Mercurial > repos > bgruening > hicexplorer_hicpca
changeset 16:77919cc3618e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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--- a/hicPCA.xml Tue Jan 10 18:56:55 2023 +0000 +++ b/hicPCA.xml Wed Oct 18 10:39:52 2023 +0000 @@ -7,11 +7,17 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && + mkdir output && @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext' @CHROMOSOME_LIST@ - --outputFileName pca1.$outputFormat pca2.$outputFormat + #set $eigenvectors = ' '.join([ '\'%s\'' % $eigenvector for $eigenvector in str($whichEigenvectors).split(' ') ]) + --whichEigenvectors $eigenvectors + + #set $eigenvectors_output = ' '.join([ '\'output/pca%s.%s\'' % ($eigenvector, $outputFormat) for $eigenvector in str($whichEigenvectors).split(' ') ]) + + --outputFileName $eigenvectors_output --format $outputFormat #if $ligation_factor: @@ -37,8 +43,6 @@ --obsexpMatrix obsexp.$matrix_h5_cooler.ext #end if - && mv pca1.$outputFormat pca1 - && mv pca2.$outputFormat pca2 #if $pearsonMatrix: && mv pearson.$matrix_h5_cooler.ext pearson #end if @@ -50,48 +54,45 @@ ]]> </command> <inputs> - <expand macro='matrix_h5_cooler_macro' /> - <param name='outputFormat' type='select' label="Output file format"> - <option value='bigwig' selected="true">bigwig</option> + <expand macro="matrix_h5_cooler_macro" /> + <param name="outputFormat" type="select" label="Output file format"> + <option value="bigwig" selected="true">bigwig</option> <option value="bedgraph">bedgraph</option> </param> <expand macro="chromosome_list" /> + <param argument="--whichEigenvectors" optional="true" type="text" value="1 2" label="Eigenvectors to compute" help= "Define the eigenvectors that should be computed as a list. For example 1 2 5 to compute the first, second and fifth eigenvetor." /> - <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation' /> - <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed' /> + <param name="ligation_factor" type="boolean" truevalue="--ligation_factor" label="Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation" /> + <param name="ignoreMaskedBins" type="boolean" truevalue="--ignoreMaskedBins" label="This option removes the masked bins before the PCA is computed" /> <conditional name="extra_track_conditional"> - <param name='extra_track_selection' label='Extra track type' type='select'> - <option value='' selected='true'>No track</option> - <option value='gene_density'>Gene density</option> - <option value='histon_mark'>Histon mark coverage</option> + <param name="extra_track_selection" label="Extra track type" type="select"> + <option value="" selected="true">No track</option> + <option value="gene_density">Gene density</option> + <option value="histon_mark">Histon mark coverage</option> </param> - <when value='gene_density' > - <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign' /> + <when value="gene_density" > + <param name="extraTrack" type="data" format="bed" label="Correlate PCA with e.g. gene density or histon marks to flip sign" /> </when> - <when value='histon_mark'> - <param name='extraTrack' type='data' format='bed,bigwig' label='Correlate PCA with e.g. gene density or histon marks to flip sign' /> - <param name='histonMarkType' type='select' label="Histon mark type"> - <option value='active' selected="true">active</option> + <when value="histon_mark"> + <param name="extraTrack" type="data" format="bed,bigwig" label="Correlate PCA with e.g. gene density or histon marks to flip sign" /> + <param name="histonMarkType" type="select" label="Histon mark type"> + <option value="active" selected="true">active</option> <option value="inactive">inactive</option> </param> </when> - <when value='' /> + <when value="" /> </conditional> - <param argument='--pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix' /> - <param argument='--obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix' /> + <param argument="--pearsonMatrix" type="boolean" truevalue="--pearsonMatrix" falsevalue="" label="Return internally used Pearson matrix" /> + <param argument="--obsexpMatrix" type="boolean" truevalue="--obsexpMatrix" falsevalue="" label="Return internally used observed / expected matrix" /> </inputs> <outputs> - <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1"> + <data