| Next changeset 1:3b15581e7ca7 (2020-02-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" |
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added:
hicConvertFormat.xml macros.xml static/images/SRR027956.svg static/images/SRR0279XX_perChr_eigenvector1.png static/images/diagnostic_plot.png static/images/hicAggregateContacts.png static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png static/images/hicCorrelate_Dmel_heatmap.png static/images/hicCorrelate_Dmel_scatterplot.png static/images/hicCorrelate_pearson.png static/images/hicCorrelate_pearson_scatter.png static/images/hicCorrelate_spearman.png static/images/hicCorrelate_spearman_scatter.png static/images/hicMergeMatrixBins_Xchr.png static/images/hicMergeMatrixBins_Xregion.png static/images/hicPCA.png static/images/hicPlotDistVsCounts.png static/images/hicPlotDistVsCounts_result1.png static/images/hicPlotDistVsCounts_result2.png static/images/hicPlotMatrix.png static/images/hicPlotTADs.png static/images/hicQC.png static/images/hicQC_distance.png static/images/hicQC_pairs_discarded.png static/images/hicQC_pairs_sequenced.png static/images/hicQC_read_orientation.png static/images/hicQC_unmappable_and_non_unique.png static/images/master_TADs_plot.png static/images/pulication_plots_viewpoint.png static/images/z-score.svg test-data/Li_et_al_2015.cool test-data/cHi-C/FL-E13-5_chr1.cool test-data/cHi-C/MB-E10-5_chr1.cool test-data/cHi-C/background.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png test-data/cHi-C/chicQualityControl/histogram.png test-data/cHi-C/chicQualityControl/new_referencepoints.bed test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter test-data/cHi-C/chicQualityControl/sparsity.png test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed test-data/cHi-C/referencePoints.bed test-data/cHi-C/referencePoints_chicViewpoint.bed test-data/distVsCounts.txt test-data/find_TADs/multiFDR_boundaries.bed test-data/find_TADs/multiFDR_boundaries.gff test-data/find_TADs/multiFDR_score.bedgraph test-data/find_TADs/multiFDR_tad_score.bm test-data/find_TADs/multiFDR_zscore_matrix.h5 test-data/hicAggregateContacts/test_regions.bed test-data/hicAggregateContacts_results1.png test-data/hicAverageRegions/regions.bed test-data/hicAverageRegions/result.npz test-data/hicAverageRegions/result_rangeInBins_100.npz test-data/hicAverageRegions/result_range_100000.npz test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png test-data/hicCompartmentsPolarization/pca1.bedgraph test-data/hicConvertFormat/small_test_matrix_chr4.cool test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv test-data/hicConvertFormat/small_test_matrix_chr4.homer test-data/hicConvertFormat/test_matrix.bed test-data/hicCorrectMatrix/diagnostic_plot.png test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicDetectLoops/loops.bedgraph test-data/hicFindRestrictionSites/reference_genome.fasta test-data/hicFindRestrictionSites/restriction_sites.bed test-data/hicInfo/hicInfo_output.txt test-data/hicInfo_output.txt test-data/hicMergeLoops/gm12878_10kb.bedgraph test-data/hicMergeLoops/gm12878_25kb.bedgraph test-data/hicMergeLoops/gm12878_5kb.bedgraph 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/hicPlotAverageRegions/defaults.png test-data/hicPlotAverageRegions/defaults_log.png test-data/hicPlotAverageRegions/defaults_log1p.png test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotMatrix/plot1.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/hicTransform/obs_exp_norm.h5 test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak test-data/hicValidateLocations/loops_1.bedgraph test-data/hicValidateLocations/overlap_smc3_matched_locations test-data/hicValidateLocations/overlap_smc3_statistics test-data/li_32-33mb_interactions.bedgraph test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/raw_qc_report test-data/regions.bed test-data/small_test_matrix.cool test-data/small_test_matrix_result_sorted.bam |
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| diff -r 000000000000 -r e136f22c2a0f hicConvertFormat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicConvertFormat.xml Mon Dec 16 15:28:54 2019 -0500 |
| [ |
| b'@@ -0,0 +1,375 @@\n+<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+ <description>Convert between different file formats</description>\n+ <macros>\n+ <token name="@BINARY@">hicConvertFormat</token>\n+ <token name="@SINGLE_INPUT@">\n+ #if $xml_path.inputFormat_selector == \'optionCool\':\n+ --matrices \'matrix.cool\'\n+ --inputFormat cool\n+ #if $xml_path.correctionName:\n+ --correction_name \'$xml_path.correctionName\'\n+ #end if\n+\n+ #if $xml_path.correctionDivision:\n+ --correction_division\n+ #end if\n+\n+ #if $xml_path.chromosome:\n+ #set $chromosome = \' \'.join([ \'\\\'%s\\\'\' % $chrom for $chrom in str($xml_path.chromosome).split(\' \') ])\n+\n+ --chromosome $chromosome\n+ #end if\n+\n+ #if $xml_path.loadRawValues:\n+ --load_raw_values\n+ #end if\n+ #end if\n+ #if $xml_path.inputFormat_selector == \'optionH5\':\n+ --matrices "matrix.h5"\n+ --inputFormat h5\n+\n+ #end if \n+ #if $xml_path.inputFormat_selector == \'optionHomer\':\n+ --matrices "matrix.homer"\n+ --inputFormat homer\n+\n+ #end if \n+ #if $xml_path.inputFormat_selector == \'optionHicpro\':\n+ --matrices "matrix.hicpro"\n+ --bedFileHicpro "matrix.bed"\n+ --inputFormat hicpro\n+ #end if \n+ #if $xml_path.inputFormat_selector == \'optionHic\':\n+ --matrices "matrix.hic"\n+ #if $xml_path.resolutions:\n+ #set $resolutions = \' \'.join([ \'"%s"\' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])\n+\n+ --resolutions $resolutions\n+ #end if\n+ --inputFormat hic\n+ #end if \n+ </token>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+\n+ ## single to single case\n+ \n+\n+ #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == \'singleMatrix\':\n+ #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional\n+ \n+ #if $xml_path.inputFormat_selector == \'optionCool\':\n+ ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&\n+\n+ #end if\n+ #if $xml_path.inputFormat_selector == \'optionH5\':\n+ ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&\n+\n+ #end if\n+ #if $xml_path.inputFormat_selector == \'optionHomer\':\n+ ln -s "$xml_path.matrixHomer" "matrix.homer" && \n+\n+ #end if\n+\n+ #if $xml_path.inputFormat_selector == \'optionHicpro\':\n+ ln -s "$xml_path.matrixHicpro" "matrix.hicpro" && \n+ ln -s "$xml_path.bedHicpro" "matrix.bed" &&\n+ #end if\n+\n+ #if $xml_path.inputFormat_selector == \'optionHic\':\n+ ln -s "$xml_path.matrixHic" "matrix.hic" &&\n+ #end if\n+\n+\n+\n+ @BINARY@ \n+ @SINGLE_INPUT@\n+ \n+ \n+ --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector\n+ --outFileName \'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector\'\n+\n+ #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == \'ginteractions\':\n+ && mv \'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv\' matrix_out\n+\n+ #else:\n+ && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out\n+ #end if\n+ #end'..b'="output_converted_matrix" ftype="cool">\n+ <assert_contents>\n+ <has_h5_keys keys=\'bins,chroms,indexes,pixels\'/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name=\'outputSingleMultiple_conditional\'>\n+ <param name=\'outputSingleMultiple_selector\' value=\'singleMatrix\'/>\n+ <conditional name=\'inputFormat_conditional\'>\n+ <param name=\'inputFormat_selector\' value=\'optionCool\'/>\n+ <param name=\'matrix_h5_cooler\' value=\'hicConvertFormat/small_test_matrix_chr4.cool\'/>\n+ </conditional>\n+ \n+ <conditional name=\'outputFormat_conditional\'>\n+ <param name=\'outputFormat_selector\' value=\'homer\'/>\n+ </conditional>\n+ </conditional>\n+ <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000"/>\n+ </test>\n+ <test>\n+ <conditional name=\'outputSingleMultiple_conditional\'>\n+ <param name=\'outputSingleMultiple_selector\' value=\'singleMatrix\'/>\n+ <conditional name=\'inputFormat_conditional\'>\n+ <param name=\'inputFormat_selector\' value=\'optionCool\'/>\n+ <param name=\'matrix_h5_cooler\' value=\'hicConvertFormat/small_test_matrix_chr4.cool\'/>\n+ </conditional>\n+ \n+ <conditional name=\'outputFormat_conditional\'>\n+ <param name=\'outputFormat_selector\' value=\'ginteractions\'/>\n+ </conditional>\n+ </conditional>\n+ <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/>\n+ \n+ </test>\n+ <test>\n+ <conditional name=\'outputSingleMultiple_conditional\'>\n+ <param name=\'outputSingleMultiple_selector\' value=\'multipleMatrix\'/>\n+ <conditional name=\'resolutionOrManyToOne_conditional\'>\n+ <param name=\'resolutionOrManyToOne_selector\' value=\'resolution_option\'/>\n+ <param name=\'resolutions\' value=\'5000 10000 20000\'/>\n+ <conditional name=\'inputFormat_conditional\'>\n+ <param name=\'inputFormat_selector\' value=\'optionH5\'/>\n+ <param name=\'matrix_h5_cooler\' value=\'small_test_matrix.h5\'/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="output_converted_matrix" ftype="cool">\n+ <assert_contents>\n+ <has_h5_keys keys=\'resolutions\'/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Converting between different Hi-C interaction formats\n+=====================================================\n+\n+Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool,\n+and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files\n+from one format with different resolutions and creates a mcool file. Each original file is stored under the path e.g. ::/resolutions/10000.\n+A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and\n+all output files too.\n+For input and output of cooler files special options are available, for all other formats they will be ignored.\n+HiCPro file format needs an additional bed file as input.\n+\n+| For more information about HiCExplorer please consider our documentation on readthedocs.io_\n+\n+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html\n+]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r e136f22c2a0f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Dec 16 15:28:54 2019 -0500 |
| [ |
| b'@@ -0,0 +1,699 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+ <token name="@WRAPPER_VERSION@">3.3.1</token>\n+ <token name="@USE_RANGE@">\n+ #if $use_range.select_use_range == "yes_use_range":\n+ --range $range_min:$range_max\n+ #end if\n+ </token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <token name="@CHROMOSOME_LIST@">\n+ #if $chromosome_list:\n+ #set $chromosomes = []\n+ #for $chrom in $chromosome_list:\n+ #silent $chromosomes.append("\'%s\'" % $chrom.chromosomes)\n+ #end for\n+ #set $chromosome_string = \' \'.join($chromosomes)\n+ --chromosomes $chromosome_string\n+ #end if\n+ </token>\n+\n+ <xml name="chromosome_list">\n+ <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">\n+ <param argument="--chromosomes" type="text" value="" >\n+ <validator type="empty_field" />\n+ </param>\n+ </repeat>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.1133705</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n+ </xml>\n+ <xml name="use_range">\n+ <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->\n+ <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">\n+ <option value="no_use_range">No restriction</option>\n+ <option value="yes_use_range">Only consider counts within a range</option>\n+ </param>\n+ <when value="no_use_range"/>\n+ <when value="yes_use_range">\n+ <expand macro=\'range\' />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="range">\n+ <param name=\'range_min\' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>\n+ <param name=\'range_max\' label="Maximum range to consider interactions" type="integer" value="" min="0"/>\n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summe'..b'/>\n+ <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="track_input_h5_macro">\n+ <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n+ </xml>\n+ <xml name="track_input_bed_macro">\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_macro">\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n+ </xml>\n+ <xml name="track_input_bigwig_macro">\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_matrix_macro">\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_tabular_macro">\n+ <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n+ </xml>\n+ <xml name="plot_title">\n+ <param name="title" type="text" optional="true" label="Plot title"/>\n+ </xml>\n+\n+ <xml name="spacer_macro">\n+ <param name="spacer_width" type="float" value="" optional="True"\n+ label="Include spacer at the end of the track." help="Width of the spacer." />\n+ </xml>\n+ <xml name="fontsize_macro">\n+ <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r e136f22c2a0f static/images/z-score.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/z-score.svg Mon Dec 16 15:28:54 2019 -0500 |
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| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/background.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/background.bed Mon Dec 16 15:28:54 2019 -0500 |
