| Previous changeset 7:8ad23dfdaabb (2023-01-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 |
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modified:
hicNormalize.xml macros.xml test-data/cHi-C/chicQualityControl/histogram.png test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report test-data/cHi-C/chicQualityControl/sparsity.png test-data/cHi-C/referencePoints_chicViewpoint.bed test-data/distVsCounts.txt test-data/hicConvertFormat/small_test_matrix_chr4.homer test-data/hicDifferentialTAD/accepted.txt test-data/hicDifferentialTAD/rejected.txt test-data/hicInfo/hicInfo_output.txt test-data/hicMergeLoops/gm12878_all.bedgraph test-data/hicPCA/pca1_test1.bw test-data/hicPCA/pca1_test2.bw test-data/hicPCA/pca1_test3.bw test-data/hicPCA/pca2_test1.bw test-data/hicPCA/pca2_test2.bw test-data/hicPCA/pca2_test3.bw test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotMatrix/plot2.pdf test-data/hicPlotMatrix/plot3_pca.svg test-data/hicPlotSVL/p_values.txt test-data/hicPlotSVL/plot.png test-data/hicPlotSVL/ratios.txt test-data/hicQuickQC/QC.log test-data/hicValidateLocations/overlap_smc3_matched_locations test-data/hicValidateLocations/overlap_smc3_statistics test-data/raw_qc_report |
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added:
test-data/cHi-C/aggregate.tar.gz test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 test-data/cHi-C/chicDifferentialTest/differential.hdf5 test-data/cHi-C/chicExportData/aggregate.tar.gz test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 test-data/cHi-C/chicViewpoint/two_matrices.hdf5 test-data/cHi-C/hg19.chrom.sizes test-data/cHi-C/plots.tar.gz test-data/cHi-C/target_list.bed test-data/hicCompartmentsPolarization/output_matrix.npz test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt test-data/hicConvertFormat/hg19.chrom.sizes test-data/hicConvertFormat/small_test_matrix_chr4.bed test-data/hicConvertFormat/small_test_matrix_chr4.hicpro test-data/hicInterIntraTAD/matrix.cool test-data/hicInterIntraTAD/output.txt test-data/hicInterIntraTAD/plot.png test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed test-data/hicTADClassifier/predicted.txt test-data/hicTADClassifier/predicted_second_classifier.txt test-data/hicTADClassifier/unittest_classifier.BIN test-data/hicTrainTADClassifier/model.BIN test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed test-data/hicTrainTADClassifier/small_test_matrix.cool |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb hicNormalize.xml --- a/hicNormalize.xml Tue Jan 10 18:40:25 2023 +0000 +++ b/hicNormalize.xml Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -28,23 +28,23 @@ ]]> </command> <inputs> - <expand macro='matrix_h5_cooler_multiple_macro' /> + <expand macro="matrix_h5_cooler_multiple_macro" /> <conditional name="normalize_conditional"> - <param name='normalize' type='select' label='Normalize matrices'> - <option value='norm_range'>0 to 1 range</option> - <option value='smallest'>Smallest read count</option> - <option value='multiplicative'>Multiply by value</option> + <param name="normalize" type="select" label="Normalize matrices"> + <option value="norm_range">0 to 1 range</option> + <option value="smallest">Smallest read count</option> + <option value="multiplicative">Multiply by value</option> </param> - <when value='norm_range' /> - <when value='smallest' /> - <when value='multiplicative'> + <when value="norm_range" /> + <when value="smallest" /> + <when value="multiplicative"> <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value" /> </when> </conditional> - <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero" /> + <param name="zero_threshold_value" type="float" value="1.0" optional="True" label="Set values below this threshold to zero" /> </inputs> <outputs> - <data format='cool' name="normalize_matrix"> + <data format="cool" name="normalize_matrix"> <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" /> <change_format> <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" /> @@ -54,7 +54,7 @@ <tests> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" /> - <param name='normalize' value='norm_range' /> + <param name="normalize" value="norm_range" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> <assert_contents> @@ -65,7 +65,7 @@ </test> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" /> - <param name='normalize' value='smallest' /> + <param name="normalize" value="smallest" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool"> <assert_contents> @@ -81,7 +81,7 @@ </test> <test> <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" /> - <param name='normalize' value='smallest' /> + <param name="normalize" value="smallest" /> <output name="normalize_matrix"> <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5"> <assert_contents> @@ -115,7 +115,7 @@ | 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> |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb macros.xml --- a/macros.xml Tue Jan 10 18:40:25 2023 +0000 +++ b/macros.xml Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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@"> |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate.tar.gz |