format="bedgraph" name="pca"> + <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" /> <change_format> - <when input="outputFormat" value="bedgraph" format="bedgraph" /> - </change_format> - </data> - <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2"> - <change_format> - <when input="outputFormat" value="bedgraph" format="bedgraph" /> + <when input="outputFormat" value="bigwig" format="bigwig" /> </change_format> </data> @@ -109,17 +110,19 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="outputFormat" value="bigwig" /> <conditional name="extra_track_conditional"> <param name="extra_track_selection" value="" /> </conditional> + <output name="pca"> + <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + </output> - <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' /> - <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' /> </test> - <test> + <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="outputFormat" value="bigwig" /> <param name="ligation_factor" value="True" /> @@ -127,11 +130,13 @@ <conditional name="extra_track_conditional"> <param name="extra_track_selection" value="" /> </conditional> + <output name="pca"> + <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + </output> - <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' /> - <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' /> </test> - <test> + <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="outputFormat" value="bigwig" /> <param name="ignoreMaskedBins" value="True" /> @@ -140,10 +145,12 @@ <param name="extra_track_selection" value="" /> </conditional> - <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' /> - <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' /> + <output name="pca"> + <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + </output> </test> - <test> + <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <param name="outputFormat" value="bigwig" /> <conditional name="extra_track_conditional"> @@ -158,18 +165,20 @@ <param name="chromosomes" value="chrXHet" /> </repeat> - <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' /> - <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' /> + <output name="pca"> + <discovered_dataset designation="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + <discovered_dataset designation="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + </output> </test> - <test> + <test expect_num_outputs="3"> <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <param name="outputFormat" value="bigwig" /> <conditional name="extra_track_conditional"> <param name="extra_track_selection" value="" /> </conditional> - <param name='pearsonMatrix' value='True' /> - <param name='obsexpMatrix' value='True' /> + <param name="pearsonMatrix" value="True" /> + <param name="obsexpMatrix" value="True" /> <repeat name="chromosome_list"> <param name="chromosomes" value="chrX" /> @@ -178,17 +187,19 @@ <param name="chromosomes" value="chrXHet" /> </repeat> - <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' /> - <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' /> + <output name="pca"> + <discovered_dataset designation="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + <discovered_dataset designation="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" /> + </output> <output name="pearson_outfile" ftype="h5"> <assert_contents> - <has_h5_keys keys='intervals,matrix' /> + <has_h5_keys keys="intervals,matrix" /> </assert_contents> </output> <output name="obsexp_outfile" ftype="h5"> <assert_contents> - <has_h5_keys keys='intervals,matrix' /> + <has_h5_keys keys="intervals,matrix" /> </assert_contents> </output> </test> @@ -201,7 +212,7 @@ `Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments. **hicPCA** computes two eigenvector files based on the input matrix for an A / B compartment analysis following the computation steps detailed by `Lieberman-Aiden et al. (2009)`_: the transformation of the contact matrix -into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the Pearson correlation matrix gives the eigenvectors +into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the obs/exp matrix gives the eigenvectors and Lieberman-Aiden shows that the values of the eigenvectors correspond to the distribution of genes and with features of open and closed chromatin. In some cases the first principal component corresponds to the two chromosomes arms and the second eigenvector to the plaid pattern. Therefore always the first two principal components needs to be returned and investigated. @@ -228,7 +239,7 @@ | For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369 +.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/ ]]> </help> <expand macro="citations" /> </tool>