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| b'@@ -0,0 +1,1002 @@\n+Relative position\tsize nbinom\tprob nbinom\tmax value\tmean value\n+-500000\t58.254577634279\t0.998604709282\t1.333333333333\t0.000105073709\n+-499000\t10.000013353187\t0.991925224088\t1.500000000000\t0.000105073709\n+-498000\t72.266262784304\t0.998828265884\t1.200000000000\t0.000111077921\n+-497000\t51.093422441771\t0.998183086351\t1.000000000000\t0.000120084239\n+-496000\t86.575220693033\t0.998899865570\t0.800000000000\t0.000123086345\n+-495000\t72.441590407550\t0.998655447638\t0.800000000000\t0.000126088451\n+-494000\t75.085350270547\t0.998668414055\t1.000000000000\t0.000129090557\n+-493000\t71.967411178924\t0.998612779641\t1.000000000000\t0.000129090557\n+-492000\t77.026231982211\t0.998763649786\t1.200000000000\t0.000123086345\n+-491000\t96.154018360868\t0.999129584825\t1.000000000000\t0.000108075815\n+-490000\t70.641792331241\t0.998918479365\t1.400000000000\t0.000099069497\n+-489000\t72.297114570842\t0.998971709245\t0.800000000000\t0.000096067391\n+-488000\t55.276417890737\t0.998907322028\t0.800000000000\t0.000078054755\n+-487000\t75.866231077639\t0.999020037562\t0.600000000000\t0.000096067391\n+-486000\t77.908114872120\t0.999075493568\t0.600000000000\t0.000093065285\n+-485000\t70.196050128375\t0.998940963837\t0.600000000000\t0.000096067391\n+-484000\t48.306835304302\t0.998789125810\t0.600000000000\t0.000078054755\n+-483000\t65.826727385050\t0.999115985283\t0.600000000000\t0.000075052649\n+-482000\t10.000003651221\t0.996523342626\t0.400000000000\t0.000045031590\n+-481000\t48.188933357556\t0.999179280048\t0.400000000000\t0.000051035802\n+-480000\t10.000001173914\t0.997216871755\t0.400000000000\t0.000036025272\n+-479000\t10.000002160096\t0.996985563716\t0.400000000000\t0.000039027378\n+-478000\t61.980720096540\t0.999287603012\t0.800000000000\t0.000057040014\n+-477000\t47.193502172887\t0.999138448161\t0.600000000000\t0.000054037908\n+-476000\t75.435666576826\t0.999477638616\t0.600000000000\t0.000051035802\n+-475000\t83.258498044933\t0.999385868055\t0.600000000000\t0.000066046332\n+-474000\t64.452927063111\t0.999206823435\t0.600000000000\t0.000066046332\n+-473000\t68.592799621533\t0.999390093904\t0.600000000000\t0.000054037908\n+-472000\t48.567204011739\t0.999139405277\t0.600000000000\t0.000054037908\n+-471000\t10.000004448331\t0.996292395667\t0.600000000000\t0.000048033696\n+-470000\t10.000000920405\t0.995831238986\t1.400000000000\t0.000054037908\n+-469000\t10.000003872489\t0.994909340544\t1.400000000000\t0.000066046332\n+-468000\t63.250123985231\t0.999022818205\t1.400000000000\t0.000081056861\n+-467000\t51.399551404579\t0.998558644000\t1.400000000000\t0.000096067391\n+-466000\t64.883458129266\t0.998762977849\t1.000000000000\t0.000105073709\n+-465000\t86.383451689662\t0.999139519880\t0.800000000000\t0.000096067391\n+-464000\t64.657320565128\t0.998830168725\t1.000000000000\t0.000099069497\n+-463000\t69.011442263596\t0.998889631783\t1.000000000000\t0.000099069497\n+-462000\t120.365580780362\t0.999304923056\t1.000000000000\t0.000108075815\n+-461000\t83.873478804403\t0.999085832019\t1.000000000000\t0.000099069497\n+-460000\t76.791436688795\t0.998822607239\t0.800000000000\t0.000117082133\n+-459000\t71.300309154477\t0.998707418591\t1.000000000000\t0.000120084239\n+-458000\t70.551044686671\t0.998794143443\t0.600000000000\t0.000111077921\n+-457000\t88.657625851365\t0.999084917164\t0.800000000000\t0.000105073709\n+-456000\t66.985331452249\t0.998825498193\t0.800000000000\t0.000102071603\n+-455000\t212.376735013798\t0.999710065148\t0.600000000000\t0.000078054755\n+-454000\t62.703317289439\t0.999261443476\t0.600000000000\t0.000060042120\n+-453000\t45.696967611307\t0.998932417121\t0.600000000000\t0.000063044226\n+-452000\t82.313181248075\t0.999548168551\t0.600000000000\t0.000048033696\n+-451000\t61.955802866608\t0.999249835457\t0.600000000000\t0.000060042120\n+-450000\t71.163546816639\t0.999118429295\t1.000000000000\t0.000081056861\n+-449000\t57.404577886000\t0.998868956077\t1.000000000000\t0.000084058967\n+-448000\t78.889496868591\t0.999175114488\t1.000000000000\t0.000084058967\n+-447000\t59.455705064746\t0.998872066360\t1.000000000000\t0.000087061073\n+-446000\t69.521205032032\t0.998763823049\t1.000000000000\t0.000111077921\n+-445000\t99.901425243691\t0.999325366218\t0.800000000000\t0.0000870'..b'92515295592\t0.998432747334\t1.400000000000\t0.000222155842\n+444000\t82.443622273366\t0.997719903159\t1.400000000000\t0.000243170584\n+445000\t70.933399279725\t0.997396373546\t1.400000000000\t0.000243170584\n+446000\t95.161892262226\t0.998095770809\t1.600000000000\t0.000234164266\n+447000\t124.614672839908\t0.998565069417\t1.200000000000\t0.000231162160\n+448000\t77.860490008359\t0.997704488044\t1.400000000000\t0.000231162160\n+449000\t65.217115835699\t0.997403641809\t1.400000000000\t0.000219153736\n+450000\t75.445932132698\t0.998007293338\t1.200000000000\t0.000198138995\n+451000\t95.181162634818\t0.998473187366\t1.000000000000\t0.000186130571\n+452000\t94.977236808895\t0.998461455130\t1.000000000000\t0.000189132677\n+453000\t71.519354123232\t0.997988008873\t1.000000000000\t0.00018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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 14274000 14279000 Eya1 673.0 -22000 7.00000 +chr1 14285000 14308000 Eya1 673.0 7000 389.40000 +chr1 14310000 14322000 Eya1 673.0 21000 54.80000 +chr1 14361000 14407000 Eya1 673.0 106000 21.20000 +chr1 14426000 14432000 Eya1 673.0 131000 2.40000 +chr1 14447000 14455000 Eya1 673.0 154000 4.40000 +chr1 14460000 14465000 Eya1 673.0 164000 3.20000 +chr1 14491000 14500000 Eya1 673.0 199000 17.65000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 19077000 19114000 Tfap2d 472.0 20000 344.80000 +chr1 19125000 19129000 Tfap2d 472.0 35000 7.80000 +chr1 19134000 19139000 Tfap2d 472.0 45000 8.40000 +chr1 19141000 19238000 Tfap2d 472.0 144000 47.40000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 4472000 4503000 Sox17 810.0 15000 566.20000 +chr1 4507000 4516000 Sox17 810.0 28000 38.80000 +chr1 4520000 4531000 Sox17 810.0 43000 10.40000 +chr1 4533000 4543000 Sox17 810.0 55000 6.80000 +chr1 4562000 4593000 Sox17 810.0 105000 25.00000 +chr1 4664000 4669000 Sox17 810.0 181000 1.20000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 14274000 14279000 Eya1 832.0 -22000 0.00000 +chr1 14285000 14308000 Eya1 832.0 7000 479.80000 +chr1 14310000 14322000 Eya1 832.0 21000 52.80000 +chr1 14361000 14407000 Eya1 832.0 106000 36.00000 +chr1 14426000 14432000 Eya1 832.0 131000 9.00000 +chr1 14447000 14455000 Eya1 832.0 154000 12.40000 +chr1 14460000 14465000 Eya1 832.0 164000 7.60000 +chr1 14491000 14500000 Eya1 832.0 199000 15.75000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 19077000 19114000 Tfap2d 800.0 20000 527.80000 +chr1 19125000 19129000 Tfap2d 800.0 35000 8.80000 +chr1 19134000 19139000 Tfap2d 800.0 45000 11.20000 +chr1 19141000 19238000 Tfap2d 800.0 144000 163.00000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 4472000 4503000 Sox17 978.0 15000 724.40000 +chr1 4507000 4516000 Sox17 978.0 28000 19.00000 +chr1 4520000 4531000 Sox17 978.0 43000 22.20000 +chr1 4533000 4543000 Sox17 978.0 55000 12.20000 +chr1 4562000 4593000 Sox17 978.0 105000 23.20000 +chr1 4664000 4669000 Sox17 978.0 181000 5.40000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed +MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed +MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed +MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 14274000 14279000 Eya1 673.0 -22000 7.00000 +chr1 14285000 14308000 Eya1 673.0 7000 389.40000 +chr1 14310000 14322000 Eya1 673.0 21000 54.80000 +chr1 14361000 14407000 Eya1 673.0 106000 21.20000 +chr1 14426000 14432000 Eya1 673.0 131000 2.40000 +chr1 14447000 14455000 Eya1 673.0 154000 4.40000 +chr1 14460000 14465000 Eya1 673.0 164000 3.20000 +chr1 14491000 14500000 Eya1 673.0 199000 17.65000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Sum