000 ID_0.01_1352 -0.062648 . 1.0 1.0 1.0 -chr3R 22605000 22695000 ID_0.01_1353 -0.011252 . 1.0 1.0 1.0 -chr3R 22695000 22780000 ID_0.01_1354 -0.089033 . 1.0 1.0 1.0 -chr3R 22780000 22885000 ID_0.01_1355 -0.04050025 . 1.0 1.0 1.0 -chr3R 22885000 22985000 ID_0.01_1356 -0.05683475 . 1.0 1.0 1.0 -chr3R 22985000 23110000 ID_0.01_1357 -0.0237815 . 1.0 1.0 1.0 -chr3R 23110000 23185000 ID_0.01_1358 -0.100625 . 1.0 1.0 1.0 -chr3R 23185000 23195000 ID_0.01_1359 -0.00294725 . 1.0 1.0 1.0 -chr3R 23195000 23415000 ID_0.01_1360 -0.00275775 . 1.0 1.0 1.0 -chr3R 23415000 23560000 ID_0.01_1361 -0.090027 . 1.0 1.0 1.0 -chr3R 23560000 23770000 ID_0.01_1362 -0.104602 . 1.0 1.0 1.0 -chr3R 23770000 23815000 ID_0.01_1363 -0.1119105 . 1.0 1.0 1.0 -chr3R 23815000 23920000 ID_0.01_1364 -0.0660765 . 1.0 1.0 1.0 -chr3R 23920000 24030000 ID_0.01_1365 -0.04218475 . 1.0 1.0 1.0 -chr3R 24030000 24160000 ID_0.01_1366 -0.05579575 . 1.0 1.0 1.0 -chr3R 24160000 24205000 ID_0.01_1367 -0.01546725 . 1.0 1.0 1.0 -chr3R 24205000 24345000 ID_0.01_1368 -0.0326015 . 1.0 1.0 1.0 -chr3R 24345000 24375000 ID_0.01_1369 -0.0623065 . 1.0 1.0 1.0 -chr3R 24375000 24450000 ID_0.01_1370 -0.0749395 . 1.0 1.0 1.0 -chr3R 24450000 24625000 ID_0.01_1371 -0.09836075 . 1.0 1.0 1.0 -chr3R 24625000 24745000 ID_0.01_1372 -0.03171375 . 1.0 1.0 1.0 -chr3R 24745000 24885000 ID_0.01_1373 -0.08589625 . 1.0 1.0 1.0 -chr3R 24885000 24995000 ID_0.01_1374 -0.09323725 . 1.0 1.0 1.0 -chr3R 24995000 25090000 ID_0.01_1375 -0.0589785 . 1.0 1.0 1.0 -chr3R 25090000 25165000 ID_0.01_1376 0.03674225 . 1.0 1.0 1.0 -chr3R 25165000 25330000 ID_0.01_1377 -0.0462465 . 1.0 1.0 1.0 -chr3R 25330000 25405000 ID_0.01_1378 -0.08303325 . 1.0 1.0 1.0 -chr3R 25405000 25570000 ID_0.01_1379 -0.00546225 . 1.0 1.0 1.0 -chr3R 25570000 25580000 ID_0.01_1380 -0.04654075 . 1.0 1.0 1.0 -chr3R 25580000 25730000 ID_0.01_1381 -0.01871575 . 1.0 1.0 1.0 -chr3R 25730000 25880000 ID_0.01_1382 -0.00858875 . 1.0 1.0 1.0 -chr3R 25880000 25990000 ID_0.01_1383 -0.10581625 . 1.0 1.0 1.0 -chr3R 25990000 26050000 ID_0.01_1384 -0.090403 . 1.0 1.0 1.0 -chr3R 26050000 26180000 ID_0.01_1385 -0.0935315 . 1.0 1.0 1.0 -chr3R 26180000 26275000 ID_0.01_1386 -0.11469275 . 1.0 1.0 1.0 -chr3R 26275000 26330000 ID_0.01_1387 -0.1002735 . 1.0 1.0 1.0 -chr3R 26330000 26490000 ID_0.01_1388 -0.092304 . 1.0 1.0 1.0 -chr3R 26490000 26565000 ID_0.01_1389 0.0627965 . 1.0 1.0 1.0 -chr3R 26565000 26640000 ID_0.01_1390 -0.01974475 . 1.0 1.0 1.0 -chr3R 26640000 26715000 ID_0.01_1391 -0.07430725 . 1.0 1.0 1.0 -chr3R 26715000 26870000 ID_0.01_1392 -0.049789 . 1.0 1.0 1.0 -chr3R 26870000 27045000 ID_0.01_1393 -0.0249905 . 1.0 1.0 1.0 -chr3R 27045000 27155000 ID_0.01_1394 -0.074189 . 1.0 1.0 1.0 -chr3R 27155000 27185000 ID_0.01_1395 -0.00609925 . 1.0 1.0 1.0 -chr3R 27185000 27250000 ID_0.01_1396 -0.01281025 . 1.0 1.0 1.0 -chr3R 27250000 27385000 ID_0.01_1397 -0.04990275 . 1.0 1.0 1.0 -chr3R 27385000 27420000 ID_0.01_1398 -0.041305 . 1.0 1.0 1.0 -chr3R 27420000 27570000 ID_0.01_1399 -0.0499295 . 1.0 1.0 1.0 -chr3R 27570000 27700000 ID_0.01_1400 -0.08094325 . 1.0 1.0 1.0 -chr3R 27700000 27750000 ID_0.01_1401 -0.01535 . 1.0 nan 1.0 -chr3R 27750000 27770000 ID_0.01_1402 0.01357725 . 1.0 nan 1.0 +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr3L 165000 260000 ID_0.01_1 -0.10316675 . nan 1.0 1.0 nan 0.0 0.0 +chr3L 260000 335000 ID_0.01_2 -0.026655 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 335000 360000 ID_0.01_3 -0.030848 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 360000 485000 ID_0.01_4 -0.0580815 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 485000 525000 ID_0.01_5 -0.07169775 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 525000 680000 ID_0.01_6 -0.1060405 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 