--- a/macros.xml Tue Jan 10 18:56:55 2023 +0000 +++ b/macros.xml Wed Oct 18 10:39:52 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 10:39:52 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 10:39:52 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 10:39:52 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 10:39:52 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 10:39:52 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 10:39:52 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 10:39:52 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 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0.000000000000 5.892229182196 2.000000000000 +chr1 14494000 14495000 Eya1 673.000000000000 194000 0.003268945022 0.000000000000 6.294126893758 2.200000000000 +chr1 14495000 14496000 Eya1 673.000000000000 195000 0.003268945022 0.000000000000 6.680269651133 2.200000000000 +chr1 14496000 14497000 Eya1 673.000000000000 196000 0.002971768202 0.000000000000 6.072972410121 2.000000000000 +chr1 14497000 14498000 Eya1 673.000000000000 197000 0.002080237741 0.000000000000 3.937080406684 1.400000000000 +chr1 14498000 14499000 Eya1 673.000000000000 198000 0.002971768202 0.000000000000 4.852424033528 2.000000000000 +chr1 14499000 14500000 Eya1 673.000000000000 199000 0.003343239227 0.000000000000 5.830530441735 2.250000000000 +chr1 14500000 14501000 Eya1 673.000000000000 200000 0.004457652303 0.000000000000 7.575723225668 3.000000000000
--- /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 10:39:52 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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0.000000000000 0.000000000000 +chr1 14185000 14186000 Eya1 832.000000000000 -115000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14186000 14187000 Eya1 832.000000000000 -114000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14187000 14188000 Eya1 832.000000000000 -113000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14188000 14189000 Eya1 832.000000000000 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14189000 14190000 Eya1 832.000000000000 -111000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14190000 14191000 Eya1 832.000000000000 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14191000 14192000 Eya1 832.000000000000 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14192000 14193000 Eya1 832.000000000000 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14193000 14194000 Eya1 832.000000000000 -107000 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14211000 14212000 Eya1 832.000000000000 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14212000 14213000 Eya1 832.000000000000 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14213000 14214000 Eya1 832.000000000000 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14214000 14215000 Eya1 832.000000000000 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14215000 14216000 Eya1 832.000000000000 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14216000 14217000 Eya1 832.000000000000 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14217000 14218000 Eya1 832.000000000000 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14218000 14219000 Eya1 832.000000000000 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14219000 14220000 Eya1 832.000000000000 -81000 0.000000000000 1.000000000000 0.000000000000 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832.000000000000 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14468000 14469000 Eya1 832.000000000000 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14469000 14470000 Eya1 832.000000000000 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14470000 14471000 Eya1 832.000000000000 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14471000 14472000 Eya1 832.000000000000 171000 0.000480769231 