of interactions Relative distance Raw target +chr1 14274000 14279000 Eya1 832.0 -22000 0.00000 +chr1 14285000 14308000 Eya1 832.0 7000 479.80000 +chr1 14310000 14322000 Eya1 832.0 21000 52.80000 +chr1 14361000 14407000 Eya1 832.0 106000 36.00000 +chr1 14426000 14432000 Eya1 832.0 131000 9.00000 +chr1 14447000 14455000 Eya1 832.0 154000 12.40000 +chr1 14460000 14465000 Eya1 832.0 164000 7.60000 +chr1 14491000 14500000 Eya1 832.0 199000 15.75000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,17 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335 +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943 +chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802 +chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943 +chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802 +chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118 +chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.43072 +chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00105 +chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.12754 +chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.40725 +chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.36639 +chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.16231 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by chi2 test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.43072 +chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00105 +chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.12754 +chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.40725 +chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.36639 +chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.16231 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744 +chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206 +chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744 +chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206 +chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094 +chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082 +chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117 +chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402 +chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847 +chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860 +chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082 +chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117 +chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402 +chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847 +chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860 +chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3 +# This file contains the p-values computed by fisher test +# To test the smoothed (float) values they were rounded up to the next integer +# +# Alpha level 0.5 +# Degrees of freedom 1 +# +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 +chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586 +chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002 +chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706 +chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523 +chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210 +chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425 +chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed +FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed +FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png |
| b |
| Binary file test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png |
| b |
| Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png |
| b |
| Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png |
| b |
| Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicQualityControl/histogram.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicQualityControl/new_referencepoints.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,35 @@ +chr1 4487435 4487435 Sox17 +chr1 14300280 14300280 Eya1 +chr1 19093103 19093103 Tfap2d +chr1 24202042 24202042 Col9a1 +chr1 33776741 33776741 Rab23 +chr1 38684089 38684089 Aff3 +chr1 42753991 42753991 Pou3f3 +chr1 52176282 52176282 Stat1 +chr1 53118507 53118507 Mstn +chr1 57028178 57028178 Satb2 +chr1 59821123 59821123 Bmpr2 +chr1 66991630 66991630 Myl1 +chr1 74648029 74648029 Stk36 +chr1 74818466 74818466 Wnt6 +chr1 75356867 75356867 Des +chr1 77511663 77511663 Epha4 +chr1 78193711 78193711 Pax3 +chr1 89102386 89102386 Chrng +chr1 93355905 93355905 Per2 +chr1 93698054 93698054 Twist2 +chr1 107677300 107677300 Tnfrsf11a +chr1 120950196 120950196 Gli2 +chr1 122499064 122499064 En1 +chr1 127808791 127808791 Lypd1 +chr1 135934092 135934092 Fmod +chr1 136186581 136186581 MyoG +chr1 164004278 164006270 mm712 +chr1 164147754 164147754 Dnm3os +chr1 165243781 165243781 Prrx1 +chr1 165333772 165333772 Gorab +chr1 169619689 169619689 Lmx1a +chr1 182823250 182823250 Lefty2 +chr1 182865170 182865170 Lefty1 +chr1 188529871 188529871 Tgfb2 +chr1 194979306 194979306 Irf6 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,45 @@ +# Created with chicQualityControl version 3.3 +# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool +chr1 4487435 4487435 Sox17 0.14485514485514486 0.16083916083916083 +chr1 14300280 14300280 Eya1 0.14285714285714285 0.1938061938061938 +chr1 19093103 19093103 Tfap2d 0.1048951048951049 0.16683316683316685 +chr1 19198995 19198995 Tfap2b 0.01898101898101898 0.016983016983016984 +chr1 24202042 24202042 Col9a1 0.10589410589410589 0.12787212787212787 +chr1 33776741 33776741 Rab23 0.15484515484515485 0.2137862137862138 +chr1 38684089 38684089 Aff3 0.11588411588411589 0.11388611388611389 +chr1 42753991 42753991 Pou3f3 0.04995004995004995 0.07592407592407592 +chr1 52176282 52176282 Stat1 0.19080919080919082 0.22777222777222778 +chr1 52557292 52557292 Nab1 0.02197802197802198 0.024975024975024976 +chr1 53118507 53118507 Mstn 0.3116883116883117 0.37462537462537465 +chr1 57028178 57028178 Satb2 0.12287712287712288 0.14385614385614387 +chr1 59821123 59821123 Bmpr2 0.14085914085914086 0.16983016983016982 +chr1 66991630 66991630 Myl1 0.0919080919080919 0.09290709290709291 +chr1 74648029 74648029 Stk36 0.2777222777222777 0.3356643356643357 +chr1 74818466 74818466 Wnt6 0.29270729270729273 0.34165834165834164 +chr1 74838593 74838593 Wnt10a 0.00999000999000999 0.008991008991008992 +chr1 74998246 74998246 Ihh 0.008991008991008992 0.003996003996003996 +chr1 75356867 75356867 Des 0.18081918081918083 0.21678321678321677 +chr1 77511663 77511663 Epha4 0.15684315684315683 0.22277722277722278 +chr1 78193711 78193711 Pax3 0.24375624375624375 0.3096903096903097 +chr1 89102386 89102386 Chrng 0.16783216783216784 0.2217782217782218 +chr1 93355905 93355905 Per2 0.15384615384615385 0.16483516483516483 +chr1 93698054 93698054 Twist2 0.22277722277722278 0.23476523476523475 +chr1 94076918 94076918 Hdac4 0.0 0.0 +chr1 107677300 107677300 Tnfrsf11a 0.14685314685314685 0.16383616383616384 +chr1 120950196 120950196 Gli2 0.13986013986013987 