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| Binary file test-data/cHi-C/aggregate.tar.gz has changed |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt --- /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 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicDifferentialTest/differential.hdf5 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicExportData/aggregate.tar.gz |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt --- /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 10:21:43 2023 +0000 |
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| b'@@ -0,0 +1,402 @@\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+chr1\t14100000\t14101000\tEya1\t673.000000000000\t-200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.000000000000\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.000000000000\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.000000000000\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.000000000000\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.000000000000\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.000000000000\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.000000000000\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.000000000000\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.000000000000\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.000000000000\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.000000000000\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.000000000000\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.000000000000\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.000000000000\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.000000000000\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.000000000000\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.000000000000\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.000000000000\t-182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.000000000000\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.000000000000\t-180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.000000000000\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.000000000000\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.000000000000\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.000000000000\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.000000000000\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.000000000000\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.000000000000\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.000000000000\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.000000000000\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.000000000000\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.000000000000\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.000000000000\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.000000000000\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.0000000000'..b'.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.000000000000\t166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.000000000000\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.000000000000\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.000000000000\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.000000000000\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.000000000000\t171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.000000000000\t172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.000000000000\t173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.000000000000\t174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.000000000000\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.000000000000\t176000\t0.000297176820\t0.000000000000\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.000000000000\t177000\t0.000297176820\t0.000000000000\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.000000000000\t178000\t0.000594353640\t0.000000000000\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.000000000000\t179000\t0.000594353640\t0.000000000000\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.000000000000\t180000\t0.001485884101\t0.000000000000\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.000000000000\t181000\t0.001188707281\t0.000000000000\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.000000000000\t182000\t0.001188707281\t0.000000000000\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.000000000000\t183000\t0.001783060921\t0.000000000000\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.000000000000\t184000\t0.002080237741\t0.000000000000\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.000000000000\t185000\t0.001188707281\t0.000000000000\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.000000000000\t186000\t0.001188707281\t0.000000000000\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.000000000000\t187000\t0.001188707281\t0.000000000000\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.000000000000\t188000\t0.000594353640\t0.000000000000\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.000000000000\t189000\t0.000297176820\t0.000000000000\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.000000000000\t190000\t0.000297176820\t0.000000000000\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.000000000000\t191000\t0.002080237741\t0.000000000000\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