0.000000000000 0.659028767461 0.400000000000 +chr1 14472000 14473000 Eya1 832.000000000000 172000 0.000480769231 0.000000000000 0.618316565296 0.400000000000 +chr1 14473000 14474000 Eya1 832.000000000000 173000 0.000480769231 0.000000000000 0.630488151323 0.400000000000 +chr1 14474000 14475000 Eya1 832.000000000000 174000 0.000480769231 0.000000000000 0.667266626197 0.400000000000 +chr1 14475000 14476000 Eya1 832.000000000000 175000 0.000480769231 0.000000000000 0.690275820369 0.400000000000 +chr1 14476000 14477000 Eya1 832.000000000000 176000 0.000240384615 0.000000000000 0.340731894279 0.200000000000 +chr1 14477000 14478000 Eya1 832.000000000000 177000 0.000480769231 0.000000000000 0.727927229038 0.400000000000 +chr1 14478000 14479000 Eya1 832.000000000000 178000 0.000480769231 0.000000000000 0.755396181293 0.400000000000 +chr1 14479000 14480000 Eya1 832.000000000000 179000 0.000480769231 0.000000000000 0.769923031050 0.400000000000 +chr1 14480000 14481000 Eya1 832.000000000000 180000 0.000480769231 0.000000000000 0.812913656138 0.400000000000 +chr1 14481000 14482000 Eya1 832.000000000000 181000 0.000240384615 0.000000000000 0.408530587410 0.200000000000 +chr1 14482000 14483000 Eya1 832.000000000000 182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14483000 14484000 Eya1 832.000000000000 183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 +chr1 14484000 14485000 Eya1 832.000000000000 184000 0.000240384615 0.000000000000 0.390595098725 0.200000000000 +chr1 14485000 14486000 Eya1 832.000000000000 185000 0.000961538462 0.000000000000 1.539846062099 0.800000000000 +chr1 14486000 14487000 Eya1 832.000000000000 186000 0.000961538462 0.000000000000 1.703659471393 0.800000000000 +chr1 14487000 14488000 Eya1 832.000000000000 187000 0.000961538462 0.000000000000 1.731286381939 0.800000000000 +chr1 14488000 14489000 Eya1 832.000000000000 188000 0.001201923077 0.000000000000 2.140962437394 1.000000000000 +chr1 14489000 14490000 Eya1 832.000000000000 189000 0.001442307692 0.000000000000 2.793209135173 1.200000000000 +chr1 14490000 14491000 Eya1 832.000000000000 190000 0.000721153846 0.000000000000 1.404771845823 0.600000000000 +chr1 14491000 14492000 Eya1 832.000000000000 191000 0.001442307692 0.000000000000 2.669066506024 1.200000000000 +chr1 14492000 14493000 Eya1 832.000000000000 192000 0.002403846154 0.000000000000 4.399560174407 2.000000000000 +chr1 14493000 14494000 Eya1 832.000000000000 193000 0.002163461538 0.000000000000 4.289571172663 1.800000000000 +chr1 14494000 14495000 Eya1 832.000000000000 194000 0.001682692308 0.000000000000 3.239907320421 1.400000000000 +chr1 14495000 14496000 Eya1 832.000000000000 195000 0.002163461538 0.000000000000 4.421153111551 1.800000000000 +chr1 14496000 14497000 Eya1 832.000000000000 196000 0.001682692308 0.000000000000 3.438674642317 1.400000000000 +chr1 14497000 14498000 Eya1 832.000000000000 197000 0.001442307692 0.000000000000 2.729727108893 1.200000000000 +chr1 14498000 14499000 Eya1 832.000000000000 198000 0.002644230769 0.000000000000 4.317607586564 2.200000000000 +chr1 14499000 14500000 Eya1 832.000000000000 199000 0.003305288462 0.000000000000 5.764345200343 2.750000000000 +chr1 14500000 14501000 Eya1 832.000000000000 200000 0.003605769231 0.000000000000 6.127958811148 3.000000000000
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 18:56:55 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:39:52 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 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:39:52 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 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 10:39:52 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 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:39:52 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 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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 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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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1.0 1.0 -chrX 1420000 1430000 ID_0.01_598 -0.02902475 . 1.0 1.0 1.0 -chrX 1430000 1505000 ID_0.01_599 -0.017421 . 1.0 1.0 1.0 -chrX 1505000 1565000 ID_0.01_600 -0.00512525 . 1.0 1.0 1.0 -chrX 1565000 1590000 ID_0.01_601 0.0740305 . 