Repository 'hicexplorer_hicdifferentialtad'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicdifferentialtad

Changeset 0:c852ad97ba28 (2021-03-16)
Next changeset 1:608538d083a2 (2023-01-12)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
added:
hicDifferentialTAD.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/hicDetectLoops.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/plot_svl.png
static/images/pulication_plots_viewpoint.png
static/images/z-score.svg
test-data/DpnII_10k.bed
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.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode.tar
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
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.txt
test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
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/plots.tar
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_failed_reference_points
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/new_referencepoints.bed_report
test-data/cHi-C/chicQualityControl/sparsity.png
test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt
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.txt
test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt
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_significant_interactions.txt
test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
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.txt
test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt
test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar
test-data/cHi-C/chicSignificantInteractions/targetFolder.tar
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.tar
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
test-data/cHi-C/chicViewpoint/viewpoints.tar
test-data/cHi-C/referencePoints.bed
test-data/cHi-C/referencePoints_chicViewpoint.bed
test-data/distVsCounts.txt
test-data/dm3_genes.bed.gz
test-data/domains.bed
test-data/find_TADs/multiFDR_boundaries.bed
test-data/find_TADs/multiFDR_boundaries.gff
test-data/find_TADs/multiFDR_domains.bed
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/hicDifferentialTAD/accepted.txt
test-data/hicDifferentialTAD/multiNone_domains.bed
test-data/hicDifferentialTAD/rejected.txt
test-data/hicFindRestrictionSites/reference_genome.fasta
test-data/hicFindRestrictionSites/restriction_sites.bed
test-data/hicHyperoptDetectLoops/hyperopt_results.txt
test-data/hicHyperoptDetectLoops/loops.bedgraph
test-data/hicInfo/hicInfo_output.txt
test-data/hicInfo_output.txt
test-data/hicMergeDomains/100kbtad_domains.bed
test-data/hicMergeDomains/10kbtad_domains.bed
test-data/hicMergeDomains/50kbtad_domains.bed
test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf
test-data/hicMergeDomains/ctcf_sorted.bed
test-data/hicMergeDomains/merged_list.bed
test-data/hicMergeDomains/relationship.txt
test-data/hicMergeDomains/two_files_relation_ctcf.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/multiNone_domains.bed
test-data/raw_qc_report
test-data/regions.bed
test-data/small_test_R1_unsorted.sam
test-data/small_test_R2_unsorted.sam
test-data/small_test_matrix.cool
test-data/small_test_matrix.h5
test-data/small_test_matrix_result_sorted.bam
b
diff -r 000000000000 -r c852ad97ba28 hicDifferentialTAD.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicDifferentialTAD.xml Tue Mar 16 21:17:26 2021 +0000
[
@@ -0,0 +1,81 @@
+<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>searches for differential TADs</description>
+    <macros>
+        <token name="@BINARY@">hicDifferentialTAD</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix_h5_cooler_target' 'matrix_target.$matrix_h5_cooler_target.ext' &&
+        ln -s '$matrix_h5_cooler_control' 'matrix_control.$matrix_h5_cooler_control.ext' &&
+
+        @BINARY@
+
+            --targetMatrix  'matrix_target.$matrix_h5_cooler_target.ext'
+            --controlMatrix  'matrix_control.$matrix_h5_cooler_control.ext'
+
+            #if $tadDomains:
+                --tadDomains '$tadDomains'
+            #end if
+
+            #if $pValue:
+                --pValue $pValue
+            #end if
+       
+            --mode $mode_selector
+            --modeReject $modeReject
+            --outFileNamePrefix galaxy_differential_tad
+            --threads @THREADS@
+
+]]>
+    </command>
+    <inputs>
+        <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" />
+        <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" />
+
+        <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." />
+        <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' />
+        <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression">
+            <option value="intra-TAD">intra-TAD</option>
+            <option value="left-inter-TAD">left-inter-TAD</option>
+            <option value="right-inter-TAD">right-inter-TAD</option>
+            <option value="all" selected="True">all</option>
+        </param>
+
+        <param name="modeReject" type="select" label="Method to compute the differentail TAD expression">
+            <option value="one" selected="True">one</option>
+            <option value="all">all</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' />
+        <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' />
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" />
+            <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" />
+
+            <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" />
+            <param name="pValue" value="1.0" />
+            <param name="mode_selector" value="all" />
+            <param name="modeReject" value="one" />
+            <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" />
+            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Differential TAD detection
+==========================
+
+Computes if precomputed TADs are differentially expressed between two samples.
+
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+
+]]>    </help>
+    <expand macro="citations" />
+</tool>
b
diff -r 000000000000 -r c852ad97ba28 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Mar 16 21:17:26 2021 +0000
[
b'@@ -0,0 +1,675 @@\n+<macros>\n+    <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+    <token name="@TOOL_VERSION@">3.6</token>\n+    <token name="@VERSION_SUFFIX@">0</token>\n+    <token name="@USE_RANGE@">\n+        #if $use_range.select_use_range == "yes_use_range":\n+            --range $use_range.range_min:$use_range.range_max\n+        #end if\n+    </token>\n+\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="@TOOL_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+    <xml name="dpi">\n+        <param argument=\'--dpi\' type=\'integer\' optional=\'true\' min="10" max="1000" label=\'DPI for image\' help=\'Change the default resolution of the plot.\' />\n+    </xml>\n+\n+    <xml name="restrictionCutFile">\n+        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments\n+                (i.e. the region between one restriction site and the next)." />\n+    </xml>\n+\n+    <xml name="restrictionSequence">\n+        <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or\n+            &quot;dangling-ends&quot;. If not given, such statistics will not be available.">\n+            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>\n+        </param>\n+    </xml>\n+    <xml name="danglingSequence">\n+        <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.\n+                    Each restriction enzyme recognizes a different DNA sequence and,\n+                    after cutting, they leave behind a specific \xe2\x80\x98sticky\xe2\x80\x99 end or dangling end sequence.\n+                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.\n+                    For DpnII, the restriction site and dangling end sequence are the same: GATC.\n+                    This information is easily found on the description of the restriction enzyme.\n+                    The dangling sequence is used to classify and report reads whose 5\xe2\x80\x99 end starts with such sequence as dangling-end reads.\n+                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">\n+            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>\n+        </param>\n+    </xml>\n+\n+    <xml name="zMax">\n+        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />\n+        <!-- this should only be ena'..b'e 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+            <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>\n+        </param>\n+    </xml>\n+\n+    <xml name="spacer_macro">\n+        <param name="spacer_width" type="float" value="" min="0" optional="True" 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="" min="5" optional="True" label="Fontsize" />\n+    </xml>\n+</macros>\n'