680000 705000 ID_0.01_7 -0.0148855 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 705000 740000 ID_0.01_8 0.002784 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 740000 870000 ID_0.01_9 0.00949975 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 870000 1010000 ID_0.01_10 -0.09546975 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1010000 1040000 ID_0.01_11 -0.05182175 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1040000 1110000 ID_0.01_12 -0.05874875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1110000 1210000 ID_0.01_13 -0.048349 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1210000 1245000 ID_0.01_14 -0.0567565 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1245000 1300000 ID_0.01_15 -0.0641435 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1300000 1465000 ID_0.01_16 -0.091379 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1465000 1535000 ID_0.01_17 -0.01307225 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1535000 1580000 ID_0.01_18 -0.08711525 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1580000 1640000 ID_0.01_19 -0.08235875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1640000 1670000 ID_0.01_20 -0.0628755 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1670000 1735000 ID_0.01_21 -0.037945 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1735000 1815000 ID_0.01_22 -0.050313 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1815000 1850000 ID_0.01_23 -0.01723525 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1850000 1925000 ID_0.01_24 -0.0259975 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 1925000 2155000 ID_0.01_25 8.325e-05 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2155000 2260000 ID_0.01_26 -0.0401965 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2260000 2390000 ID_0.01_27 -0.07518575 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2390000 2460000 ID_0.01_28 -0.072071 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2460000 2560000 ID_0.01_29 -0.09132325 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2560000 2600000 ID_0.01_30 -0.09179675 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2600000 2740000 ID_0.01_31 -0.0934855 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2740000 2885000 ID_0.01_32 -0.08927875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2885000 2945000 ID_0.01_33 -0.08972575 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2945000 2960000 ID_0.01_34 0.029899 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 2960000 3045000 ID_0.01_35 0.0356865 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3045000 3135000 ID_0.01_36 -0.00466875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3135000 3220000 ID_0.01_37 0.055702 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3220000 3255000 ID_0.01_38 -0.059463 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3255000 3315000 ID_0.01_39 -0.045796 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3315000 3345000 ID_0.01_40 -0.05499875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3345000 3475000 ID_0.01_41 -0.04234075 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3475000 3515000 ID_0.01_42 -0.05097675 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3515000 3545000 ID_0.01_43 -0.012488 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3545000 3615000 ID_0.01_44 0.02457925 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3615000 3670000 ID_0.01_45 0.019683 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3670000 3765000 ID_0.01_46 0.09945325 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3765000 3785000 ID_0.01_47 -0.047454 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3785000 3825000 