1.0 1.0 1.0 -chrX 1590000 1750000 ID_0.01_602 0.06838375 . 1.0 1.0 1.0 -chrX 1750000 1785000 ID_0.01_603 -0.03990825 . 1.0 1.0 1.0 -chrX 1785000 1825000 ID_0.01_604 -0.05312125 . 1.0 1.0 1.0 -chrX 1825000 1890000 ID_0.01_605 -0.044828 . 1.0 1.0 1.0 -chrX 1890000 1970000 ID_0.01_606 -0.00133675 . 1.0 1.0 1.0 -chrX 1970000 2055000 ID_0.01_607 -0.05727125 . 1.0 1.0 1.0 -chrX 2055000 2095000 ID_0.01_608 -0.05727125 . 1.0 1.0 1.0 -chrX 2095000 2145000 ID_0.01_609 -0.041714 . 1.0 1.0 1.0 -chrX 2145000 2270000 ID_0.01_610 -0.06873975 . 1.0 1.0 1.0 -chrX 2270000 2340000 ID_0.01_611 -0.05920325 . 1.0 1.0 1.0 -chrX 2340000 2375000 ID_0.01_612 -0.0411735 . 1.0 1.0 1.0 -chrX 2375000 2465000 ID_0.01_613 -0.04582175 . 1.0 1.0 1.0 -chrX 2465000 2505000 ID_0.01_614 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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 6865000 6935000 ID_0.01_665 -0.04908775 . 1.0 1.0 1.0 -chrX 6935000 7145000 ID_0.01_666 -0.055925 . 1.0 1.0 1.0 -chrX 7145000 7215000 ID_0.01_667 -0.06873975 . 1.0 1.0 1.0 -chrX 7215000 7355000 ID_0.01_668 -0.06873975 . 1.0 1.0 1.0 -chrX 7355000 7420000 ID_0.01_669 -0.04076175 . 1.0 1.0 1.0 -chrX 7420000 7580000 ID_0.01_670 0.0143445 . 1.0 1.0 1.0 -chrX 7580000 7670000 ID_0.01_671 -0.06873975 . 1.0 1.0 1.0 -chrX 7670000 7735000 ID_0.01_672 -0.01522375 . 1.0 1.0 1.0 -chrX 7735000 7830000 ID_0.01_673 0.03931675 . 1.0 1.0 1.0 -chrX 7830000 7945000 ID_0.01_674 -0.055925 . 1.0 1.0 1.0 -chrX 7945000 8290000 ID_0.01_675 -0.06873975 . 1.0 1.0 1.0 -chrX 8290000 8365000 ID_0.01_676 -0.05644675 . 1.0 1.0 1.0 -chrX 8365000 8435000 ID_0.01_677 -0.03096525 . 1.0 1.0 1.0 -chrX 8435000 8505000 ID_0.01_678 -0.06873975 . 1.0 1.0 1.0 -chrX 8505000 8600000 ID_0.01_679 -0.06388975 . 1.0 1.0 1.0 -chrX 8600000 8745000 ID_0.01_680 -0.04374075 . 1.0 1.0 1.0 -chrX 8745000 9000000 ID_0.01_681 -0.0553685 . 1.0 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 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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 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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 -chr2R 3085000 3175000 ID_0.01_863 -0.0731445 . 1.0 1.0 1.0 -chr2R 3175000 3290000 ID_0.01_864 -0.05878075 . 1.0 1.0 1.0 -chr2R 3290000 3375000 ID_0.01_865 -0.01696725 . 1.0 1.0 1.0 -chr2R 3375000 3415000 ID_0.01_866 -0.0744495 . 1.0 1.0 1.0 -chr2R 3415000 3475000 ID_0.01_867 -0.05353175 . 1.0 1.0 1.0 -chr2R 3475000 3515000 ID_0.01_868 -0.05957825 . 1.0 1.0 1.0 -chr2R 3515000 3595000 ID_0.01_869 -0.06716425 . 1.0 1.0 1.0 -chr2R 3595000 3615000 ID_0.01_870 -0.084495 . 1.0 1.0 1.0 -chr2R 3615000 3665000 ID_0.01_871 -0.0779385 . 1.0 1.0 1.0 -chr2R 3665000 3715000 ID_0.01_872 -0.08312075 . 1.0 1.0 1.0 -chr2R 3715000 3785000 ID_0.01_873 -0.100358 . 1.0 1.0 1.0 -chr2R 3785000 3810000 ID_0.01_874 -0.06729025 . 1.0 1.0 1.0 -chr2R 3810000 3850000 ID_0.01_875 -0.0448405 . 1.0 1.0 1.0 -chr2R 3850000 3890000 ID_0.01_876 -0.038473 . 1.0 1.0 1.0 -chr2R 3890000 3960000 ID_0.01_877 -0.06617275 . 1.0 1.0 1.0 -chr2R 3960000 3990000 ID_0.01_878 -0.072878 . 1.0 1.0 1.0 -chr2R 3990000 4045000 ID_0.01_879 -0.0701055 . 1.0 1.0 1.0 -chr2R 4045000 4070000 ID_0.01_880 -0.06933775 . 1.0 1.0 1.0 -chr2R 4070000 4145000 ID_0.01_881 -0.06263575 . 1.0 1.0 1.0 -chr2R 4145000 4170000 ID_0.01_882 0.009935 . 1.0 1.0 1.0 -chr2R 4170000 4255000 ID_0.01_883 -0.00889125 . 1.0 1.0 1.0 -chr2R 4255000 4275000 ID_0.01_884 -0.00908825 . 1.0 1.0 1.0 -chr2R 4275000 4320000 ID_0.01_885 -0.00831525 . 1.0 1.0 1.0 -chr2R 4320000 4470000 ID_0.01_886 0.035654 . 1.0 1.0 1.0 -chr2R 4470000 4540000 ID_0.01_887 -0.0553405 . 1.0 1.0 1.0 -chr2R 4540000 4655000 ID_0.01_888 -0.04982025 . 1.0 1.0 1.0 -chr2R 4655000 4775000 ID_0.01_889 -0.0096625 . 1.0 1.0 1.0 -chr2R 4775000 4830000 ID_0.01_890 0.032808 . 1.0 1.0 1.0 -chr2R 4830000 4875000 ID_0.01_891 -0.01447775 . 1.0 1.0 1.0 -chr2R 4875000 4915000 ID_0.01_892 -0.05841325 . 1.0 1.0 1.0 -chr2R 4915000 4985000 ID_0.01_893 -0.057465 . 1.0 1.0 1.0 -chr2R 4985000 5060000 ID_0.01_894 -0.064272 . 1.0 1.0 1.0 -chr2R 5060000 5195000 ID_0.01_895 -0.100123 . 1.0 1.0 1.0 -chr2R 5195000 5330000 ID_0.01_896 0.003422 . 1.0 1.0 1.0 -chr2R 5330000 5355000 ID_0.01_897 -0.01467775 . 1.0 1.0 1.0 -chr2R 5355000 5450000 ID_0.01_898 -0.02147775 . 