b
diff -r 000000000000 -r c852ad97ba28 static/images/SRR027956.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/SRR027956.svg Tue Mar 16 21:17:26 2021 +0000
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diff -r 000000000000 -r c852ad97ba28 test-data/DpnII_10k.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DpnII_10k.bed Tue Mar 16 21:17:26 2021 +0000
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/background.txt
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+++ b/test-data/cHi-C/background.txt Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,1002 @@\n+Relative position\tsize nbinom\tprob nbinom\tmax value\tmean value\n+-500000\t137.858473011804\t0.995405146787\t1.333333333333\t0.000543195980\n+-499000\t147.229076328303\t0.996053553980\t1.500000000000\t0.000497929648\n+-498000\t157.681167397960\t0.997075439230\t1.200000000000\t0.000394787078\n+-497000\t162.845011818209\t0.997421060405\t1.000000000000\t0.000359407866\n+-496000\t131.489161266395\t0.997174285891\t0.800000000000\t0.000318157645\n+-495000\t139.387908705363\t0.997380157213\t0.800000000000\t0.000311747258\n+-494000\t127.546293271132\t0.997238202254\t1.000000000000\t0.000305871070\n+-493000\t138.234947009504\t0.997287467570\t1.000000000000\t0.000319169812\n+-492000\t118.867084591776\t0.996746150847\t1.200000000000\t0.000333308009\n+-491000\t136.692711366757\t0.997596976644\t1.000000000000\t0.000279357932\n+-490000\t110.311895489180\t0.996860907065\t1.400000000000\t0.000296511490\n+-489000\t93.139811319915\t0.996396505949\t0.800000000000\t0.000287526293\n+-488000\t135.496044758383\t0.997607137097\t0.800000000000\t0.000277417947\n+-487000\t127.813813219580\t0.997234940661\t0.600000000000\t0.000303499976\n+-486000\t138.353019519830\t0.997370872576\t0.600000000000\t0.000311310637\n+-485000\t117.734214653130\t0.997150703846\t0.600000000000\t0.000287526293\n+-484000\t253.906771790139\t0.998721633870\t0.600000000000\t0.000277417947\n+-483000\t113.681955345001\t0.997258633583\t0.600000000000\t0.000266748026\n+-482000\t106.528817763059\t0.997446977501\t0.400000000000\t0.000232798277\n+-481000\t142.203512694686\t0.998164187841\t0.400000000000\t0.000223247579\n+-480000\t127.178039312326\t0.998116433009\t0.400000000000\t0.000204862484\n+-479000\t104.775871359451\t0.997936356279\t0.400000000000\t0.000184945298\n+-478000\t199.346310733692\t0.998727253220\t0.800000000000\t0.000216243733\n+-477000\t102.578276783249\t0.997550077888\t0.600000000000\t0.000219495518\n+-476000\t115.721950704400\t0.997595872644\t0.600000000000\t0.000241851543\n+-475000\t133.590972420114\t0.997943339775\t0.600000000000\t0.000234738263\n+-474000\t121.058775531555\t0.997410576803\t0.600000000000\t0.000268272300\n+-473000\t116.067738306830\t0.997619790696\t0.600000000000\t0.000236379789\n+-472000\t117.774900215669\t0.997459234865\t0.600000000000\t0.000256078105\n+-471000\t121.831143225353\t0.997650971922\t0.600000000000\t0.000248318162\n+-470000\t134.822925091174\t0.997041915657\t1.400000000000\t0.000341437473\n+-469000\t103.392243655163\t0.996159986674\t1.400000000000\t0.000341437473\n+-468000\t111.136948584269\t0.996810190304\t1.400000000000\t0.000307293726\n+-467000\t129.988284689535\t0.997433199130\t1.400000000000\t0.000287526293\n+-466000\t153.993902006927\t0.997480526600\t1.000000000000\t0.000331953099\n+-465000\t130.282565336089\t0.997421189028\t0.800000000000\t0.000287526293\n+-464000\t159.205319877438\t0.997931488108\t1.000000000000\t0.000281685915\n+-463000\t200.080959774898\t0.998171319733\t1.000000000000\t0.000312984350\n+-462000\t175.989753108966\t0.997447645086\t1.000000000000\t0.000384117157\n+-461000\t114.224052458199\t0.996401665926\t1.000000000000\t0.000352107394\n+-460000\t138.963759454412\t0.997361370093\t0.800000000000\t0.000317049082\n+-459000\t111.930590040859\t0.996761748733\t1.000000000000\t0.000310397703\n+-458000\t107.124635031856\t0.997129990391\t0.600000000000\t0.000263191385\n+-457000\t139.559368871572\t0.997725277767\t0.800000000000\t0.000271597990\n+-456000\t106.592655742084\t0.996971373730\t0.800000000000\t0.000276401764\n+-455000\t105.663670670915\t0.996933630757\t0.600000000000\t0.000277417947\n+-454000\t147.317172515235\t0.998101427721\t0.600000000000\t0.000243883909\n+-453000\t115.200337131843\t0.997742238764\t0.600000000000\t0.000224068342\n+-452000\t110.519882697522\t0.997936122327\t0.600000000000\t0.000195107127\n+-451000\t131.087083287591\t0.997969853868\t0.600000000000\t0.000227624982\n+-450000\t95.084412725215\t0.997080205489\t1.000000000000\t0.000242600310\n+-449000\t272.366855639715\t0.998970374155\t1.000000000000\t0.000239006231\n+-448000\t141.867214995723\t0.997803130066\t1.000000000000\t0.000265562479\n+-447000\t132.860415377154\t0.997595083877\t1.000000000000\t0.000275046853\n+-446000\t138.835886797127\t0.997236708437\t1.000000000000\t0.000332452276\n+-445000\t183.'..b'000000000\t0.000382823833\n+444000\t144.859828494596\t0.996903162520\t1.400000000000\t0.000384117157\n+445000\t181.127453398191\t0.997559041921\t1.400000000000\t0.000384117157\n+446000\t160.136119588827\t0.997366406029\t1.600000000000\t0.000359893553\n+447000\t153.653411583530\t0.997172630419\t1.200000000000\t0.000375581220\n+448000\t141.661704353510\t0.997163979271\t1.400000000000\t0.000345930071\n+449000\t124.591789049055\t0.996755483579\t1.400000000000\t0.000346179660\n+450000\t140.232016383950\t0.997067070092\t1.200000000000\t0.000352107394\n+451000\t136.018310879152\t0.997198243244\t1.000000000000\t0.000330767552\n+452000\t246.419596102391\t0.998452925685\t1.000000000000\t0.000325917588\n+453000\t133.267828865974\t0.997093260709\t1.000000000000\t0.000330767552\n+454000\t111.562325167782\t0.996668013833\t1.000000000000\t0.000325432591\n+455000\t136.735744503062\t0.997168723327\t1.000000000000\t0.000331395194\n+456000\t107.078418601392\t0.996473504625\t1.000000000000\t0.000323467080\n+457000\t129.245163973247\t0.997085556223\t1.000000000000\t0.000322468725\n+458000\t105.576577704040\t0.996545373786\t1.000000000000\t0.000312171404\n+459000\t127.868794891999\t0.997409239339\t0.800000000000\t0.000283033695\n+460000\t106.303153236011\t0.997074941993\t0.600000000000\t0.000266120383\n+461000\t126.838873099817\t0.997248182634\t0.800000000000\t0.000298757789\n+462000\t142.511212214533\t0.997018798351\t0.800000000000\t0.000363705134\n+463000\t110.665900101286\t0.996960672273\t0.800000000000\t0.000288455796\n+464000\t95.203501929856\t0.995744217821\t1.800000000000\t0.000347324326\n+465000\t137.363904547769\t0.997021971833\t1.800000000000\t0.000352107394\n+466000\t118.557203735630\t0.996290881001\t2.400