ID_0.01_48 -0.041084 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3825000 3900000 ID_0.01_49 -0.06101175 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 3900000 4000000 ID_0.01_50 -0.0684535 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4000000 4120000 ID_0.01_51 -0.03007875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4120000 4165000 ID_0.01_52 -0.0807515 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4165000 4200000 ID_0.01_53 -0.088488 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4200000 4220000 ID_0.01_54 -0.098724 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4220000 4270000 ID_0.01_55 -0.088911 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4270000 4365000 ID_0.01_56 -0.11633575 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4365000 4405000 ID_0.01_57 -0.0944955 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4405000 4490000 ID_0.01_58 -0.07463925 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4490000 4625000 ID_0.01_59 0.00287075 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4625000 4650000 ID_0.01_60 0.04064075 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3L 4650000 4790000 ID_0.01_61 0.03764975 . 1.0 1.0 1.0 0.0 0.0 0.0 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ID_0.01_1395 -0.00609925 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27185000 27250000 ID_0.01_1396 -0.01281025 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27250000 27385000 ID_0.01_1397 -0.04990275 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27385000 27420000 ID_0.01_1398 -0.041305 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27420000 27570000 ID_0.01_1399 -0.0499295 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27570000 27700000 ID_0.01_1400 -0.08094325 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27700000 27750000 ID_0.01_1401 -0.01535 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27750000 27770000 ID_0.01_1402 0.01357725 . 1.0 nan 1.0 0.0 nan 0.0
--- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,8 +1,8 @@ -# Matrix information file. Created with HiCExplorer's hicInfo version 3.4 +# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2 File: matrix_name.h5 Size: 33,754 Bin_length: 5000 -Sum of matrix: 35778.0 +Sum of matrix: 37321.0 Chromosomes:length: chr2L: 23011544 bp; chr2LHet: 368872 bp; chr2R: 21146708 bp; chr2RHet: 3288761 bp; chr3L: 24543557 bp; chr3LHet: 2555491 bp; chr3R: 27905053 bp; chr3RHet: 2517507 bp; chr4: 1351857 bp; chrM: 19517 bp; chrUextra: 29004656 bp; chrU: 10049037 bp; chrX: 22422827 bp; chrXHet: 204112 bp; chrYHet: 347038 bp; Non-zero elements: 69,213 Minimum (non zero): 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,22 @@ +# Created with HiCExplorer's hicInterIntraTAD version 3.7.2 +# Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio +chr2 17100000 18100000 region_0 0 + 0 148.64980341892507 0 1.0 0 90 0 90 289.00804022517053 100 100 1.0 0.0 0.5143448718696884 0.5143448718696884 +chr2 18100000 19100000 region_1 0 + 162.1124908492847 211.04026046280666 1.0 1.0 100 140 100 140 277.9356647725957 100 100 1.0 0.583273438412172 0.7593133491359512 1.3425867875481232 +chr2 19100000 20600000 region_2 0 + 223.14353637851622 150.01947633135822 1.0 1.0 150 90 150 90 556.143932925097 225 225 1.0 0.4012334274777925 0.269749371430369 0.6709827989081616 +chr2 20600000 21300000 region_3 0 + 171.34866125986417 274.4679914622871 1.0 1.0 105 84 105 84 149.85761183392816 49 49 1.0 1.1434097952244984 1.8315251931710472 2.9749349883955456 +chr2 21300000 22600000 region_4 0 + 283.89289960594425 768.874984677404 1.0 1.0 91 208 91 208 24180.36424789467 169 169 1.0 0.011740637845464306 0.03179749390021485 0.04353813174567915 +chr2 22600000 24300000 