1.0 1.0 1.0 -chr2R 5450000 5545000 ID_0.01_899 -0.0567315 . 1.0 1.0 1.0 -chr2R 5545000 5580000 ID_0.01_900 -0.0327795 . 1.0 1.0 1.0 -chr2R 5580000 5720000 ID_0.01_901 -0.03009575 . 1.0 1.0 1.0 -chr2R 5720000 5845000 ID_0.01_902 -0.0983935 . 1.0 1.0 1.0 -chr2R 5845000 6000000 ID_0.01_903 -0.0755875 . 1.0 1.0 1.0 -chr2R 6000000 6120000 ID_0.01_904 -0.09680125 . 1.0 1.0 1.0 -chr2R 6120000 6285000 ID_0.01_905 -0.038396 . 1.0 1.0 1.0 -chr2R 6285000 6305000 ID_0.01_906 0.01654825 . 1.0 1.0 1.0 -chr2R 6305000 6455000 ID_0.01_907 0.017505 . 1.0 1.0 1.0 -chr2R 6455000 6500000 ID_0.01_908 -0.02162925 . 1.0 1.0 1.0 -chr2R 6500000 6630000 ID_0.01_909 -0.071321 . 1.0 1.0 1.0 -chr2R 6630000 6720000 ID_0.01_910 -0.05926 . 1.0 1.0 1.0 -chr2R 6720000 6785000 ID_0.01_911 -0.08033825 . 1.0 1.0 1.0 -chr2R 6785000 6870000 ID_0.01_912 -0.1052695 . 1.0 1.0 1.0 -chr2R 6870000 6895000 ID_0.01_913 -0.06038725 . 1.0 1.0 1.0 -chr2R 6895000 7025000 ID_0.01_914 -0.07233 . 1.0 1.0 1.0 -chr2R 7025000 7050000 ID_0.01_915 0.0061175 . 1.0 1.0 1.0 -chr2R 7050000 7185000 ID_0.01_916 0.00824475 . 1.0 1.0 1.0 -chr2R 7185000 7300000 ID_0.01_917 -0.07265075 . 1.0 1.0 1.0 -chr2R 7300000 7475000 ID_0.01_918 -0.0765185 . 1.0 1.0 1.0 -chr2R 7475000 7560000 ID_0.01_919 0.00986175 . 1.0 1.0 1.0 -chr2R 7560000 7600000 ID_0.01_920 -0.06929 . 1.0 1.0 1.0 -chr2R 7600000 7735000 ID_0.01_921 -0.0675465 . 1.0 1.0 1.0 -chr2R 7735000 7790000 ID_0.01_922 -0.03059125 . 1.0 1.0 1.0 -chr2R 7790000 7910000 ID_0.01_923 -0.04697575 . 1.0 1.0 1.0 -chr2R 7910000 8025000 ID_0.01_924 0.01008175 . 1.0 1.0 1.0 -chr2R 8025000 8135000 ID_0.01_925 -0.079754 . 1.0 1.0 1.0 -chr2R 8135000 8215000 ID_0.01_926 0.0761755 . 1.0 1.0 1.0 -chr2R 8215000 8225000 ID_0.01_927 0.0145305 . 1.0 1.0 1.0 -chr2R 8225000 8325000 ID_0.01_928 0.04205975 . 1.0 1.0 1.0 -chr2R 8325000 8340000 ID_0.01_929 -0.06201275 . 1.0 1.0 1.0 -chr2R 8340000 8555000 ID_0.01_930 -0.06089675 . 1.0 1.0 1.0 -chr2R 8555000 8640000 ID_0.01_931 -0.08516325 . 1.0 1.0 1.0 -chr2R 8640000 8715000 ID_0.01_932 -0.05181275 . 1.0 1.0 1.0 -chr2R 8715000 8830000 ID_0.01_933 -0.07001 . 1.0 1.0 1.0 -chr2R 8830000 8950000 ID_0.01_934 -0.09537375 . 1.0 1.0 1.0 -chr2R 8950000 9040000 ID_0.01_935 -0.102756 . 1.0 1.0 1.0 -chr2R 9040000 9110000 ID_0.01_936 -0.05077875 . 1.0 1.0 1.0 -chr2R 9110000 9230000 ID_0.01_937 -0.0870745 . 1.0 1.0 1.0 -chr2R 9230000 9300000 ID_0.01_938 0.0546225 . 1.0 1.0 1.0 -chr2R 9300000 9440000 ID_0.01_939 -0.07234375 . 1.0 1.0 1.0 -chr2R 9440000 9500000 ID_0.01_940 -0.01500425 . 1.0 1.0 1.0 -chr2R 9500000 9690000 ID_0.01_941 -0.04233375 . 1.0 1.0 1.0 -chr2R 9690000 9755000 ID_0.01_942 -0.04501625 . 1.0 1.0 1.0 -chr2R 9755000 9840000 ID_0.01_943 0.00135075 . 1.0 1.0 1.0 -chr2R 9840000 9910000 ID_0.01_944 -0.05264025 . 1.0 1.0 1.0 -chr2R 9910000 10060000 ID_0.01_945 -0.06264125 . 1.0 1.0 1.0 -chr2R 10060000 10185000 ID_0.01_946 -0.09217875 . 1.0 1.0 1.0 -chr2R 10185000 10210000 ID_0.01_947 -0.097835 . 1.0 1.0 1.0 -chr2R 10210000 10390000 ID_0.01_948 -0.0976975 . 1.0 1.0 1.0 -chr2R 10390000 10410000 ID_0.01_949 -0.0279585 . 1.0 1.0 1.0 -chr2R 10410000 10510000 ID_0.01_950 -0.0029855 . 1.0 1.0 1.0 -chr2R 10510000 10605000 ID_0.01_951 -0.04224275 . 1.0 1.0 1.0 -chr2R 10605000 10680000 ID_0.01_952 -0.05759525 . 1.0 1.0 1.0 -chr2R 10680000 10730000 ID_0.01_953 -0.05716625 . 1.0 1.0 1.0 -chr2R 10730000 10795000 ID_0.01_954 -0.046105 . 1.0 1.0 1.0 -chr2R 10795000 10915000 ID_0.01_955 -0.0852145 . 1.0 1.0 1.0 -chr2R 10915000 11015000 ID_0.01_956 -0.06458275 . 1.0 1.0 1.0 -chr2R 11015000 11050000 ID_0.01_957 0.02882475 . 1.0 1.0 1.0 -chr2R 11050000 11080000 ID_0.01_958 0.01121875 . 1.0 1.0 1.0 -chr2R 11080000 11115000 ID_0.01_959 -0.0504035 . 1.0 1.0 1.0 -chr2R 11115000 11170000 ID_0.01_960 -0.0388235 . 1.0 1.0 1.0 -chr2R 11170000 11215000 ID_0.01_961 -0.06728375 . 1.0 1.0 1.0 -chr2R 11215000 11325000 ID_0.01_962 -0.0353375 . 1.0 1.0 1.0 -chr2R 11325000 11375000 ID_0.01_963 0.03372075 . 1.0 1.0 1.0 -chr2R 11375000 11420000 ID_0.01_964 0.01379025 . 1.0 1.0 1.0 -chr2R 11420000 11505000 ID_0.01_965 -0.0516025 . 1.0 1.0 1.0 -chr2R 11505000 11590000 ID_0.01_966 -0.07983725 . 1.0 1.0 1.0 -chr2R 11590000 11660000 ID_0.01_967 -0.063507 . 1.0 1.0 1.0 -chr2R 11660000 11715000 ID_0.01_968 -0.0660395 . 1.0 1.0 1.0 -chr2R 11715000 11835000 ID_0.01_969 -0.07628875 . 