000000000\t0.000376758591\n+467000\t104.819090517074\t0.995525960971\t2.800000000000\t0.000402408450\n+468000\t114.597405436879\t0.995690757202\t2.800000000000\t0.000423382467\n+469000\t129.271097317921\t0.997170331551\t1.400000000000\t0.000314762670\n+470000\t192.030681022578\t0.997984998366\t1.400000000000\t0.000330423361\n+471000\t148.206038001898\t0.997389657398\t1.000000000000\t0.000331090883\n+472000\t97.546089803069\t0.995843333605\t1.200000000000\t0.000347128098\n+473000\t95.851837787801\t0.995983996487\t1.200000000000\t0.000330056224\n+474000\t99.818854582017\t0.996557343281\t1.000000000000\t0.000294342649\n+475000\t148.008769541300\t0.997902427625\t0.600000000000\t0.000265562479\n+476000\t148.345768593866\t0.997933098098\t0.600000000000\t0.000262644210\n+477000\t123.596807612976\t0.997297923191\t0.600000000000\t0.000284531228\n+478000\t204.246569441019\t0.998287432528\t1.000000000000\t0.000298757789\n+479000\t132.924248355030\t0.997278666969\t0.800000000000\t0.000309427710\n+480000\t136.416688826340\t0.997425348906\t0.800000000000\t0.000301268359\n+481000\t118.446922382493\t0.997078476496\t1.000000000000\t0.000296247219\n+482000\t118.529156084928\t0.997003411887\t1.200000000000\t0.000304092749\n+483000\t190.680584441799\t0.998045921750\t1.000000000000\t0.000318674975\n+484000\t192.305361142196\t0.998005560472\t1.200000000000\t0.000328791641\n+485000\t171.354362305989\t0.997464844394\t1.200000000000\t0.000373052054\n+486000\t120.791244594597\t0.996480163123\t1.600000000000\t0.000364199971\n+487000\t230.056159698575\t0.998148828248\t1.600000000000\t0.000364199971\n+488000\t195.433175858843\t0.997957440166\t1.400000000000\t0.000341437473\n+489000\t126.632801152788\t0.996613466031\t1.600000000000\t0.000367303948\n+490000\t169.329748474940\t0.997643487089\t1.200000000000\t0.000341437473\n+491000\t136.266699963976\t0.997144438338\t1.000000000000\t0.000336264178\n+492000\t132.474984457930\t0.997281892907\t1.000000000000\t0.000312171404\n+493000\t143.910368825532\t0.997529065543\t1.200000000000\t0.000304092749\n+494000\t115.246894063938\t0.997187873361\t1.200000000000\t0.000278027657\n+495000\t170.264731113853\t0.997728931336\t1.200000000000\t0.000331682117\n+496000\t150.361715442266\t0.997070480810\t1.200000000000\t0.000380834105\n+497000\t132.494299731452\t0.996465234668\t1.400000000000\t0.000400817903\n+498000\t197.912620506313\t0.997679641998\t1.200000000000\t0.000393395349\n+499000\t142.734281997358\t0.996531092376\t1.000000000000\t0.000426796841\n+500000\t10.000000000000\tnan\t0.000000000000\t0.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode.tar
b
Binary file test-data/cHi-C/chicAggregateStatistic/batch_mode.tar has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 673.0 138000  523.00000
+chr1 14444000 14467000 Eya1 673.0 166000   10.00000
+chr1 14476000 14501000 Eya1 673.0 200000   30.25000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,5 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19118000 Tfap2d 472.0 24000  349.00000
+chr1 19120000 19274000 Tfap2d 472.0 180000   86.00000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,5 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4480000 4549000 Sox17 810.0 61000  640.00000
+chr1 4555000 4688000 Sox17 810.0 200000   73.18333
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 832.0 138000  645.00000
+chr1 14444000 14467000 Eya1 832.0 166000   25.00000
+chr1 14476000 14501000 Eya1 832.0 200000   26.15000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,5 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19118000 Tfap2d 800.0 24000  534.00000
+chr1 19120000 19274000 Tfap2d 800.0 180000  214.00000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,5 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4480000 4549000 Sox17 978.0 61000  798.00000
+chr1 4555000 4688000 Sox17 978.0 200000   82.93333
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 673.0 138000  523.00000
+chr1 14444000 14467000 Eya1 673.0 166000   10.00000
+chr1 14476000 14501000 Eya1 673.0 200000   30.25000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 832.0 138000  645.00000
+chr1 14444000 14467000 Eya1 832.0 166000   25.00000
+chr1 14476000 14501000 Eya1 832.0 200000   26.15000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 0.97540
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.05733
+chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.18635
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 0.97540
+chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.05733
+chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.18635
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25577
+chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00599
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25577
+chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00599
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.65155
+chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.70460
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.65155
+chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.70460
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.23380
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.23380
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19122000 19131000 Tfap2d 37000 472.00000 10.20000 800.00000 15.80000 0.69206
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19188000 19232000 Tfap2d 138000 472.00000 23.40000 800.00000 115.00000 0.00000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 19122000 19131000 Tfap2d 37000 472.00000 10.20000 800.00000 15.80000 0.69206
+chr1 19188000 19232000 Tfap2d 138000 472.00000 23.40000 800.00000 115.00000 0.00000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4512000 4529000 Sox17 41000 810.00000 24.80000 978.00000 33.20000 0.69177
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4534000 4544000 Sox17 56000 810.00000 7.00000 978.00000 13.20000 0.37830
+chr1 4585000 4590000 Sox17 102000 810.00000 8.00000 978.00000 2.40000 0.12513
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 4512000 4529000 Sox17 41000 810.00000 24.80000 978.00000 33.20000 0.69177
+chr1 4534000 4544000 Sox17 56000 810.00000 7.00000 978.00000 13.20000 0.37830
+chr1 4585000 4590000 Sox17 102000 810.00000 8.00000 978.00000 2.40000 0.12513
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013
+chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3
+# 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
+#
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000
+chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013
+chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
\ No newline at end of file
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicPlotViewpoint/batchMode/plots.tar
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicQualityControl/histogram.png
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diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,47 @@
+# Created with chicQualityControl version 3.6
+# A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
+# Used Matrices 0_matrix.cool 1_matrix.cool
+# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
+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 c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,13 @@
+# Created with chicQualityControl version 3.6
+# QC report for matrices: 0_matrix.cool 1_matrix.cool 
+#Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
+
+Number of reference points: 43
+Number of accepted reference points: 35
+Number of rejected reference points: 8
+Number of faulty reference points: 0
+
+
+A faulty reference point is caused by the non-presence of the chromosome in one of the given matrices.