region_5 0 + 789.804014201572 321.70053830625835 1.0 1.0 221 238 221 238 659.9593561049022 289 289 1.0 1.1967464464221198 0.48745507633219043 1.6842015227543101 +chr2 24300000 25800000 region_6 0 + 340.44705127228065 836.790681935677 1.0 1.0 255 720 255 720 598.8884085354028 225 225 1.0 0.5684649200422041 1.3972397361673277 1.965704656209532 +chr2 25800000 30700000 region_7 0 + 852.3657188383157 1593.0953595672838 1.0 1.0 735 1421 735 1421 4153.286346671477 2401 2401 1.0 0.20522681262307327 0.3835746506724779 0.5888014632955512 +chr2 30700000 33700000 region_8 0 + 1644.3620053137968 315.02407146145276 1.0 1.0 1470 240 1470 240 1873.0714290428866 900 900 1.0 0.8778960480722525 0.16818582920910052 1.046081877281353 +chr2 33700000 34600000 region_9 0 + 351.38600814451206 204.32883091037917 1.0 1.0 270 153 270 153 245.00889544594847 81 81 1.0 1.434176532672184 0.8339649486541041 2.268141481326288 +chr2 34600000 36400000 region_10 0 + 213.88883777381795 379.5343566721307 1.0 1.0 162 288 162 288 770.6376988509402 324 324 1.0 0.27754785172427593 0.49249388816305717 0.7700417398873332 +chr2 36400000 38100000 region_11 0 + 399.4783208321819 189.4340956757372 1.0 1.0 306 136 306 136 635.9658356069232 289 289 1.0 0.6281443097504547 0.29786835246417603 0.9260126622146307 +chr2 38100000 39000000 region_12 0 + 209.82145375215833 74.59004956153072 1.0 1.0 153 45 153 45 229.67774089590498 81 81 1.0 0.9135471854334115 0.3247595925951596 1.2383067780285713 +chr2 39000000 39600000 region_13 0 + 87.2296637584025 120.04828267162685 1.0 1.0 54 72 54 72 114.2377217834551 36 36 1.0 0.7635802114799864 1.0508637672168046 1.814443978696791 +chr2 39600000 40900000 region_14 0 + 127.68593516818584 348.8073054441913 1.0 1.0 78 247 78 247 447.58733970743407 169 169 1.0 0.2852760206569915 0.7793055667575172 1.0645815874145086 +chr2 40900000 42900000 region_15 0 + 363.6155543954171 330.73139298156053 1.0 1.0 260 240 260 240 912.1015373488856 400 400 1.0 0.3986568813953566 0.3626037008367121 0.7612605822320687 +chr2 42900000 44200000 region_16 0 + 353.76150800590995 305.3562724757596 1.0 1.0 260 208 260 208 434.0150296605763 169 169 1.0 0.8150904550069866 0.7035615165552332 1.51865197156222 +chr2 44200000 45900000 region_17 0 + 321.3851510623236 309.7368872510572 1.0 1.0 221 221 221 221 667.4121186463332 289 289 1.0 0.4815392799791639 0.4640863996885097 0.9456256796676736 +chr2 45900000 47300000 region_18 0 + 330.1441180225245 330.3028710611577 1.0 1.0 238 238 238 238 509.86032585858186 196 196 1.0 0.6475187444062777 0.6478301101481911 1.2953488545544687 +chr2 47300000 49100000 region_19 0 + 330.3028710611577 0 1.0 0 238 0 238 0 737.4495555644096 324 324 1.0 0.44789893568836614 0.0 0.44789893568836614
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,20 @@ +chr2 17100000 18100000 ID_0.01_10 -0.230354000000 . 17100000 18100000 51,160,44 +chr2 18100000 19100000 ID_0.01_11 -0.513536500000 . 18100000 19100000 31,120,180 +chr2 19100000 20600000 ID_0.01_12 -0.420252500000 . 19100000 20600000 51,160,44 +chr2 20600000 21300000 ID_0.01_13 -0.998086500000 . 20600000 21300000 31,120,180 +chr2 21300000 22600000 ID_0.01_14 -0.859866000000 . 21300000 22600000 51,160,44 +chr2 22600000 24300000 ID_0.01_15 -0.281294000000 . 22600000 24300000 31,120,180 +chr2 24300000 25800000 ID_0.01_16 -1.036617500000 . 24300000 25800000 51,160,44 +chr2 25800000 30700000 ID_0.01_17 -0.147124500000 . 25800000 30700000 31,120,180 +chr2 30700000 33700000 ID_0.01_18 -1.013445500000 . 30700000 33700000 51,160,44 +chr2 33700000 34600000 ID_0.01_19 -1.338090000000 . 33700000 34600000 31,120,180 +chr2 34600000 36400000 ID_0.01_20 -0.632501500000 . 34600000 36400000 51,160,44 +chr2 36400000 38100000 ID_0.01_21 -0.925006000000 . 