.000000000000\t192000\t0.003268945022\t0.000000000000\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.000000000000\t193000\t0.002971768202\t0.000000000000\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.000000000000\t194000\t0.003268945022\t0.000000000000\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.000000000000\t195000\t0.003268945022\t0.000000000000\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.000000000000\t196000\t0.002971768202\t0.000000000000\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.000000000000\t197000\t0.002080237741\t0.000000000000\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.000000000000\t198000\t0.002971768202\t0.000000000000\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.000000000000\t199000\t0.003343239227\t0.000000000000\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.000000000000\t200000\t0.004457652303\t0.000000000000\t7.575723225668\t3.000000000000\n' |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig |
| b |
| Binary file test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig has changed |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt --- /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 10:21:43 2023 +0000 |
| b |
| b'@@ -0,0 +1,402 @@\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+chr1\t14100000\t14101000\tEya1\t832.000000000000\t-200000\t0.000400641026\t0.028365821799\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.000000000000\t-199000\t0.000300480769\t0.036748857670\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.000000000000\t-198000\t0.000240384615\t0.042850447268\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.000000000000\t-197000\t0.000240384615\t0.042850447268\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.000000000000\t-196000\t0.000240384615\t0.042850447268\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.000000000000\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.000000000000\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.000000000000\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.000000000000\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.000000000000\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.000000000000\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.000000000000\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.000000000000\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.000000000000\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.000000000000\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.000000000000\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.000000000000\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.000000000000\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.000000000000\t-182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.000000000000\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.000000000000\t-180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.000000000000\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.000000000000\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.000000000000\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.000000000000\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.000000000000\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.000000000000\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.000000000000\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.000000000000\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.000000000000\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.000000000000\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.000000000000\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.000000000000\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.000000000000\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.0000000000'..b'.000000000000\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.000000000000\t166000\t0.000240384615\t0.000000000000\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.000000000000\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.000000000000\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.000000000000\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.000000000000\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.000000000000\t171000\t0.000480769231\t0.000000000000\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.000000000000\t172000\t0.000480769231\t0.000000000000\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.000000000000\t173000\t0.000480769231\t0.000000000000\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.000000000000\t174000\t0.000480769231\t0.000000000000\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.000000000000\t175000\t0.000480769231\t0.000000000000\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.000000000000\t176000\t0.000240384615\t0.000000000000\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.000000000000\t177000\t0.000480769231\t0.000000000000\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.000000000000\t178000\t0.000480769231\t0.000000000000\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.000000000000\t179000\t0.000480769231\t0.000000000000\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.000000000000\t180000\t0.000480769231