+It can also be caused by the non-presence of valid Hi-C reads in a region, especially at the chromosome ends.
+Please check the results of hicInfo to validate this for your data.
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicQualityControl/sparsity.png
b
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.00283251424532149354 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.00000000000000000000 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.00001082770154392509 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.00008828123932902443 3.51709033858399999772 9.80000000000000071054
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,8 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1
+# /tmp/output_target_8dty7wuh/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
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,8 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.00706210137955387562 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10178166638720864690 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04060984916018672841 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.02428991556274540109 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000047362266253348 19.28508294646199772160 7.59999999999999875655
+chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000000011102 56.96782483342801128856 20.64999999999999857891
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.05859241166597439765 4.79015312599299925012 49.79999999999999715783
+chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602988210 13.72351582211000042832 9.00000000000000000000
+chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000003774758 22.36493893927400122834 12.39999999999999857891
+chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00000409886448993202 12.15366029908999934150 7.59999999999999964473
+chr1 14491000 14501000 Eya1 832.0 200000 0.02253605769199999720 0.00000000000000011102 41.39757163433100117800 18.75000000000000000000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
+# 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 c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
+# targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
+# 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 c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.00283251424532149354 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.00000000000000000000 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.00001082770154392509 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.00008828123932902443 3.51709033858399999772 9.80000000000000071054
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,8 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.00000000000000000000 4.06818820852600016025 28.80000000000000071054
+chr1 19104000 19106000 Tfap2d 472.0 11000 0.02245762711799999950 0.00000021753312740014 3.62722049649999966903 10.59999999999999964473
+chr1 19109000 19114000 Tfap2d 472.0 18000 0.03940677966200000631 0.00000013791919284412 9.61739201792699915927 18.60000000000000142109
+chr1 19125000 19129000 Tfap2d 472.0 33000 0.01652542372999999884 0.19640940181488197869 7.28507499155399962376 7.79999999999999982236
+chr1 19227000 19233000 Tfap2d 472.0 137000 0.01186440677899999914 0.19195463066672580066 14.41899403645599875290 5.59999999999999964473
+chr1 19097000 19098000 Tfap2d 472.0 4000 0.02542372881399999895 0.00000000000002398082 1.62514514601700010843 12.00000000000000000000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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 0.00000000034537894766 11.55191083898800030738 27.80000000000000071054
+chr1 4585000 4590000 Sox17 810.0 98000 0.00987654320999999807 0.08235176084316242484 8.98479195802099894763 8.00000000000000000000
+chr1 4484000 4485000 Sox17 810.0 -3000 0.03283950617300000069 0.00000000000000000000 1.52393745982299999575 26.60000000000000142109
+chr1 4499000 4500000 Sox17 810.0 12000 0.00987654320999999981 0.00000762924143549171 1.65903762227799989049 8.00000000000000000000
+chr1 4501000 4502000 Sox17 810.0 14000 0.00765432098799999957 0.00092861255189025105 1.57677828943600006895 6.20000000000000017764
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,8 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1
+# /tmp/output_target_83sqy1lg/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
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,11 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1
+# /tmp/output_target_83sqy1lg/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 19097000 19098000
+chr1 19104000 19106000
+chr1 19109000 19114000
+chr1 19125000 19129000
+chr1 19227000 19233000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,9 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1
+# /tmp/output_target_83sqy1lg/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 4484000 4485000
+chr1 4499000 4502000
+chr1 4509000 4515000
+chr1 4585000 4590000
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
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 0.00132401127244263783 9.15400589712000112286 7.00000000000000000000
+chr1 14295000 14372000 Eya1 673.0 -1000 0.73997028231099992723 0.00000273538672768137 71.55022378473699973256 497.99999999999977262632
+chr1 14391000 14404000 Eya1 673.0 99000 0.01485884100899999803 0.00000099822649402004 12.71460890380599906280 10.00000000000000000000
+chr1 14405000 14431000 Eya1 673.0 126000 0.01485884100399999762 0.00000000706881753132 16.50018487636599928692 10.00000000000000532907
+chr1 14447000 14465000 Eya1 673.0 150000 0.01485884100799999760 0.00000000163091362637 20.98645213257099939597 10.00000000000000177636
+chr1 14476000 14501000 Eya1 673.0 200000 0.04494799405200000653 0.00000000000000011102 81.22289233532099217427 30.24999999999999644729
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
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 19088000 19093000 Tfap2d 472.0 -1000 0.25550847457600001089 0.10302839603584690309 8.11832748109999968733 120.59999999999999431566
+chr1 19094000 19118000 Tfap2d 472.0 1000 0.38686440678100009194 0.02157410618457478169 32.83428528261499934615 182.60000000000005115908
+chr1 19124000 19141000 Tfap2d 472.0 33000 0.04661016949300000184 0.00000000000393274302 22.39995010446000023308 22.00000000000000000000
+chr1 19143000 19150000 Tfap2d 472.0 52000 0.01059322034000000079 0.01905738347386221054 7.00310519245599927274 5.00000000000000000000
+chr1 19153000 19185000 Tfap2d 472.0 65000 0.03177966102100000800 0.00000000000269295697 24.96572554191800108470 14.99999999999999467093
+chr1 19186000 19210000 Tfap2d 472.0 108000 0.03177966101800000498 0.00000001275562755421 29.45424687062300250773 15.00000000000000000000
+chr1 19215000 19251000 Tfap2d 472.0 137000 0.04237288135900001140 0.00000000000112376775 56.40252329690899557590 19.99999999999999644729
+chr1 19252000 19264000 Tfap2d 472.0 163000 0.01694915254200000249 0.00000062934133893133 24.34766306781100198009 8.00000000000000000000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,9 @@
+# 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 4480000 4518000 Sox17 810.0 0 0.76049382715799984656 0.00000000602330973987 45.61581246979399395514 616.00000000000011368684
+chr1 4520000 4549000 Sox17 810.0 44000 0.02962962962900000247 0.00000000000001332268 17.03851209048299963911 24.00000000000000710543
+chr1 4557000 4578000 Sox17 810.0 75000 0.02592592592600001522 0.00000000000051858517 20.41795056780900097237 21.00000000000000355271
+chr1 4582000 4590000 Sox17 810.0 98000 0.01111111110999999860 0.00013740149648666655 9.96981855628800062163 9.00000000000000000000
+chr1 4592000 4634000 Sox17 810.0 116000 0.02839506171900002887 0.00000000000000011102 32.07927393785299585716 22.99999999999999289457
+chr1 4641000 4670000 Sox17 810.0 169000 0.01604938270900000546 0.00000000034415081895 23.33313824700799798961 12.99999999999999644729
+chr1 4671000 4688000 Sox17 810.0 191000 0.00763374485400000052 0.00000023615040700697 14.23725687309200438335 6.18333333333300050327
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,5 @@
+# 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 14290000 14439000 Eya1 832.0 -1000 0.77524038462200028921 0.00000003592597119795 124.40376311550902244107 645.00000000000000000000
+chr1 14444000 14467000 Eya1 832.0 149000 0.03004807692100000191 0.00000000000000011102 43.43355247431500032462 25.00000000000000000000
+chr1 14484000 14501000 Eya1 832.0 200000 0.02902644230799999656 0.00000000000000011102 53.10190206687700253951 24.15000000000000213163
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+# 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 19083000 Tfap2d 800.0 -15000 0.01875000000000000278 0.00009145581248537482 9.05078678760400023862 15.00000000000000000000
+chr1 19084000 19118000 Tfap2d 800.0 0 0.64874999999999971578 0.00000005045883955113 44.36507725070399033029 518.99999999999988631316
+chr1 19120000 19249000 Tfap2d 800.0 105000 0.25625000000000008882 0.00000000000000011102 244.06286621622496113559 204.99999999999994315658
+chr1 19258000 19274000 Tfap2d 800.0 169000 0.01000000000000000021 0.00000152506365280747 14.62211731845800244400 8.00000000000000000000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
--- /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_significant_interactions.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,8 @@
+# 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 4480000 4549000 Sox17 978.0 0 0.81595092025199977837 0.00000000000956168478 62.24249077437998067808 797.99999999999988631316
+chr1 4555000 4575000 Sox17 978.0 78000 0.02147239264300000727 0.00000000000005484502 17.04008783523400438753 21.00000000000000000000
+chr1 4577000 4591000 Sox17 978.0 93000 0.00715746421499999924 0.00023632212134716557 6.23881980673299985085 6.99999999999999911182
+chr1 4599000 4632000 Sox17 978.0 128000 0.01738241309700000112 0.00000000000000011102 20.66516512408400174650 16.99999999999999289457
+chr1 4634000 4662000 Sox17 978.0 169000 0.01635991820800000371 0.00000000000171385128 23.27331220218900398322 15.99999999999999644729