36400000 38100000 31,120,180 +chr2 38100000 39000000 ID_0.01_22 -0.911804000000 . 38100000 39000000 51,160,44 +chr2 39000000 39600000 ID_0.01_23 -0.474157000000 . 39000000 39600000 31,120,180 +chr2 39600000 40900000 ID_0.01_24 -0.483398000000 . 39600000 40900000 51,160,44 +chr2 40900000 42900000 ID_0.01_25 -0.701614500000 . 40900000 42900000 31,120,180 +chr2 42900000 44200000 ID_0.01_26 -0.658489500000 . 42900000 44200000 51,160,44 +chr2 44200000 45900000 ID_0.01_27 -1.406743500000 . 44200000 45900000 31,120,180 +chr2 45900000 47300000 ID_0.01_28 -0.656308000000 . 45900000 47300000 51,160,44 +chr2 47300000 49100000 ID_0.01_29 -0.003388500000 . 47300000 49100000 31,120,180 \ No newline at end of file
--- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 11:00:15 2023 +0000 @@ -7,7 +7,7 @@ 1 1050000 1075000 1 1175000 1200000 0.001 1 1310000 1320000 1 1410000 1420000 0.001 1 1710000 1720000 1 1830000 1840000 0.001 -1 1870000 1880000 1 3340000 3350000 0.0019430592210407133 +1 1870000 1880000 1 3340000 3350000 0.0019430592210407 1 2080000 2090000 1 3330000 3340000 0.001 1 2110000 2120000 1 2710000 2720000 0.001 1 2120000 2130000 1 2480000 2490000 0.001 @@ -101,7 +101,7 @@ 1 13160000 13170000 1 14520000 14530000 0.001 1 13320000 13330000 1 13440000 13450000 0.001 1 13335000 13340000 1 13540000 13545000 0.001 -1 13350000 13360000 1 13630000 13640000 0.008992888101929171 +1 13350000 13360000 1 13630000 13640000 0.0089928881019291 1 13475000 13500000 1 13700000 13725000 0.001 1 13550000 13575000 1 14325000 14350000 0.001 1 13690000 13700000 1 15390000 15400000 0.001 @@ -151,7 +151,7 @@ 1 21100000 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--- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.6 +# Created with HiCExplorer's hicPlotSVL 3.7.2 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum # Short range contacts: <= 2000000 0_small_test_matrix.h5 1_small_test_matrix.h5 1.0
--- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 11:00:15 2023 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.6 +# Created with HiCExplorer's hicPlotSVL 3.7.2 # Short range vs long range contacts per chromosome: raw data # Short range contacts: <= 2000000 # 0_small_test_matrix.h5 1_small_test_matrix.h5
--- a/test-data/hicQuickQC/QC.log Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 11:00:15 2023 +0000 @@ -1,5 +1,5 @@ -File /tmp/tmp12xmnm2f.h5 +File /var/folders/nm/9sgmbhhj6gn_h8b308xvhm0w0000gt/T/tmp8sucpx99.h5 Sequenced reads 983 Min rest. site distance 300 Max library insert size 1000 @@ -12,7 +12,7 @@ Low mapping quality 164 (16.68) # count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end GATC 1 (0.33) +dangling end GATC (restriction sequence GATC) 1 (0.33) self ligation (removed) 0 (0.00) One mate not close to rest site 0 (0.00) same fragment 84 (28.00)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed Wed Oct 18 11:00:15 2023 +0000 @@ -0,0 +1,26 @@ +chr2L 800001 1550001 ID_0.01_1 0.022884658057 . 800001 1550001 31,120,180 +chr2L 1550001 2100001 ID_0.01_2 -0.744086372037 . 1550001 2100001 51,160,44 +chr2L 2100001 2400001 ID_0.01_3 0.311391232701 . 2100001 2400001 31,120,180 +chr2L 2400001 2750001 ID_0.01_4 0.078149036231 . 2400001 2750001 51,160,44 +chr2L 2750001 3700001 ID_0.01_5 -0.648971714281 . 2750001 3700001 31,120,180 +chr2L 3700001 4200001 ID_0.01_6 -0.133385571846 . 3700001 4200001 51,160,44 +chr2L 4200001 5050001 ID_0.01_7 -0.598347187435 . 4200001 5050001 31,120,180 +chr2L 5050001 5450001 ID_0.01_8 -0.589296128895 . 5050001 5450001 51,160,44 +chr2L 5450001 6550001 ID_0.01_9 -0.463215188679 . 5450001 6550001 31,120,180 +chr2L 6550001 7250001 ID_0.01_10 -0.739312227247 . 6550001 7250001 51,160,44 +chr2L 7250001 7650001 ID_0.01_11 -0.558267533146 . 7250001 7650001 31,120,180 +chr2L 7650001 8100001 ID_0.01_12 -0.164474310036 . 