\t0.000000000000\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.000000000000\t181000\t0.000240384615\t0.000000000000\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.000000000000\t182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.000000000000\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.000000000000\t184000\t0.000240384615\t0.000000000000\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.000000000000\t185000\t0.000961538462\t0.000000000000\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.000000000000\t186000\t0.000961538462\t0.000000000000\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.000000000000\t187000\t0.000961538462\t0.000000000000\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.000000000000\t188000\t0.001201923077\t0.000000000000\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.000000000000\t189000\t0.001442307692\t0.000000000000\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.000000000000\t190000\t0.000721153846\t0.000000000000\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.000000000000\t191000\t0.001442307692\t0.000000000000\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.000000000000\t192000\t0.002403846154\t0.000000000000\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.000000000000\t193000\t0.002163461538\t0.000000000000\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.000000000000\t194000\t0.001682692308\t0.000000000000\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.000000000000\t195000\t0.002163461538\t0.000000000000\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.000000000000\t196000\t0.001682692308\t0.000000000000\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.000000000000\t197000\t0.001442307692\t0.000000000000\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.000000000000\t198000\t0.002644230769\t0.000000000000\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.000000000000\t199000\t0.003305288462\t0.000000000000\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.000000000000\t200000\t0.003605769231\t0.000000000000\t6.127958811148\t3.000000000000\n' 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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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. |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/hg19.chrom.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/hg19.chrom.sizes Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/referencePoints_chicViewpoint.bed --- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/cHi-C/target_list.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/target_list.bed Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/distVsCounts.txt --- a/test-data/distVsCounts.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 10:21:43 2023 +0000 |
| b |
| b'@@ -1,600 +1,600 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\t27870\t1.0\n+551\tsmall_test_matrix_h5\tall\t2760000\t7.178235589692053e-05\t27862\t1.0\n+552\tsmall_test_matrix_h5\tall\t2765000\t0.00014360594528613484\t27854\t1.0\n+553\tsmall_test_matrix_h5\tall\t2770000\t0.00025138260432378077\t27846\t1.0\n+554\tsmall_test_matrix_h5\tall\t2775000\t0.00014368848336805806\t27838\t1.0\n+555\tsmall_test_matrix_h5\tall\t2780000\t0.00014372978799856272\t27830\t1.0\n+556\tsmall_test_matrix_h5\tall\t2785000\t0.0001437711163827187\t27822\t1.0\n+557\tsmall_test_matrix_h5\tall\t2790000\t0.00025167181994678936\t27814\t1.0\n+558\tsmall_test_matrix_h5\tall\t2795000\t0.0001438538444939941\t27806\t1.0\n+559\tsmall_test_matrix_h5\tall\t2800000\t0.00010792143319663285\t27798\t1.0\n+560\tsmall_test_matrix_h5\tall\t2805000\t0.00021590500179920834\t27790\t1.0\n+561\tsmall_test_matrix_h5\tall\t2810000\t0.00017997264415808796\t27782\t1.0\n+562\tsmall_test_matrix_h5\tall\t2815000\t3.600489666594657e-05\t27774\t1.0\n+563\tsmall_test_matrix_h5\tall\t2820000\t0.0002160916228480876\t27766\t1.0\n+564\tsmall_test_matrix_h5\tall\t2825000\t0.000144102601051949\t27758\t1.0\n+565\tsmall_test_matrix_h5\tall\t2830000\t0.00014414414414414415\t27750\t1.0\n+566\tsmall_test_matrix_h5\tall\t2835000\t0.0002523249945930358\t27742\t1.0\n+567\tsmall_test_matrix_h5\tall\t2840000\t0.00018028412778538978\t27734\t1.0\n+568\tsmall_test_matrix_h5\tall\t2845000\t0.00010820168794633196\t27726\t1.0\n+569\tsmall_test_matrix_h5\tall\t2850000\t0.00018038819539649325\t27718\t1.0\n+570\tsmall_test_matrix_h5\tall\t2855000\t7.217610970768675e-05\t27710\t1.0\n+571\tsmall_test_matrix_h5\tall\t2860000\t0.0003248862897985705\t27702\t1.0\n+572\tsmall_test_matrix_h5\tall\t2865000\t0.00018054452227919405\t27694\t1.0\n+573\tsmall_test_matrix_h5\tall\t2870000\t0.0002889547063497797\t27686\t1.0\n+574\tsmall_test_matrix_h5\tall\t2875000\t0.00036129778163162076\t27678\t1.0\n+575\tsmall_test_matrix_h5\tall\t2880000\t0.00014456089627755693\t27670\t1.0\n+576\tsmall_test_matrix_h5\tall\t2890000\t0.00021696680407897592\t27654\t1.0\n+577\tsmall_test_matrix_h5\tall\t2895000\t0.0001808579903060117\t27646\t1.0\n+578\tsmall_test_matrix_h5\tall\t2900000\t7.236413633403285e-05\t27638\t1.0\n+579\tsmall_test_matrix_h5\tall\t2905000\t0.0002533478103510677\t27630\t1.0\n+580\tsmall_test_matrix_h5\tall\t2910000\t0.00010860907971906451\t27622\t1.0\n+581\tsmall_test_matrix_h5\tall\t2915000\t0.00010864054465126386\t27614\t