+chr1 4663000 4688000 Sox17 978.0 200000 0.02242672120499999977 0.00000000000000011102 39.41625174041998747043 21.93333333333300316781
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,9 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 14274000 14279000
+chr1 14290000 14439000
+chr1 14444000 14467000
+chr1 14484000 14501000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 19077000 19118000
+chr1 19120000 19274000
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 4480000 4549000
+chr1 4555000 4688000
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar
b
Binary file test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar has changed
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicSignificantInteractions/targetFolder.tar
b
Binary file test-data/cHi-C/chicSignificantInteractions/targetFolder.tar has changed
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1.tar
b
Binary file test-data/cHi-C/chicViewpoint/output_1.tar has changed
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.999999994943\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t141350"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.998003530647\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.999352809734\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.999664588125\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.999918251505\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.989304103068\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.999999999417\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.997208984795\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.999780212263\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.981475867334\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.944032684304\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.999936032663\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.999594131731\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t1.000000000000\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t1.000000000000\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t1.000000000000\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t1.000000000000\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.000000000000\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t1.000000000000\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t1.000000000000\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.000000000000\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.000000000000\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t1.000000000000\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t1.000000000000\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t1.000000000000\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t1.000000000000\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t1.000000000000\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t1.000000000000\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.000000000000\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.000000000000\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.000000000000\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.000000000000\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.000000000000\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.000000000000\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.000000000000\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.000000000000\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.000000000000\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t0.000000000000\t7.575723225668\t3.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t1.000000000000\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t1.000000000000\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.999999994943\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t"..b'4\t0.998003530647\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.000647190266\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.000335411875\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.000081748495\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.989304103068\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t1.000000000000\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.999999999417\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.997208984795\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.999780212263\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.981475867334\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.944032684304\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.999936032663\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.999594131731\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t1.000000000000\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t1.000000000000\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t1.000000000000\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t1.000000000000\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t1.000000000000\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t1.000000000000\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t1.000000000000\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t1.000000000000\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t1.000000000000\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t1.000000000000\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.999999994943\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000"..b'0.000493827160\t1.000000000000\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.998003530647\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.999352809734\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.999664588125\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.999918251505\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.989304103068\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t1.000000000000\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.000000000583\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.002791015205\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.000219787737\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.981475867334\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.944032684304\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.999936032663\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.999594131731\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t1.000000000000\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t1.000000000000\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t1.000000000000\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t1.000000000000\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t1.000000000000\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t1.000000000000\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t1.000000000000\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t1.000000000000\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t1.000000000000\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t1.000000000000\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t1.000000000000\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t1.000000000000\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t1.000000000000\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t1.000000000000\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t1.000000000000\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t1.000000000000\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t1.000000000000\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t1.000000000000\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t1.000000000000\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t1.000000000000\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t1.000000000000\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t1.000000000000\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t1.000000000000\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t1.000000000000\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t1.000000000000\t0.699377466512\t0.333333333333\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t1.000000000000\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t1.000000000000\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.999999994943\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t1.000000000000\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t141350"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.001996469353\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.000647190266\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.000335411875\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.999918251505\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.989304103068\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.999999999417\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.997208984795\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.999780212263\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.981475867334\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.944032684304\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.999936032663\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.999594131731\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t1.000000000000\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t1.000000000000\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t1.000000000000\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t1.000000000000\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t1.000000000000\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t1.000000000000\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t1.000000000000\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t1.000000000000\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t1.000000000000\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t1.000000000000\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t1.000000000000\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.000000000000\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.000000000000\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t1.000000000000\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.000000000000\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.000000000000\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.000000000000\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.000000000000\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.000000000000\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.000000000000\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.000000000000\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.000000000000\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.000000000000\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t0.000000000000\t6.127958811148\t3.