0.2007992007992008 +chr1 122499064 122499064 En1 0.1008991008991009 0.11988011988011989 +chr1 127808791 127808791 Lypd1 0.18681318681318682 0.22977022977022976 +chr1 135934092 135934092 Fmod 0.3516483516483517 0.4145854145854146 +chr1 136186581 136186581 MyoG 0.07392607392607392 0.09090909090909091 +chr1 152313295 152313295 Prg4 0.00999000999000999 0.006993006993006993 +chr1 164004278 164006270 mm712 0.26173826173826176 0.2867132867132867 +chr1 164147754 164147754 Dnm3os 0.24875124875124874 0.24675324675324675 +chr1 165243781 165243781 Prrx1 0.36063936063936064 0.34065934065934067 +chr1 165333772 165333772 Gorab 0.36863136863136864 0.3956043956043956 +chr1 169619689 169619689 Lmx1a 0.11888111888111888 0.16783216783216784 +chr1 170362300 170362300 Pbx1 0.003996003996003996 0.002997002997002997 +chr1 180249284 180249284 Gm16586 0.0 0.0 +chr1 182823250 182823250 Lefty2 0.27472527472527475 0.33266733266733267 +chr1 182865170 182865170 Lefty1 0.25674325674325676 0.3086913086913087 +chr1 188529871 188529871 Tgfb2 0.13486513486513488 0.16583416583416583 +chr1 194979306 194979306 Irf6 0.12987012987012986 0.15284715284715283 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +chr1 19198995 19198995 Tfap2b +chr1 52557292 52557292 Nab1 +chr1 74838593 74838593 Wnt10a +chr1 74998246 74998246 Ihh +chr1 94076918 94076918 Hdac4 +chr1 152313295 152313295 Prg4 +chr1 170362300 170362300 Pbx1 +chr1 180249284 180249284 Gm16586 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicQualityControl/sparsity.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473 +chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000 +chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946 +chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054 +chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655 +chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev +# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 14274000 14278000 +chr1 14296000 14298000 +chr1 14314000 14319000 +chr1 14480000 14488000 +chr1 14491000 14501000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000 +chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605 +chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109 +chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783 +chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109 +chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev +# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: loose p-value with 0.5 +# Used p-value: 0.2 +# +chr1 14274000 14279000 +chr1 14285000 14308000 +chr1 14310000 14322000 +chr1 14361000 14395000 +chr1 14491000 14500000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473 +chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000 +chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946 +chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054 +chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655 +chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14295000 14298000 Eya1 832.0 -3000 0.05985576923100000002 0.06113759528369666629 4.79015312599299925012 49.79999999999999715783 +chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000 +chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891 +chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473 +chr1 14491000 14501000 Eya1 832.0 200000 0.02253605769199999720 0.00000000000003064216 41.39757163433100117800 18.75000000000000000000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3 +# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 14274000 14278000 +chr1 14296000 14298000 +chr1 14314000 14319000 +chr1 14480000 14488000 +chr1 14491000 14501000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3 +# targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 14295000 14298000 +chr1 14426000 14432000 +chr1 14447000 14455000 +chr1 14460000 14465000 +chr1 14491000 14501000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473 +chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000 +chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946 +chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054 +chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655 +chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 19089000 19091000 Tfap2d 472.0 -3000 0.06101694915199999680 0.18835888966198111039 4.06818820852600016025 28.80000000000000071054 +chr1 19104000 19106000 Tfap2d 472.0 11000 0.02245762711799999950 0.11671915718551462149 3.62722049649999966903 10.59999999999999964473 +chr1 19109000 19114000 Tfap2d 472.0 18000 0.03940677966200000631 0.00080680261510490681 9.61739201792699915927 18.60000000000000142109 +chr1 19125000 19129000 Tfap2d 472.0 33000 0.01652542372999999884 0.00829653069244939978 7.28507499155399962376 7.79999999999999982236 +chr1 19133000 19138000 Tfap2d 472.0 41000 0.01949152542399999744 0.00041957482022692005 9.72184228688099949522 9.19999999999999928946 +chr1 19197000 19202000 Tfap2d 472.0 108000 0.01059322033899999863 0.00398884532051024809 10.24326734149200035517 5.00000000000000000000 +chr1 19227000 19233000 Tfap2d 472.0 137000 0.01186440677899999914 0.00244241040005155341 14.41899403645599875290 5.59999999999999964473 +chr1 19254000 19261000 Tfap2d 472.0 163000 0.01355932203300000069 0.00004326025137579848 19.68794216164500454624 6.39999999999999946709 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 4509000 4515000 Sox17 810.0 23000 0.03432098765399999724 0.00000160319175224188 11.55191083898800030738 27.80000000000000071054 +chr1 4561000 4567000 Sox17 810.0 75000 0.01432098765400000029 0.00000102319718320310 11.23656007944399881637 11.59999999999999964473 +chr1 4585000 4590000 Sox17 810.0 98000 0.00987654320999999807 0.00037019878415911478 8.98479195802099894763 8.00000000000000000000 +chr1 4652000 4658000 Sox17 810.0 169000 0.00740740740700000008 0.00005538687174366785 11.12107213938599947767 6.00000000000000000000 +chr1 4499000 4500000 Sox17 810.0 12000 0.00987654320999999981 0.15859163588059266292 1.65903762227799989049 8.00000000000000000000 +chr1 4501000 4502000 Sox17 810.0 14000 0.00765432098799999957 0.17926099806325068720 1.57677828943600006895 6.20000000000000017764 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev +# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 14274000 14278000 +chr1 14296000 14298000 +chr1 14314000 14319000 +chr1 14480000 14488000 +chr1 14491000 14501000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev +# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 19089000 19091000 +chr1 19104000 19106000 +chr1 19109000 19114000 +chr1 19125000 19129000 +chr1 19133000 19138000 +chr1 19197000 19202000 +chr1 19227000 19233000 +chr1 19254000 19261000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev +# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed +# Mode: x-fold background with 1.5 +# Used p-value: 0.2 +# +chr1 4499000 4502000 +chr1 4509000 4515000 +chr1 4561000 4567000 +chr1 4585000 4590000 +chr1 4652000 4658000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000 +chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605 +chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109 +chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783 +chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109 +chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 19097000 19099000 Tfap2d 472.0 4000 0.04322033898299999788 0.18510915606880684603 3.09466471690400002359 20.39999999999999857891 +chr1 19103000 19106000 Tfap2d 472.0 11000 0.03305084745700000159 0.03717817323565530963 5.08894228542100002244 15.60000000000000142109 +chr1 19110000 19114000 Tfap2d 472.0 18000 0.03135593220400000047 0.00456343459440844423 7.84960476513000049437 14.79999999999999893419 +chr1 19126000 19129000 Tfap2d 472.0 33000 0.01271186440799999991 0.01781395819889997068 5.68520760692500015665 6.00000000000000000000 +chr1 19134000 19137000 Tfap2d 472.0 41000 0.01271186440799999991 0.00778984492262324579 6.25346808942800080899 6.00000000000000000000 +chr1 19162000 19198000 Tfap2d 472.0 69000 0.02966101695299999674 0.00000060908645727054 24.93693789855100106934 14.00000000000000532907 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 4483000 4496000 Sox17 810.0 0 0.64098765432000004427 0.00000017949046104970 15.90973968251499925941 519.20000000000004547474 +chr1 4497000 4503000 Sox17 810.0 12000 0.04592592592699999698 0.00009501601454375841 8.17222136878799965132 37.19999999999999573674 +chr1 4507000 4516000 Sox17 810.0 23000 0.04790123456699999643 0.00000000479943529363 15.54534421085400097695 38.80000000000000426326 +chr1 4533000 4543000 Sox17 810.0 46000 0.00839506173000000022 0.00536916279076038450 5.36115769549400056349 6.79999999999999893419 +chr1 4562000 4565000 Sox17 810.0 75000 0.00814814814800000030 0.00087160464483748701 6.21039574622800039094 6.59999999999999964473 +chr1 4567000 4585000 Sox17 810.0 81000 0.00814814814699999987 0.00084968562666110081 6.38963961746400066488 6.60000000000000053291 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 14295000 14303000 Eya1 832.0 -1000 0.51754807692400006669 0.00019954744684358428 10.99424166368200062038 430.60000000000002273737 +chr1 14304000 14307000 Eya1 832.0 4000 0.03052884615399999862 0.12043367620410594387 2.40926082355099957510 25.39999999999999857891 +chr1 14311000 14322000 Eya1 832.0 11000 0.05841346153899999727 0.00001294028787446333 12.63215080382700250539 48.59999999999999431566 +chr1 14369000 14382000 Eya1 832.0 69000 0.00793269231000000123 0.00220510219722336309 6.44339861264899926852 6.59999999999999875655 +chr1 14391000 14407000 Eya1 832.0 106000 0.01201923077000000006 0.00000515283260571486 11.00547257592000072179 10.00000000000000000000 +chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000 +chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891 +chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473 +chr1 14491000 14500000 Eya1 832.0 199000 0.01893028846099999857 0.00000000000000932587 35.26961282318300305860 15.75000000000000000000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 19077000 19082000 Tfap2d 800.0 -15000 0.01675000000000000100 0.00195382844240210574 8.20856302019300088091 13.40000000000000035527 +chr1 19083000 19095000 Tfap2d 800.0 0 0.41274999999999995026 0.00011621308769860228 18.49630381537900092326 330.19999999999998863132 +chr1 19096000 19114000 Tfap2d 800.0 3000 0.17700000000000001843 0.00042447176642534945 22.86014655871399980924 141.59999999999999431566 +chr1 19125000 19129000 Tfap2d 800.0 33000 0.01099999999999999936 0.00379145119303403444 4.83882643603000062171 8.80000000000000071054 +chr1 19135000 19139000 Tfap2d 800.0 43000 0.01175000000000000003 0.00015657417058367873 6.23967021246500053167 9.40000000000000035527 +chr1 19141000 19170000 Tfap2d 800.0 49000 0.02125000000000001193 0.00000543603606051324 15.65207577841900032922 17.00000000000000355271 +chr1 19195000 19208000 Tfap2d 800.0 105000 0.04900000000000001577 0.00000000000000000000 47.90516101420298866742 39.20000000000000284217 +chr1 19209000 19238000 Tfap2d 800.0 124000 0.09275000000000004075 0.00000000000000000000 112.06129567939001390187 74.20000000000000284217 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 +#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target +chr1 4472000 4492000 Sox17 978.0 0 0.66196319018500004994 0.00000000202165995056 17.41734930604599895787 647.40000000000009094947 +chr1 4493000 4496000 Sox17 978.0 6000 0.02576687116499999652 0.03614683764250059550 2.69049295166299984317 25.20000000000000284217 +chr1 4497000 4503000 Sox17 978.0 12000 0.03946830265799999848 0.00007297810251505332 7.02344214143100042946 38.60000000000000142109 +chr1 4520000 4531000 Sox17 978.0 37000 0.02269938650399999994 0.00000000003034350549 10.91808266157200080215 22.20000000000000284217 +chr1 4562000 4566000 Sox17 978.0 78000 0.00920245398800000058 0.00000732123325153378 7.15040494335099996448 9.00000000000000000000 +chr1 4569000 4593000 Sox17 978.0 93000 0.01022494887899999885 0.00001986913191398543 8.54218878677400006438 9.99999999999999822364 +chr1 4664000 4669000 Sox17 978.0 179000 0.00552147239400000052 0.00001416173948909361 8.93206575494200016863 5.40000000000000035527 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed +MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed +MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed +MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3 +# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed +# Mode: loose p-value with 0.5 +# Used p-value: 0.2 +# +chr1 14274000 14279000 +chr1 14285000 14308000 +chr1 14310000 14322000 +chr1 14361000 14407000 +chr1 14426000 14432000 +chr1 14447000 14455000 +chr1 14460000 14465000 +chr1 14491000 14500000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3 +# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed +# Mode: loose p-value with 0.5 +# Used p-value: 0.2 +# +chr1 19077000 19114000 +chr1 19125000 19129000 +chr1 19134000 19139000 +chr1 19141000 19238000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3 +# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed +# Mode: loose p-value with 0.5 +# Used p-value: 0.2 +# +chr1 4472000 4503000 +chr1 4507000 4516000 +chr1 4520000 4531000 +chr1 4533000 4543000 +chr1 4562000 4593000 +chr1 4664000 4669000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed +FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed +FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,3 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed +MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed +FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed +MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed +FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed +MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n' |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/referencePoints.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/referencePoints.