1.0\n+582\tsmall_test_matrix_h5\tall\t2920000\t0.00021734405564007825\t27606\t1.0\n+583\tsmall_test_matrix_h5\tall\t2925000\t0.00010870352924124937\t27598\t1.0\n+584\tsmall_test_matrix_h5\tall\t2930000\t0.0001812250815512867\t27590\t1.0\n+585\tsmall_test_matrix_h5\tall\t2935000\t0.00010876658690450294\t27582\t1.0\n+586\tsmall_test_matrix_h5\tall\t2940000\t0.00014506419090447523\t27574\t1.0\n+587\tsmall_test_matrix_h5\tall\t2945000\t0.000290212580715374\t27566\t1.0\n+588\tsmall_test_matrix_h5\tall\t2950000\t0.0001451484142535743\t27558\t1.0\n+589\tsmall_test_matrix_h5\tall\t2955000\t0.00025408348457350274\t27550\t1.0\n+590\tsmall_test_matrix_h5\tall\t2960000\t0.00010892455159392927\t27542\t1.0\n+591\tsmall_test_matrix_h5\tall\t2965000\t7.263746640517178e-05\t27534\t1.0\n+592\tsmall_test_matrix_h5\tall\t2970000\t3.6329288672527794e-05\t27526\t1.0\n+593\tsmall_test_matrix_h5\tall\t2975000\t7.26797005596337e-05\t27518\t1.0\n+594\tsmall_test_matrix_h5\tall\t2980000\t0.00010905125408942203\t27510\t1.0\n+595\tsmall_test_matrix_h5\tall\t2985000\t0.00021816595156715876\t27502\t1.0\n+596\tsmall_test_matrix_h5\tall\t2990000\t0.00010911471593802284\t27494\t1.0\n+597\tsmall_test_matrix_h5\tall\t2995000\t0.00014552863275849522\t27486\t1.0\n+598\tsmall_test_matrix_h5\tall\t3000000\t0.00029114200451270107\t27478\t1.0\n' |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicCompartmentsPolarization/output_matrix.npz |
| b |
| Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt Wed Oct 18 10:21:43 2023 +0000 |
| b |
| b'@@ -0,0 +1,8688 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|
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicConvertFormat/hg19.chrom.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/hg19.chrom.sizes Wed Oct 18 10:21:43 2023 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicConvertFormat/small_test_matrix_chr4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/small_test_matrix_chr4.bed Wed Oct 18 10:21:43 2023 +0000 |
| b |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicConvertFormat/small_test_matrix_chr4.hicpro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/small_test_matrix_chr4.hicpro Wed Oct 18 10:21:43 2023 +0000 |
| b |
| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicConvertFormat/small_test_matrix_chr4.homer |
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| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicDifferentialTAD/accepted.txt --- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:21:43 2023 +0000 |
| b |
| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicDifferentialTAD/rejected.txt --- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:21:43 2023 +0000 |
| b |
| b"@@ -1,1402 +1,1406 @@\n-# Created with HiCExplorer's hicDifferentialTAD version 3.6\n+# Created with HiCExplorer's hicDifferentialTAD version 3.7.2\n # 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.\n # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one \n-# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n-chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\tnan\t1.0\t1.0\n-chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t1.0\t1.0\t1.0\n-chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t1.0\t1.0\t1.0\n-chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t1.0\t1.0\t1.0\n-chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t1.0\t1.0\t1.0\n-chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t1.0\t1.0\t1.0\n-chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t1.0\t1.0\t1.0\n-chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t1.0\t1.0\t1.0\n-chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t1.0\t1.0\t1.0\n-chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t1.0\t1.0\t1.0\n-chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1.0\t1.0\t1.0\n-chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1.0\t1.0\t1.0\n-chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1.0\t1.0\t1.0\n-chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1.0\t1.0\t1.0\n-chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1.0\t1.0\t1.0\n-chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1.0\t1.0\t1.0\n-chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1.0\t1.0\t1.0\n-chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1.0\t1.0\t1.0\n-chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1.0\t1.0\t1.0\n-chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1.0\t1.0\t1.0\n-chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1.0\t1.0\t1.0\n-chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1.0\t1.0\t1.0\n-chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1.0\t1.0\t1.0\n-chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1.0\t1.0\t1.0\n-chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1.0\t1.0\t1.0\n-chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t1.0\t1.0\t1.0\n-chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t1.0\t1.0\t1.0\n-chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t1.0\t1.0\t1.0\n-chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t1.0\t1.0\t1.0\n-chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t1.0\t1.0\t1.0\n-chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t1.0\t1.0\t1.0\n-chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t1.0\t1.0\t1.0