7650001 8100001 51,160,44 +chr2L 8100001 8950001 ID_0.01_13 -0.618832592666 . 8100001 8950001 31,120,180 +chr2L 8950001 10450001 ID_0.01_14 -0.547147684409 . 8950001 10450001 51,160,44 +chr2L 10450001 10800001 ID_0.01_15 -0.938748995456 . 10450001 10800001 31,120,180 +chr2L 10800001 11600001 ID_0.01_16 -0.305174734420 . 10800001 11600001 51,160,44 +chr2L 11600001 12300001 ID_0.01_17 -0.941807294590 . 11600001 12300001 31,120,180 +chr2L 12300001 12650001 ID_0.01_18 -0.124089226194 . 12300001 12650001 51,160,44 +chr2L 12650001 13150001 ID_0.01_19 -0.535969778416 . 12650001 13150001 31,120,180 +chr2L 13150001 13800001 ID_0.01_20 -0.246694822549 . 13150001 13800001 51,160,44 +chr2L 13800001 14200001 ID_0.01_21 -0.220174816848 . 13800001 14200001 31,120,180 +chr2L 14200001 15650001 ID_0.01_22 -0.512329343230 . 14200001 15650001 51,160,44 +chr2L 15650001 16250001 ID_0.01_23 -0.711741883911 . 15650001 16250001 31,120,180 +chr2L 16250001 17550001 ID_0.01_24 -0.917923384534 . 16250001 17550001 51,160,44 +chr2L 17550001 17850001 ID_0.01_25 -0.423222465610 . 17550001 17850001 31,120,180 +chr2L 17850001 18550001 ID_0.01_26 -0.274143371604 . 17850001 18550001 51,160,44 \ No newline at end of file
--- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 11:00:15 2023 +0000 @@ -1,6 +1,6 @@ chr1 1050000 1060000 chr1 1180000 1190000 0.001 chr1 1710000 1720000 chr1 1830000 1840000 0.001 -chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407133 +chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407 chr1 2120000 2130000 chr1 2310000 2320000 0.001 chr1 2120000 2130000 chr1 2480000 2490000 0.001 chr1 2130000 2140000 chr1 3570000 3580000 0.001 @@ -79,7 +79,7 @@ chr1 29200000 29210000 chr1 29520000 29530000 0.001 chr1 29210000 29220000 chr1 29360000 29370000 0.001 chr1 29560000 29570000 chr1 31180000 31190000 0.001 -chr1 29560000 29570000 chr1 30580000 30590000 0.00321287751564984 +chr1 29560000 29570000 chr1 30580000 30590000 0.0032128775156498 chr1 30260000 30270000 chr1 30850000 30860000 0.001 chr1 31270000 31280000 chr1 31380000 31390000 0.001 chr1 31650000 31660000 chr1 32010000 32020000 0.001 @@ -96,7 +96,7 @@ chr1 35910000 35920000 chr1 36190000 36200000 0.001 chr1 36030000 36040000 chr1 36180000 36190000 0.001 chr1 36610000 36620000 chr1 36750000 36760000 0.001 -chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961147 +chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961 chr1 37160000 37170000 chr1 37780000 37790000 0.001 chr1 38020000 38030000 chr1 38140000 38150000 0.001 chr1 38490000 38500000 chr1 39050000 39060000 0.001
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 11:00:15 2023 +0000 @@ -1,5 +1,5 @@ -# HiCExplorer hicValidateLocations 3.6 -# Overlap of loop file /tmp/tmpd80q3k6g/files/a/4/0/dataset_a40f2565-c94b-4e73-9b47-ec233d99bda8.dat with protein file /tmp/tmpd80q3k6g/files/7/1/1/dataset_7116b645-b87b-49a2-a957-3ebe53aba250.dat +# HiCExplorer hicValidateLocations 3.7.2 +# Overlap of loop file /tmp/tmpjjk1hb59/files/a/8/9/dataset_a8916559-7d4d-42e7-b157-fdc26b57c5e2.dat with protein file /tmp/tmpjjk1hb59/files/e/5/a/dataset_e5ab267d-b489-4abc-88ce-c408eadfd25b.dat # Protein peaks: 3097 Matched Loops: 530
--- a/test-data/raw_qc_report Tue Jan 10 18:43:10 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 11:00:15 2023 +0000 @@ -1,5 +1,5 @@ -File matrix.h5 +File matrix.cool Sequenced reads 983 Min rest. site distance 300 Max library insert size 1000 @@ -12,7 +12,7 @@ Low mapping quality 164 (16.68) # count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end GATC 1 (0.33) +dangling end GATC (restriction sequence GATC) 1 (0.33) self ligation (removed) 0 (0.00) One mate not close to rest site 0 (0.00) same fragment 84 (28.00)