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.999999994943\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t"..b'0\t0.998003530647\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.999352809734\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.999664588125\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.999918251505\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.989304103068\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t1.000000000000\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.999999999417\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.997208984795\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.999780212263\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.981475867334\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.944032684304\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.999936032663\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.999594131731\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t1.000000000000\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t1.000000000000\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t1.000000000000\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t1.000000000000\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t1.000000000000\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t1.000000000000\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t1.000000000000\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t1.000000000000\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t1.000000000000\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t1.000000000000\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t1.000000000000\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t1.000000000000\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t1.000000000000\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t1.000000000000\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t1.000000000000\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t1.000000000000\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t1.000000000000\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t1.000000000000\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t1.000000000000\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t1.000000000000\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t1.000000000000\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3.1\n+# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.999999994943\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000"..b'0.000613496933\t1.000000000000\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.998003530647\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.999352809734\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.999664588125\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.999918251505\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.989304103068\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t1.000000000000\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.999999999417\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.002791015205\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.000219787737\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.981475867334\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.944032684304\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.999936032663\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.999594131731\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t1.000000000000\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.000000000000\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.000000000000\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.000000000000\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.000000000000\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.000000000000\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t1.000000000000\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t1.000000000000\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t1.000000000000\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t1.000000000000\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t1.000000000000\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.000000000000\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.000000000000\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t1.000000000000\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.000000000000\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.000000000000\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t1.000000000000\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.000000000000\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t1.000000000000\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t1.000000000000\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t1.000000000000\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.000000000000\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t1.000000000000\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.000000000000\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.000000000000\t2.316956024029\t1.333333333333\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t1.000000000000\t0.0"..b'08665\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t1.000000000000\t1.591533108618\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t1.000000000000\t0.780082358626\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t1.000000000000\t0.813852157891\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t1.000000000000\t0.377777473345\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t1.000000000000\t0.387710125250\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t1.000000000000\t0.804681391196\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t1.000000000000\t0.853631790099\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t1.000000000000\t2.209060071856\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t1.000000000000\t1.740739337114\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t1.000000000000\t1.946633238000\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t1.000000000000\t2.611109005672\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t1.000000000000\t3.150313631272\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t1.000000000000\t1.707263580199\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t1.000000000000\t1.814813352082\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t1.000000000000\t1.806605148755\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t1.000000000000\t0.912259118375\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t1.000000000000\t0.475667144687\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t1.000000000000\t0.488628585681\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t1.000000000000\t3.452466352281\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t1.000000000000\t5.155266499539\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t1.000000000000\t4.559079214345\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t1.000000000000\t5.423459548891\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t1.000000000000\t5.638713926662\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t1.000000000000\t5.019309740274\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t1.000000000000\t3.323229640928\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t1.000000000000\t4.181187622141\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t1.000000000000\t4.818931539295\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t6.794212212290\t3.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\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\t0.009736859396\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.016726462474\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.023000625561\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.023000625561\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+c"..b'4\t0.000000000000\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.000000000000\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.000000000000\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.000000000000\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.000000000000\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.000000000000\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.000000000000\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.000000000000\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.000000000000\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.000000000000\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.000000000000\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.000000000000\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.000000000000\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.000000000000\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.000000000000\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.000000000000\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.000000000000\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.000000000000\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.000000000000\