\n-chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t1.0\t1.0\t1.0\n-chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t1.0\t1.0\t1.0\n-chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t1.0\t1.0\t1.0\n-chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t1.0\t1.0\t1.0\n-chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t1.0\t1.0\t1.0\n-chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t1.0\t1.0\t1.0\n-chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t1.0\t1.0\t1.0\n-chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t1.0\t1.0\t1.0\n-chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t1.0\t1.0\t1.0\n-chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t1.0\t1.0\t1.0\n-chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t1.0\t1.0\t1.0\n-chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t1.0\t1.0\t1.0\n-chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t1.0\t1.0\t1.0\n-chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t1.0\t1.0\t1.0\n-chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t1.0\t1.0\t1.0\n-chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t1.0\t1.0\t1.0\n-chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t1.0\t1.0\t1.0\n-chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t1.0\t1.0\t1.0\n-chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t1.0\t1.0\t1.0\n-chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t1.0\t1.0\t1.0\n-chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t1.0\t1.0\t1.0\n-chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t1.0\t1.0\t1.0\n-chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t1.0\t1.0\t1.0\n-chr3L\t4270000\t4365000\tID_0.01_56\t-0.11633575\t.\t1.0\t1.0\t1.0\n-chr3L\t4365000\t4405000\tID_0.01_57\t-0.0944955\t.\t1.0\t1.0\t1.0\n-chr3L\t4405000\t4490000\tID_0.01_58\t-0.07463925\t.\t1.0\t1.0\t1.0\n-chr3L\t4490000\t4625000\tID_0.01_59\t0.00287075\t.\t1.0\t1.0\t1.0\n-chr3L\t4625000\t4650000\tI"..b'.0\t0.0\t0.0\t0.0\n+chr3R\t22380000\t22500000\tID_0.01_1350\t-0.055847\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22500000\t22520000\tID_0.01_1351\t-0.0631105\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22520000\t22605000\tID_0.01_1352\t-0.062648\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22605000\t22695000\tID_0.01_1353\t-0.011252\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22695000\t22780000\tID_0.01_1354\t-0.089033\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22780000\t22885000\tID_0.01_1355\t-0.04050025\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.05683475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.0237815\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.00294725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.00275775\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.1119105\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.0660765\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.04218475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.05579575\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.01546725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.0326015\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.0623065\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.0749395\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.09836075\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.03171375\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.08589625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.09323725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.0589785\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.03674225\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.0462465\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.08303325\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.00546225\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.04654075\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.01871575\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.00858875\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.10581625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.0935315\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.11469275\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.1002735\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.0627965\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.01974475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.07430725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.0249905\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.00609925\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.01281025\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.04990275\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.0499295\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.08094325\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.01535\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.01357725\t.\t1.0\tnan\t1.0\t0.0\tnan\t0.0\n' |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicInfo/hicInfo_output.txt --- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:21:43 2023 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicInterIntraTAD/matrix.cool |
| b |