1.0 1.0 1.0 -chr2R 11835000 11885000 ID_0.01_970 -0.03699875 . 1.0 1.0 1.0 -chr2R 11885000 11990000 ID_0.01_971 -0.0252265 . 1.0 1.0 1.0 -chr2R 11990000 12025000 ID_0.01_972 -0.08639 . 1.0 1.0 1.0 -chr2R 12025000 12105000 ID_0.01_973 -0.09129175 . 1.0 1.0 1.0 -chr2R 12105000 12260000 ID_0.01_974 -0.0914255 . 1.0 1.0 1.0 -chr2R 12260000 12345000 ID_0.01_975 -0.0480015 . 1.0 1.0 1.0 -chr2R 12345000 12450000 ID_0.01_976 -0.0352425 . 1.0 1.0 1.0 -chr2R 12450000 12580000 ID_0.01_977 -0.10245475 . 1.0 1.0 1.0 -chr2R 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 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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 -chr3R 15935000 16115000 ID_0.01_1268 0.06661075 . 1.0 1.0 1.0 -chr3R 16115000 16155000 ID_0.01_1269 -0.087499 . 1.0 1.0 1.0 -chr3R 16155000 16295000 ID_0.01_1270 -0.0530865 . 1.0 1.0 1.0 -chr3R 16295000 16350000 ID_0.01_1271 0.05583375 . 1.0 1.0 1.0 -chr3R 16350000 16445000 ID_0.01_1272 0.02853525 . 1.0 1.0 1.0 -chr3R 16445000 16565000 ID_0.01_1273 -0.094774 . 1.0 1.0 1.0 -chr3R 16565000 16670000 ID_0.01_1274 -0.07276575 . 1.0 1.0 1.0 -chr3R 16670000 16700000 ID_0.01_1275 -0.067027 . 1.0 1.0 1.0 -chr3R 16700000 16770000 ID_0.01_1276 -0.05248575 . 1.0 1.0 1.0 -chr3R 16770000 16805000 ID_0.01_1277 -0.036296 . 1.0 1.0 1.0 -chr3R 16805000 16910000 ID_0.01_1278 -0.0365275 . 1.0 1.0 1.0 -chr3R 16910000 17105000 ID_0.01_1279 -0.11469275 . 1.0 1.0 1.0 -chr3R 17105000 17215000 ID_0.01_1280 -0.05478675 . 1.0 1.0 1.0 -chr3R 17215000 17315000 ID_0.01_1281 -0.07937775 . 1.0 1.0 1.0 -chr3R 17315000 17425000 ID_0.01_1282 -0.017845 . 1.0 1.0 1.0 -chr3R 17425000 17490000 ID_0.01_1283 -0.072665 . 1.0 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 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21820000 21845000 ID_0.01_1342 -0.00145975 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 21845000 21950000 ID_0.01_1343 0.0360515 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 21950000 21990000 ID_0.01_1344 0.002742 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 21990000 22075000 ID_0.01_1345 0.00713375 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22075000 22220000 ID_0.01_1346 -0.087915 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22220000 22270000 ID_0.01_1347 0.0614505 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22270000 22310000 ID_0.01_1348 -0.02575325 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22310000 22380000 ID_0.01_1349 -0.04946475 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22380000 22500000 ID_0.01_1350 -0.055847 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22500000 22520000 ID_0.01_1351 -0.0631105 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22520000 22605000 ID_0.01_1352 -0.062648 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22605000 22695000 ID_0.01_1353 -0.011252 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22695000 22780000 ID_0.01_1354 -0.089033 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22780000 22885000 ID_0.01_1355 -0.04050025 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22885000 22985000 ID_0.01_1356 -0.05683475 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 22985000 23110000 ID_0.01_1357 -0.0237815 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23110000 23185000 ID_0.01_1358 -0.100625 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23185000 23195000 ID_0.01_1359 -0.00294725 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23195000 23415000 ID_0.01_1360 -0.00275775 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23415000 23560000 ID_0.01_1361 -0.090027 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23560000 23770000 ID_0.01_1362 -0.104602 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23770000 23815000 ID_0.01_1363 -0.1119105 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23815000 23920000 ID_0.01_1364 -0.0660765 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 23920000 24030000 ID_0.01_1365 -0.04218475 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24030000 24160000 ID_0.01_1366 -0.05579575 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24160000 24205000 ID_0.01_1367 -0.01546725 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24205000 24345000 ID_0.01_1368 -0.0326015 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24345000 24375000 ID_0.01_1369 -0.0623065 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24375000 24450000 ID_0.01_1370 -0.0749395 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24450000 24625000 ID_0.01_1371 -0.09836075 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24625000 24745000 ID_0.01_1372 -0.03171375 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24745000 24885000 ID_0.01_1373 -0.08589625 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24885000 24995000 ID_0.01_1374 -0.09323725 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 24995000 25090000 ID_0.01_1375 -0.0589785 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25090000 25165000 ID_0.01_1376 0.03674225 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25165000 25330000 ID_0.01_1377 -0.0462465 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25330000 25405000 ID_0.01_1378 -0.08303325 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25405000 25570000 ID_0.01_1379 -0.00546225 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25570000 25580000 ID_0.01_1380 -0.04654075 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25580000 25730000 ID_0.01_1381 -0.01871575 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25730000 25880000 ID_0.01_1382 -0.00858875 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25880000 25990000 ID_0.01_1383 -0.10581625 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 25990000 26050000 ID_0.01_1384 -0.090403 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26050000 26180000 ID_0.01_1385 -0.0935315 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26180000 26275000 ID_0.01_1386 -0.11469275 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26275000 26330000 ID_0.01_1387 -0.1002735 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26330000 26490000 ID_0.01_1388 -0.092304 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26490000 26565000 ID_0.01_1389 0.0627965 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26565000 26640000 ID_0.01_1390 -0.01974475 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26640000 26715000 ID_0.01_1391 -0.07430725 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26715000 26870000 ID_0.01_1392 -0.049789 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 26870000 27045000 ID_0.01_1393 -0.0249905 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27045000 27155000 ID_0.01_1394 -0.074189 . 1.0 1.0 1.0 0.0 0.0 0.0 +chr3R 27155000 27185000 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 18:56:55 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:39:52 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 10:39:52 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 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:39:52 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 21125000 1 22350000 22375000 0.001 1 21310000 21315000 1 21520000 21525000 0.001 1 21360000 21370000 1 21470000 21480000 0.001 -1 21575000 21600000 1 21675000 21700000 0.0010553575253769206 +1 21575000 21600000 1 21675000 21700000 0.0010553575253769 1 21900000 21910000 1 22900000 22910000 0.001 1 21930000 21940000 1 22690000 22700000 0.001 1 22020000 22030000 1 22280000 22290000 0.001 @@ -203,11 +203,11 @@ 1 29550000 29575000 1 31175000 31200000 0.001 1 29560000 29570000 1 30840000 30850000 0.001 1 29560000 29570000 1 30310000 30320000 0.001 -1 29560000 29570000 1 30580000 30590000 0.00321287751564984 +1 29560000 29570000 1 30580000 30590000 0.0032128775156498 1 29780000 29790000 1 30840000 30850000 0.001 1 29870000 29880000 1 30020000 30030000 0.001 1 29870000 29880000 1 31120000 31130000 0.001 -1 30030000 30040000 1 31120000 31130000 0.001105560265853574 +1 30030000 30040000 1 31120000 31130000 0.0011055602658535 1 30260000 30270000 1 30850000 30860000 0.001 1 30260000 30270000 1 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--- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:39:52 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 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:39:52 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 18:56:55 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 10:39:52 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)