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000493827160\t1.000000000000\t0.626563751378\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t1.000000000000\t0.661173939568\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t1.000000000000\t0.648142502908\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t1.000000000000\t0.676200620074\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t1.000000000000\t1.386332452855\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t1.000000000000\t1.243833473318\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t1.000000000000\t1.245632721235\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t1.000000000000\t1.897031040397\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t1.000000000000\t1.999321931024\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t1.000000000000\t1.499232064694\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t1.000000000000\t1.166577475118\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t1.000000000000\t1.116847870700\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t1.000000000000\t0.614969855182\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t1.000000000000\t0.301316248499\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t1.000000000000\t0.317940593070\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t1.000000000000\t0.313881777236\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t1.000000000000\t0.322134462090\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t1.000000000000\t0.668580958364\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t1.000000000000\t0.354626046134\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t1.000000000000\t0.367085784780\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t1.000000000000\t0.361579498110\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t1.000000000000\t0.404346965794\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t1.000000000000\t0.373926115317\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t1.000000000000\t0.354626046134\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t1.000000000000\t0.376965859861\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t1.000000000000\t0.375260884294\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t1.000000000000\t0.757963440329\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t1.000000000000\t0.395214800462\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t1.000000000000\t0.405983997732\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t1.000000000000\t1.229370293696\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t1.000000000000\t1.168179917236\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t1.000000000000\t1.136392707872\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t1.000000000000\t1.228952281617\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t1.000000000000\t1.277728778668\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t1.000000000000\t0.834072951902\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t1.000000000000\t0.788900722520\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t1.000000000000\t0.347399909840\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t1.000000000000\t0.444875298484\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t1.000000000000\t0.627229741958\t0.333333333333\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\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\t0.028365821799\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.036748857670\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.042850447268\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.042850447268\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.042850447268\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t1.000000000000\t0"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.000000000000\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.000000000000\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.000000000000\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.000000000000\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.000000000000\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.000000000000\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.000000000000\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.000000000000\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.000000000000\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.000000000000\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.000000000000\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.000000000000\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.000000000000\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.000000000000\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.000000000000\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.000000000000\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.000000000000\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.000000000000\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.000000000000\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.000000000000\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.000000000000\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.000000000000\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.000000000000\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.000000000000\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.000000000000\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.000000000000\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.000000000000\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.000000000000\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.000000000000\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.000000000000\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.000000000000\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.000000000000\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t0.000000000000\t6.127958811148\t3.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr"..b'0\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t1.000000000000\t0.350915402129\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t1.000000000000\t0.629690695867\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t1.000000000000\t0.945902347688\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t1.000000000000\t0.960371964201\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t1.000000000000\t1.156750545807\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t1.000000000000\t0.910783479301\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t1.000000000000\t0.885869770168\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t1.000000000000\t0.565404234542\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t1.000000000000\t0.933985467557\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t1.000000000000\t0.610165403210\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t1.000000000000\t0.965744551450\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t1.000000000000\t0.953415898353\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t1.000000000000\t0.978483428599\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t1.000000000000\t0.676938220343\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t1.000000000000\t0.718117743421\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t1.000000000000\t0.371674357090\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t1.000000000000\t0.409401302867\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t1.000000000000\t0.366099241837\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t1.000000000000\t1.135800575275\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t1.000000000000\t1.077176615132\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t1.000000000000\t1.145033799329\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t1.000000000000\t0.759903290695\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t1.000000000000\t0.767437983333\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t1.000000000000\t0.411058797704\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t1.000000000000\t0.414912474122\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t1.000000000000\t0.394260722067\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t1.000000000000\t0.767065077813\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t1.000000000000\t0.829542790092\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t1.000000000000\t0.431233462800\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t1.000000000000\t0.422249431901\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t1.000000000000\t0.399380990776\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