| Binary file test-data/hicInterIntraTAD/matrix.cool has changed |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicInterIntraTAD/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicInterIntraTAD/plot.png |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicMergeLoops/gm12878_all.bedgraph --- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:21:43 2023 +0000 |
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| b'@@ -7,7 +7,7 @@\n 1\t1050000\t1075000\t1\t1175000\t1200000\t0.001\n 1\t1310000\t1320000\t1\t1410000\t1420000\t0.001\n 1\t1710000\t1720000\t1\t1830000\t1840000\t0.001\n-1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407133\n+1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407\n 1\t2080000\t2090000\t1\t3330000\t3340000\t0.001\n 1\t2110000\t2120000\t1\t2710000\t2720000\t0.001\n 1\t2120000\t2130000\t1\t2480000\t2490000\t0.001\n@@ -101,7 +101,7 @@\n 1\t13160000\t13170000\t1\t14520000\t14530000\t0.001\n 1\t13320000\t13330000\t1\t13440000\t13450000\t0.001\n 1\t13335000\t13340000\t1\t13540000\t13545000\t0.001\n-1\t13350000\t13360000\t1\t13630000\t13640000\t0.008992888101929171\n+1\t13350000\t13360000\t1\t13630000\t13640000\t0.0089928881019291\n 1\t13475000\t13500000\t1\t13700000\t13725000\t0.001\n 1\t13550000\t13575000\t1\t14325000\t14350000\t0.001\n 1\t13690000\t13700000\t1\t15390000\t15400000\t0.001\n@@ -151,7 +151,7 @@\n 1\t21100000\t21125000\t1\t22350000\t22375000\t0.001\n 1\t21310000\t21315000\t1\t21520000\t21525000\t0.001\n 1\t21360000\t21370000\t1\t21470000\t21480000\t0.001\n-1\t21575000\t21600000\t1\t21675000\t21700000\t0.0010553575253769206\n+1\t21575000\t21600000\t1\t21675000\t21700000\t0.0010553575253769\n 1\t21900000\t21910000\t1\t22900000\t22910000\t0.001\n 1\t21930000\t21940000\t1\t22690000\t22700000\t0.001\n 1\t22020000\t22030000\t1\t22280000\t22290000\t0.001\n@@ -203,11 +203,11 @@\n 1\t29550000\t29575000\t1\t31175000\t31200000\t0.001\n 1\t29560000\t29570000\t1\t30840000\t30850000\t0.001\n 1\t29560000\t29570000\t1\t30310000\t30320000\t0.001\n-1\t29560000\t29570000\t1\t30580000\t30590000\t0.00321287751564984\n+1\t29560000\t29570000\t1\t30580000\t30590000\t0.0032128775156498\n 1\t29780000\t29790000\t1\t30840000\t30850000\t0.001\n 1\t29870000\t29880000\t1\t30020000\t30030000\t0.001\n 1\t29870000\t29880000\t1\t31120000\t31130000\t0.001\n-1\t30030000\t30040000\t1\t31120000\t31130000\t0.001105560265853574\n+1\t30030000\t30040000\t1\t31120000\t31130000\t0.0011055602658535\n 1\t30260000\t30270000\t1\t30850000\t30860000\t0.001\n 1\t30260000\t30270000\t1\t31170000\t31180000\t0.001\n 1\t30425000\t30450000\t1\t30525000\t30550000\t0.001\n@@ -228,7 +228,7 @@\n 1\t34100000\t34125000\t1\t35200000\t35225000\t0.001\n 1\t34300000\t34325000\t1\t34400000\t34425000\t0.001\n 1\t34350000\t34360000\t1\t34450000\t34460000\t0.001\n-1\t34570000\t34580000\t1\t35070000\t35080000\t0.0026399240525339608\n+1\t34570000\t34580000\t1\t35070000\t35080000\t0.0026399240525339\n 1\t34925000\t34950000\t1\t35050000\t35075000\t0.001\n 1\t35320000\t35330000\t1\t35760000\t35770000\t0.001\n 1\t35650000\t35660000\t1\t36230000\t36240000\t0.001\n@@ -241,7 +241,7 @@\n 1\t36610000\t36620000\t1\t36750000\t36760000\t0.001\n 1\t36775000\t36800000\t1\t36875000\t36900000\t0.001\n 1\t37020000\t37030000\t1\t38100000\t38110000\t0.001\n-1\t37040000\t37050000\t1\t37780000\t37790000\t0.0030468037205961147\n+1\t37040000\t37050000\t1\t37780000\t37790000\t0.0030468037205961\n 1\t37060000\t37070000\t1\t37890000\t37900000\t0.001\n 1\t37160000\t37170000\t1\t37780000\t37790000\t0.001\n 1\t37190000\t37200000\t1\t37290000\t37300000\t0.001\n@@ -256,7 +256,7 @@\n 1\t38950000\t38960000\t1\t39050000\t39060000\t0.001\n 1\t39070000\t39080000\t1\t39290000\t39300000\t0.001\n 1\t39330000\t39340000\t1\t39450000\t39460000\t0.001\n-1\t39550000\t39575000\t1\t39650000\t39675000\t0.0012254650005710432\n+1\t39550000\t39575000\t1\t39650000\t39675000\t0.001225465000571\n 1\t39560000\t39570000\t1\t40000000\t40010000\t0.001\n 1\t39560000\t39570000\t1\t39720000\t39730000\t0.001\n 1\t39790000\t39800000\t1\t39910000\t39920000\t0.001\n@@ -338,7 +338,7 @@\n 1\t55125000\t55150000\t1\t55250000\t55275000\t0.001\n 1\t55600000\t55625000\t1\t55725000\t55750000\t0.001\n 1\t55600000\t55610000\t1\t57060000\t57070000\t0.001\n-1\t55600000\t55610000\t1\t57180000\t57190000\t0.004934547993800267\n+1\t55600000\t55610000\t1\t57180000\t57190000\t0.0049345479938002\n 1\t55825000\t55850000\t1\t57050000\t57075000\t0.001\n 1\t55940000\t55950000\t1\t56870000\t56880000\t0.001\n 1\t56025000\t56050000\t1\t57825000\t57850000\t0.001\n@@ -377,14 +377,14 @@\n 1\t64150000\t64160000\t1\t64600000\t64610000\t0.001\n 1\t64225000\t64250000\t1\t64325000\t64350000\t0.001\n 1\t64600000\t64610000\t1\t64700000\t64710000\t0.001\n-1\t64725000\t64750000\t1\t66150000\t66175000\t0.0036618652715747655\n+1\t64725000\t64750000\t1\t66150000\t66175000\t0.0036618652715747\n 1\t64730000\t64740000\t1\t65140000\t65150000\t0.001\n 1\t64730000\t64740000\t1\t65500000\t65510000\t0'..b'4803309559888334\n+1\t73380000\t73390000\t1\t74050000\t74060000\t0.0048033095598883\n 1\t74300000\t74310000\t1\t74930000\t74940000\t0.001\n 1\t74300000\t74325000\t1\t74450000\t74475000\t0.001\n 1\t74310000\t74320000\t1\t75150000\t75160000\t0.001\n@@ -426,7 +426,7 @@\n 1\t75230000\t75240000\t1\t75670000\t75680000\t0.001\n 1\t75240000\t75250000\t1\t76060000\t76070000\t0.001\n 