| Previous changeset 7:0d6c2ff54c76 (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:
hicDetectLoops.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 0d6c2ff54c76 -r 0410b6aada45 hicDetectLoops.xml --- a/hicDetectLoops.xml Tue Jan 10 19:20:16 2023 +0000 +++ b/hicDetectLoops.xml Wed Oct 18 10:41:24 2023 +0000 |
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| @@ -53,21 +53,21 @@ </command> <inputs> <expand macro="matrix_h5_cooler_macro" /> - <param argument="--peakWidth" type="integer" optional='true' label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." /> - <param argument="--windowSize" type="integer" optional='true' label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak + <param argument="--peakWidth" type="integer" optional="true" label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." /> + <param argument="--windowSize" type="integer" optional="true" label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" /> <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates. For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given. - This does NOT influence the p-value for the neighborhood testing." value='0.05' /> - <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value='5' /> + This does NOT influence the p-value for the neighborhood testing." value="0.05" /> + <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value="5" /> <!-- new--> - <param argument="--obsExpThreshold" type="float" label="Obs/exp interaction threshold" help= "The minimum number of obs/exp interactions a detected peaks needs to have to be considered" value='1.5' /> + <param argument="--obsExpThreshold" type="float" label="Obs/exp interaction threshold" help= "The minimum number of obs/exp interactions a detected peaks needs to have to be considered" value="1.5" /> - <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value='0.05' /> - <param argument="--maxLoopDistance" optional='true' type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value='2000000' /> - <param argument="--chromosomes" optional='true' type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." /> - <param argument="--region" optional='true' type="text" label="Chromosomes to include" help= "The format is chr:start-end." /> + <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value="0.05" /> + <param argument="--maxLoopDistance" optional="true" type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value="2000000" /> + <param argument="--chromosomes" optional="true" type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." /> + <param argument="--region" optional="true" type="text" label="Chromosomes to include" help= "The format is chr:start-end." /> <param argument="--expected" type="select" label="Method to compute the expected value"> <option value="mean" selected="True">mean</option> <option value="mean_nonzero">mean_nonzero</option> @@ -75,7 +75,7 @@ </param> </inputs> <outputs> - <data name='output_loops' from_work_dir='output_loop.bedgraph' format='bedgraph' label='Computed loops' /> + <data name="output_loops" from_work_dir="output_loop.bedgraph" format="bedgraph" label="Computed loops" /> </outputs> <tests> <test> |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 macros.xml --- a/macros.xml Tue Jan 10 19:20:16 2023 +0000 +++ b/macros.xml Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicDifferentialTest/differential.hdf5 |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicExportData/aggregate.tar.gz |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/cHi-C/referencePoints_chicViewpoint.bed --- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/distVsCounts.txt --- a/test-data/distVsCounts.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicCompartmentsPolarization/output_matrix.npz |
| b |
| Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed |
| b |
| diff -r 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 2023 +0000 |
| b |
| b'@@ -0,0 +1,8688 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|
| b |
| diff -r 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 2023 +0000 |
| b |
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| b |
| diff -r 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicConvertFormat/small_test_matrix_chr4.homer |
| b |
| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/hicDifferentialTAD/accepted.txt --- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:41:24 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 |
| b |
| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/hicDifferentialTAD/rejected.txt --- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicInfo/hicInfo_output.txt --- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicInterIntraTAD/matrix.cool |
| b |
| Binary file test-data/hicInterIntraTAD/matrix.cool has changed |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 test-data/hicInterIntraTAD/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:41:24 2023 +0000 |
| b |
| @@ -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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicInterIntraTAD/plot.png |
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| diff -r 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicMergeLoops/gm12878_all.bedgraph --- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicPlotSVL/p_values.txt --- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicPlotSVL/ratios.txt --- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicQuickQC/QC.log --- a/test-data/hicQuickQC/QC.log Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 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 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicValidateLocations/overlap_smc3_matched_locations --- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/hicValidateLocations/overlap_smc3_statistics --- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:41:24 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 0d6c2ff54c76 -r 0410b6aada45 test-data/raw_qc_report --- a/test-data/raw_qc_report Tue Jan 10 19:20:16 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 10:41:24 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) |