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,43 @@ +chr1 4487435 4487435 Sox17 +chr1 14300280 14300280 Eya1 +chr1 19093103 19093103 Tfap2d +chr1 19198995 19198995 Tfap2b +chr1 24202042 24202042 Col9a1 +chr1 33776741 33776741 Rab23 +chr1 38684089 38684089 Aff3 +chr1 42753991 42753991 Pou3f3 +chr1 52176282 52176282 Stat1 +chr1 52557292 52557292 Nab1 +chr1 53118507 53118507 Mstn +chr1 57028178 57028178 Satb2 +chr1 59821123 59821123 Bmpr2 +chr1 66991630 66991630 Myl1 +chr1 74648029 74648029 Stk36 +chr1 74818466 74818466 Wnt6 +chr1 74838593 74838593 Wnt10a +chr1 74998246 74998246 Ihh +chr1 75356867 75356867 Des +chr1 77511663 77511663 Epha4 +chr1 78193711 78193711 Pax3 +chr1 89102386 89102386 Chrng +chr1 93355905 93355905 Per2 +chr1 93698054 93698054 Twist2 +chr1 94076918 94076918 Hdac4 +chr1 107677300 107677300 Tnfrsf11a +chr1 120950196 120950196 Gli2 +chr1 122499064 122499064 En1 +chr1 127808791 127808791 Lypd1 +chr1 135934092 135934092 Fmod +chr1 136186581 136186581 MyoG +chr1 152313295 152313295 Prg4 +chr1 164004278 164006270 mm712 +chr1 164147754 164147754 Dnm3os +chr1 165243781 165243781 Prrx1 +chr1 165333772 165333772 Gorab +chr1 169619689 169619689 Lmx1a +chr1 170362300 170362300 Pbx1 +chr1 180249284 180249284 Gm16586 +chr1 182823250 182823250 Lefty2 +chr1 182865170 182865170 Lefty1 +chr1 188529871 188529871 Tgfb2 +chr1 194979306 194979306 Irf6 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/cHi-C/referencePoints_chicViewpoint.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +chr1 4487435 4487435 Sox17 +chr1 14300280 14300280 Eya1 +chr1 19093103 19093103 Tfap2d + |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/distVsCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/distVsCounts.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b'@@ -0,0 +1,600 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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/find_TADs/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_score.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/find_TADs/multiFDR_tad_score.bm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_tad_score.bm Mon Dec 16 15:28:54 2019 -0500 |
| b |
| b'@@ -0,0 +1,24113 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| diff -r 000000000000 -r e136f22c2a0f test-data/find_TADs/multiFDR_zscore_matrix.h5 |
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| Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicAggregateContacts/test_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicAggregateContacts/test_regions.bed Mon Dec 16 15:28:54 2019 -0500 |
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| @@ -0,0 +1,55 @@ +2R 5441451 5441452 msl2_peak_1532 9.54697 +2R 8291271 8291272 msl2_peak_1644 7.36770 +2R 14575573 14575574 msl2_peak_1947 4.41313 +3L 628463 628464 msl2_peak_2780 11.60203 +3L 3903421 3903422 msl2_peak_2958 4.32242 +3L 8759529 8759530 msl2_peak_3195 4.10429 +3R 2901523 2901524 msl2_peak_4559 2.22040 +3R 3932152 3932153 msl2_peak_4603 9.59945 +3R 11851634 11851635 msl2_peak_4969 8.43238 +3R 20545331 20545332 msl2_peak_5267 4.72876 +X 147841 147842 msl2_peak_22671 16.59036 +X 366894 366895 msl2_peak_22686 25.37647 +X 517100 517101 msl2_peak_22694 8.54298 +X 548547 548548 msl2_peak_22696 27.53758 +X 656427 656428 msl2_peak_22697 14.11897 +X 692287 692288 msl2_peak_22698 15.96065 +X 818016 818017 msl2_peak_22713 10.66184 +X 937135 937136 msl2_peak_22717 67.84654 +X 1112721 1112722 msl2_peak_22727 26.81313 +X 1268823 1268824 msl2_peak_22735 29.73846 +X 1356647 1356648 msl2_peak_22736 9.58288 +X 1375009 1375010 msl2_peak_22738 4.49598 +X 1375616 1375617 msl2_peak_22739 128.36397 +X 1409093 1409094 msl2_peak_22742 14.72497 +X 1588015 1588016 msl2_peak_22757 102.61334 +X 1679121 1679122 msl2_peak_22767 16.12354 +X 1754043 1754044 msl2_peak_22769 20.51431 +X 1775025 1775026 msl2_peak_22773 43.05813 +X 1787755 1787756 msl2_peak_22774 142.73460 +X 1798236 1798237 msl2_peak_22775 80.66115 +X 1819545 1819546 msl2_peak_22777 11.21560 +X 1918989 1918990 msl2_peak_22793 74.48118 +X 1956476 1956477 msl2_peak_22794 32.73601 +X 1972291 1972292 msl2_peak_22795 37.39349 +X 2007235 2007236 msl2_peak_22798 11.21560 +X 2015927 2015928 msl2_peak_22799 68.80555 +X 2044335 2044336 msl2_peak_22804 36.60362 +X 2050114 2050115 msl2_peak_22805 47.23102 +X 2072937 2072938 msl2_peak_22807 52.37415 +X 2126007 2126008 msl2_peak_22808 42.23372 +X 2162302 2162303 msl2_peak_22810 78.64520 +X 2237610 2237611 msl2_peak_22817 43.05813 +X 2340287 2340288 msl2_peak_22825 14.72497 +X 2493295 2493296 msl2_peak_22827 23.47760 +X 2503119 2503120 msl2_peak_22828 80.83590 +X 2520611 2520612 msl2_peak_22839 17.87077 +X 2521079 2521080 msl2_peak_22840 60.08352 +X 2613112 2613113 msl2_peak_22844 43.87985 +X 2628624 2628625 msl2_peak_22847 115.37079 +X 3382405 3382406 msl2_peak_22879 6.13203 +X 3593688 3593689 msl2_peak_22908 10.66184 +X 3596515 3596516 msl2_peak_22909 6.59200 +X 3755342 3755343 msl2_peak_22919 164.76546 +X 3848197 3848198 msl2_peak_22920 74.65739 +X 4021813 4021814 msl2_peak_22929 32.73601 |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicAggregateContacts_results1.png |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicAverageRegions/regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicAverageRegions/regions.bed Mon Dec 16 15:28:54 2019 -0500 |
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| @@ -0,0 +1,6 @@ +chr2L 2500000 +chr2L 3500000 +chr2L 4500000 +chr2L 5500000 +chr2L 7000000 +chr2L 19000000 |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicAverageRegions/result.npz |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicAverageRegions/result_range_100000.npz |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicCompartmentsPolarization/pca1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicCompartmentsPolarization/pca1.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicConvertFormat/small_test_matrix_chr4.cool |
| b |
| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.cool has changed |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv Mon Dec 16 15:28:54 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicConvertFormat/small_test_matrix_chr4.homer |
| b |
| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicConvertFormat/test_matrix.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicConvertFormat/test_matrix.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicCorrectMatrix/diagnostic_plot.png |
| b |
| Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 |
| b |
| Binary file test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicCorrelate_heatmap_result1.png |
| b |
| Binary file test-data/hicCorrelate_heatmap_result1.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicCorrelate_scatter_result1.png |
| b |