1\t75720000\t75730000\t1\t76090000\t76100000\t0.001\n-1\t75725000\t75750000\t1\t75825000\t75850000\t0.0015043592556291366\n+1\t75725000\t75750000\t1\t75825000\t75850000\t0.0015043592556291\n 1\t76370000\t76380000\t1\t77190000\t77200000\t0.001\n 1\t76610000\t76620000\t1\t77590000\t77600000\t0.001\n 1\t76630000\t76640000\t1\t77360000\t77370000\t0.001\n@@ -481,7 +481,7 @@\n 1\t87590000\t87600000\t1\t88410000\t88420000\t0.001\n 1\t87750000\t87775000\t1\t89050000\t89075000\t0.001\n 1\t87750000\t87775000\t1\t88400000\t88425000\t0.001\n-1\t87800000\t87825000\t1\t87900000\t87925000\t0.003919529137873564\n+1\t87800000\t87825000\t1\t87900000\t87925000\t0.0039195291378735\n 1\t88260000\t88270000\t1\t88360000\t88370000\t0.001\n 1\t89125000\t89150000\t1\t89325000\t89350000\t0.001\n 1\t89450000\t89475000\t1\t89825000\t89850000\t0.001\n@@ -631,7 +631,7 @@\n 1\t120775000\t120800000\t1\t121075000\t121100000\t0.001\n 1\t121240000\t121250000\t1\t121340000\t121350000\t0.001\n 1\t121350000\t121375000\t1\t121450000\t121475000\t0.001\n-1\t142525000\t142550000\t1\t142625000\t142650000\t0.007224819791140677\n+1\t142525000\t142550000\t1\t142625000\t142650000\t0.0072248197911406\n 1\t142540000\t142550000\t1\t142960000\t142970000\t0.001\n 1\t142540000\t142550000\t1\t143540000\t143550000\t0.001\n 1\t142560000\t142570000\t1\t142730000\t142740000\t0.001\n@@ -655,7 +655,7 @@\n 1\t143880000\t143890000\t1\t144160000\t144170000\t0.0114591711614241\n 1\t144150000\t144175000\t1\t145325000\t145350000\t0.001\n 1\t144150000\t144175000\t1\t145775000\t145800000\t0.001\n-1\t144170000\t144180000\t1\t144510000\t144520000\t0.0010944871943884217\n+1\t144170000\t144180000\t1\t144510000\t144520000\t0.0010944871943884\n 1\t144180000\t144190000\t1\t145980000\t145990000\t0.001\n 1\t144210000\t144220000\t1\t145750000\t145760000\t0.001\n 1\t144210000\t144220000\t1\t144320000\t144330000\t0.001\n@@ -669,7 +669,7 @@\n 1\t144620000\t144630000\t1\t145300000\t145310000\t0.001\n 1\t144675000\t144700000\t1\t144950000\t144975000\t0.001\n 1\t144810000\t144820000\t1\t146230000\t146240000\t0.001\n-1\t144825000\t144850000\t1\t146450000\t146475000\t0.005463291888438761\n+1\t144825000\t144850000\t1\t146450000\t146475000\t0.0054632918884387\n 1\t144830000\t144840000\t1\t145370000\t145380000\t0.001\n 1\t144850000\t144860000\t1\t146020000\t146030000\t0.001\n 1\t144910000\t144920000\t1\t145050000\t145060000\t0.001\n@@ -789,7 +789,7 @@\n 1\t157550000\t157560000\t1\t157650000\t157660000\t0.001\n 1\t157730000\t157740000\t1\t157830000\t157840000\t0.001\n 1\t157930000\t157940000\t1\t158090000\t158100000\t0.001\n-1\t157950000\t157960000\t1\t159050000\t159060000\t0.026660483087000208\n+1\t157950000\t157960000\t1\t159050000\t159060000\t0.0266604830870002\n 1\t158150000\t158175000\t1\t158950000\t158975000\t0.001\n 1\t158170000\t158180000\t1\t158290000\t158300000\t0.001\n 1\t158170000\t158175000\t1\t158465000\t158470000\t0.001\n@@ -948,7 +948,7 @@\n 1\t185110000\t185120000\t1\t186330000\t186340000\t0.001\n 1\t185250000\t185275000\t1\t186275000\t186300000\t0.001\n 1\t185280000\t185290000\t1\t185560000\t185570000\t0.001\n-1\t185280000\t185290000\t1\t185380000\t185390000\t0.009307972819450458\n+1\t185280000\t185290000\t1\t185380000\t185390000\t0.0093079728194504\n 1\t185780000\t185790000\t1\t186180000\t186190000\t0.001\n 1\t186450000\t186460000\t1\t186950000\t186960000\t0.001\n 1\t186460000\t186470000\t1\t186560000\t186570000\t0.001\n@@ -1161,9 +1161,9 @@\n 1\t229850000\t229860000\t1\t230440000\t230450000\t0.001\n 1\t229860000\t229870000\t1\t229970000\t229980000\t0.001\n 1\t230225000\t230250000\t1\t230325000\t230350000\t0.001\n-1\t230770000\t230780000\t1\t231740000\t231750000\t0.03373828183610245\n+1\t230770000\t230780000\t1\t231740000\t231750000\t0.0337382818361024\n 1\t231050000\t231060000\t1\t231340000\t231350000\t0.001\n-1\t231050000\t231075000\t1\t231150000\t231175000\t0.001796188746513645\n+1\t231050000\t231075000\t1\t231150000\t231175000\t0.0017961887465136\n 1\t231060000\t231070000\t1\t231730000\t231740000\t0.001\n 1\t231475000\t231500000\t1\t231725000\t231750000\t0.001\n 1\t231990000\t232000000\t1\t233140000\t233150000\t0.001\n' |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicPlotSVL/p_values.txt --- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicPlotSVL/ratios.txt --- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicQuickQC/QC.log --- a/test-data/hicQuickQC/QC.log Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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) |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicTADClassifier/unittest_classifier.BIN |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicTrainTADClassifier/small_test_matrix.cool |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicValidateLocations/overlap_smc3_matched_locations --- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/hicValidateLocations/overlap_smc3_statistics --- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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 |
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| diff -r 8ad23dfdaabb -r 6d042c96aceb test-data/raw_qc_report --- a/test-data/raw_qc_report Tue Jan 10 18:40:25 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 10:21:43 2023 +0000 |
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| @@ -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) |