| Binary file test-data/hicCorrelate_scatter_result1.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicFindRestrictionSites/reference_genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindRestrictionSites/reference_genome.fasta Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>chr1 +CTACGGTACGAACGTACGGTACGcgtaCGNAGTCATG |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicFindRestrictionSites/restriction_sites.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindRestrictionSites/restriction_sites.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +chr1 5 9 . 0 + +chr1 13 17 . 0 + +chr1 18 22 . 0 + +chr1 24 28 . 0 + |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicInfo/hicInfo_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Matrix information file. Created with HiCExplorer's hicInfo version 3.3 +File: matrix_name.h5 +Size: 33,754 +Bin_length: 5000 +Sum of matrix: 35778.0 +Chromosomes: chr2L, chr2LHet, chr2R, chr2RHet, chr3L, chr3LHet, chr3R, chr3RHet, chr4, chrM, chrUextra, chrU, chrX, chrXHet, chrYHet +Non-zero elements: 69,213 +Minimum (non zero): 1 +Maximum: 8 +NaN bins: 0 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicInfo_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInfo_output.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# Matrix information file. Created with HiCExplorer's hicInfo version 3.1 +File: matrix_name.h5 +Size: 3,383 +Bin_length: 50000 +Sum of matrix: 32798.5 +Chromosomes: chr2RHet, chr3RHet, chr2LHet, chr4, chrYHet, chr3L, chr2L, chrU, chrX, chrXHet, chr2R, chr3R, chrUextra, chrM, chr3LHet +Non-zero elements: 45,981 +Minimum (non zero): 1 +Maximum: 68 +NaN bins: 664 \ No newline at end of file |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicMergeLoops/gm12878_10kb.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicMergeLoops/gm12878_10kb.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicMergeLoops/gm12878_25kb.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicMergeLoops/gm12878_25kb.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicMergeLoops/gm12878_5kb.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicMergeLoops/gm12878_5kb.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicMergeLoops/gm12878_all.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicPlotSVL/p_values.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Mon Dec 16 15:28:54 2019 -0500 |
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| @@ -0,0 +1,4 @@ +# Created with HiCExplorer's hicPlotSVL 3.3 +# 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 000000000000 -r e136f22c2a0f test-data/hicPlotSVL/plot.png |
| b |
| Binary file test-data/hicPlotSVL/plot.png has changed |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicPlotSVL/ratios.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +# Created with HiCExplorer's hicPlotSVL 3.3 +# Short range vs long range contacts per chromosome: raw data +# Short range contacts: <= 2000000 +# 0_small_test_matrix.h5 1_small_test_matrix.h5 +# Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000 +chr2L 4.7639676113360325 11767 2470 4.7639676113360325 11767 2470 +chr3L 4.8960869565217395 11261 2300 4.8960869565217395 11261 2300 +chr4 |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicQuickQC/QC.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicQuickQC/QC.log Mon Dec 16 15:28:54 2019 -0500 |
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| @@ -0,0 +1,29 @@ + +File /tmp/tmpp4d6khlj.h5 +Sequenced reads 983 +Min rest. site distance 300 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Hi-C contacts 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +Low mapping quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 0 (0.00) +self ligation (removed) 0 (0.00) +One mate not close to rest site 0 (0.00) +same fragment 85 (28.33) +self circle 0 (0.00) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +Intra short range (< 20kb) 61 (28.37) +Intra long range (>= 20kb) 130 (60.47) +Read pair type: inward pairs 42 (19.53) +Read pair type: outward pairs 66 (30.70) +Read pair type: left pairs 48 (22.33) +Read pair type: right pairs 35 (16.28) |
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| diff -r 000000000000 -r e136f22c2a0f test-data/hicTransform/obs_exp_norm.h5 |
| b |
| Binary file test-data/hicTransform/obs_exp_norm.h5 has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicValidateLocations/loops_1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicValidateLocations/loops_1.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicValidateLocations/overlap_smc3_matched_locations --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Mon Dec 16 15:28:54 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/hicValidateLocations/overlap_smc3_statistics --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +# HiCExplorer hicValidateLocations 3.3 +# Overlap of loop file /tmp/tmpo82hqd2o/files/4/a/4/dataset_4a45db46-19b9-4b40-9d5b-d049a100e2aa.dat with protein file /tmp/tmpo82hqd2o/files/3/5/8/dataset_358b0ce7-ab08-46fc-8968-195d416429ca.dat +# +Protein peaks: 3097 +Matched Loops: 530 +Total Loops: 1007 +Loops match protein: 0.5263157894736842 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/li_32-33mb_interactions.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/li_32-33mb_interactions.bedgraph Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +X 3139841 3367043 X 2851659 3139841 28764.634828529033 +X 3139841 3367043 X 3139841 3367043 139691.503741355060 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/li_viewpoint_32-33Mb.png |
| b |
| Binary file test-data/li_viewpoint_32-33Mb.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/li_viewpoint_32Mb.png |
| b |
| Binary file test-data/li_viewpoint_32Mb.png has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/raw_qc_report --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_qc_report Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,29 @@ + +File matrix.cool +Sequenced reads 983 +Min rest. site distance 300 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Hi-C contacts 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +Low mapping quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 0 (0.00) +self ligation (removed) 0 (0.00) +One mate not close to rest site 0 (0.00) +same fragment 85 (28.33) +self circle 0 (0.00) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +Intra short range (< 20kb) 61 (28.37) +Intra long range (>= 20kb) 130 (60.47) +Read pair type: inward pairs 42 (19.53) +Read pair type: outward pairs 66 (30.70) +Read pair type: left pairs 48 (22.33) +Read pair type: right pairs 35 (16.28) |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regions.bed Mon Dec 16 15:28:54 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chrX 10000000 15000000 +chrX 18000000 22000000 |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/small_test_matrix.cool |
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| Binary file test-data/small_test_matrix.cool has changed |
| b |
| diff -r 000000000000 -r e136f22c2a0f test-data/small_test_matrix_result_sorted.bam |
| b |
| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