--- /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.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t1.000000000000\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\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4323"..b'0.000613496933\t0.000000000000\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.000000000000\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.000000000000\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.000000000000\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.000000000000\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.000000000000\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.000000000000\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.000000000000\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.000000000000\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.000000000000\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.000000000000\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.000000000000\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.000000000000\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.000000000000\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.000000000000\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.000000000000\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.000000000000\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.000000000000\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.000000000000\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.000000000000\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.000000000000\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.000000000000\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.000000000000\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.000000000000\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.000000000000\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.000000000000\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.000000000000\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.000000000000\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.000000000000\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.000000000000\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.000000000000\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.000000000000\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.000000000000\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.000000000000\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.000000000000\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.000000000000\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.000000000000\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.000000000000\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.000000000000\t2.316956024029\t1.333333333333\n'
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/chicViewpoint/viewpoints.tar
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Binary file test-data/cHi-C/chicViewpoint/viewpoints.tar has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/cHi-C/referencePoints.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/referencePoints.bed Tue Mar 16 21:17:26 2021 +0000
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
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diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,4 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+
b
diff -r 000000000000 -r c852ad97ba28 test-data/distVsCounts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/distVsCounts.txt Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,600 @@\n+\tMatrix\tChromosome\tDistance\tContacts\n+0\tsmall_test_matrix_h5\tall\t0\t0.09142620133910055\n+1\tsmall_test_matrix_h5\tall\t5000\t0.07741782506891134\n+2\tsmall_test_matrix_h5\tall\t10000\t0.04433044715929309\n+3\tsmall_test_matrix_h5\tall\t15000\t0.03461983446557299\n+4\tsmall_test_matrix_h5\tall\t20000\t0.027541995607526563\n+5\tsmall_test_matrix_h5\tall\t25000\t0.023782660332541568\n+6\tsmall_test_matrix_h5\tall\t30000\t0.02002019841977069\n+7\tsmall_test_matrix_h5\tall\t35000\t0.01967193628907643\n+8\tsmall_test_matrix_h5\tall\t40000\t0.017480230691479873\n+9\tsmall_test_matrix_h5\tall\t45000\t0.015494884606233642\n+10\tsmall_test_matrix_h5\tall\t50000\t0.014013686402856293\n+11\tsmall_test_matrix_h5\tall\t55000\t0.012799142755089891\n+12\tsmall_test_matrix_h5\tall\t60000\t0.011404919302007028\n+13\tsmall_test_matrix_h5\tall\t65000\t0.011588417540514775\n+14\tsmall_test_matrix_h5\tall\t70000\t0.01084818501519938\n+15\tsmall_test_matrix_h5\tall\t75000\t0.010554561717352416\n+16\tsmall_test_matrix_h5\tall\t80000\t0.008769313368728748\n+17\tsmall_test_matrix_h5\tall\t85000\t0.00907137741704464\n+18\tsmall_test_matrix_h5\tall\t90000\t0.008328855454056958\n+19\tsmall_test_matrix_h5\tall\t95000\t0.009049098076693346\n+20\tsmall_test_matrix_h5\tall\t100000\t0.007140723035554228\n+21\tsmall_test_matrix_h5\tall\t105000\t0.006874701099952176\n+22\tsmall_test_matrix_h5\tall\t110000\t0.006488846360863585\n+23\tsmall_test_matrix_h5\tall\t115000\t0.005354792389613497\n+24\tsmall_test_matrix_h5\tall\t120000\t0.006584066558927396\n+25\tsmall_test_matrix_h5\tall\t125000\t0.005598802395209581\n+26\tsmall_test_matrix_h5\tall\t130000\t0.005990534954771461\n+27\tsmall_test_matrix_h5\tall\t135000\t0.005393743257820928\n+28\tsmall_test_matrix_h5\tall\t140000\t0.0048564062593680676\n+29\tsmall_test_matrix_h5\tall\t145000\t0.005338291746641075\n+30\tsmall_test_matrix_h5\tall\t150000\t0.0047404740474047405\n+31\tsmall_test_matrix_h5\tall\t155000\t0.004892544122943931\n+32\tsmall_test_matrix_h5\tall\t160000\t0.004864572698336437\n+33\tsmall_test_matrix_h5\tall\t165000\t0.004025474645517904\n+34\tsmall_test_matrix_h5\tall\t170000\t0.004538077778445633\n+35\tsmall_test_matrix_h5\tall\t175000\t0.0036380036079374624\n+36\tsmall_test_matrix_h5\tall\t180000\t0.003970402454430608\n+37\tsmall_test_matrix_h5\tall\t185000\t0.0030994222436206064\n+38\tsmall_test_matrix_h5\tall\t190000\t0.0034318742850261907\n+39\tsmall_test_matrix_h5\tall\t195000\t0.0034333212865919767\n+40\tsmall_test_matrix_h5\tall\t200000\t0.0031334739379331126\n+41\tsmall_test_matrix_h5\tall\t205000\t0.0035869303110682422\n+42\tsmall_test_matrix_h5\tall\t210000\t0.0030154087386545245\n+43\tsmall_test_matrix_h5\tall\t215000\t0.002865761689291101\n+44\tsmall_test_matrix_h5\tall\t220000\t0.0026254639828590396\n+45\tsmall_test_matrix_h5\tall\t225000\t0.0027774423378818984\n+46\tsmall_test_matrix_h5\tall\t230000\t0.0027483313702394976\n+47\tsmall_test_matrix_h5\tall\t235000\t0.002265997945495196\n+48\tsmall_test_matrix_h5\tall\t240000\t0.0025691400936980503\n+49\tsmall_test_matrix_h5\tall\t245000\t0.001904934687953556\n+50\tsmall_test_matrix_h5\tall\t250000\t0.00266190749871442\n+51\tsmall_test_matrix_h5\tall\t255000\t0.002511650426677964\n+52\tsmall_test_matrix_h5\tall\t260000\t0.0026942754215481487\n+53\tsmall_test_matrix_h5\tall\t265000\t0.0026650514839491215\n+54\tsmall_test_matrix_h5\tall\t270000\t0.002120762262550368\n+55\tsmall_test_matrix_h5\tall\t275000\t0.002697460144268655\n+56\tsmall_test_matrix_h5\tall\t280000\t0.0020314726660804706\n+57\tsmall_test_matrix_h5\tall\t285000\t0.002062606163552536\n+58\tsmall_test_matrix_h5\tall\t290000\t0.0020937642239417385\n+59\tsmall_test_matrix_h5\tall\t295000\t0.001973164956590371\n+60\tsmall_test_matrix_h5\tall\t300000\t0.0017917337301466792\n+61\tsmall_test_matrix_h5\tall\t305000\t0.0018532020901689148\n+62\tsmall_test_matrix_h5\tall\t310000\t0.0016107953682035073\n+63\tsmall_test_matrix_h5\tall\t315000\t0.002158710854363028\n+64\tsmall_test_matrix_h5\tall\t320000\t0.001429570824588618\n+65\tsmall_test_matrix_h5\tall\t325000\t0.0014301363193768258\n+66\tsmall_test_matrix_h5\tall\t330000\t0.0016133451036498129\n+67\tsmall_test_matrix_h5\tall\t335000\t0.0017966989463426518\n+68\tsmall_test_matrix_h5\tall\t340000\t0.0013709063214013709\n+69\tsmall_test_matrix_h5\tall\t3'..b'15\n+533\tsmall_test_matrix_h5\tall\t2670000\t7.141326858530314e-05\n+534\tsmall_test_matrix_h5\tall\t2675000\t0.0001785841845846132\n+535\tsmall_test_matrix_h5\tall\t2680000\t0.0001786352268667381\n+536\tsmall_test_matrix_h5\tall\t2685000\t0.0002858980773354299\n+537\tsmall_test_matrix_h5\tall\t2690000\t0.00010724243940802173\n+538\tsmall_test_matrix_h5\tall\t2695000\t0.00021454623471358077\n+539\tsmall_test_matrix_h5\tall\t2700000\t0.00021460762572430073\n+540\tsmall_test_matrix_h5\tall\t2705000\t0.00017889087656529517\n+541\tsmall_test_matrix_h5\tall\t2710000\t0.00010736525660296328\n+542\tsmall_test_matrix_h5\tall\t2715000\t3.57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diff -r 000000000000 -r c852ad97ba28 test-data/dm3_genes.bed.gz
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Binary file test-data/dm3_genes.bed.gz has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/domains.bed Tue Mar 16 21:17:26 2021 +0000
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b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,24113 @@\n+#{"step":15000,"minDepth":15000,"maxDepth":30000,"binsize":5000}\n+chr2L\t0\t5000\t0.000000\t0.000000\n+chr2L\t5000\t10000\t-0.260846\t-0.229327\n+chr2L\t10000\t15000\t-0.244737\t-0.217294\n+chr2L\t15000\t20000\t0.038826\t0.457739\n+chr2L\t20000\t25000\t0.248816\t0.195739\n+chr2L\t25000\t30000\t0.248816\t0.322439\n+chr2L\t30000\t35000\t-0.234167\t0.241686\n+chr2L\t35000\t40000\t0.480531\t0.299615\n+chr2L\t40000\t45000\t0.207538\t0.213937\n+chr2L\t45000\t50000\t0.207538\t0.234405\n+chr2L\t50000\t55000\t0.038826\t0.192227\n+chr2L\t55000\t60000\t0.207538\t0.234405\n+chr2L\t60000\t65000\t0.207538\t0.234405\n+chr2L\t65000\t70000\t0.207538\t0.099412\n+chr2L\t70000\t75000\t-0.234167\t-0.189929\n+chr2L\t75000\t80000\t-0.234167\t-0.057202\n+chr2L\t80000\t85000\t-0.234167\t-0.057202\n+chr2L\t85000\t90000\t0.296739\t0.075525\n+chr2L\t90000\t95000\t0.176728\t0.178248\n+chr2L\t95000\t100000\t0.707634\t0.178248\n+chr2L\t100000\t105000\t0.038826\t0.011046\n+chr2L\t105000\t110000\t-0.234167\t-0.057202\n+chr2L\t110000\t115000\t-0.234167\t-0.069183\n+chr2L\t115000\t120000\t0.248816\t0.075082\n+chr2L\t120000\t125000\t0.248816\t0.075082\n+chr2L\t125000\t130000\t-0.234167\t0.075082\n+chr2L\t130000\t135000\t0.176728\t0.057060\n+chr2L\t135000\t140000\t0.176728\t0.057060\n+chr2L\t140000\t145000\t0.207538\t0.064762\n+chr2L\t145000\t150000\t0.753523\t0.221726\n+chr2L\t150000\t155000\t0.207538\t0.085230\n+chr2L\t155000\t160000\t-0.234167\t-0.025196\n+chr2L\t160000\t165000\t-0.234167\t-0.025196\n+chr2L\t165000\t170000\t-0.234167\t0.063544\n+chr2L\t170000\t175000\t0.248816\t0.063544\n+chr2L\t175000\t180000\t0.779722\t0.063544\n+chr2L\t180000\t185000\t0.207538\t0.173970\n+chr2L\t185000\t190000\t0.618432\t0.155948\n+chr2L\t190000\t195000\t0.618432\t0.023221\n+chr2L\t195000\t200000\t-0.234167\t-0.189929\n+chr2L\t200000\t205000\t0.038826\t-0.121680\n+chr2L\t205000\t210000\t-0.234167\t-0.069183\n+chr2L\t210000\t215000\t0.248816\t-0.069183\n+chr2L\t215000\t220000\t0.248816\t0.374742\n+chr2L\t220000\t225000\t0.248816\t0.195827\n+chr2L\t225000\t230000\t0.248816\t0.195827\n+chr2L\t230000\t235000\t0.248816\t0.195827\n+chr2L\t235000\t240000\t0.248816\t0.075082\n+chr2L\t240000\t245000\t-0.234167\t0.075082\n+chr2L\t245000\t250000\t-0.234167\t-0.045664\n+chr2L\t250000\t255000\t-0.234167\t0.103511\n+chr2L\t255000\t260000\t0.176728\t0.206234\n+chr2L\t260000\t265000\t0.176728\t0.206234\n+chr2L\t265000\t270000\t0.480531\t0.426450\n+chr2L\t270000\t275000\t0.207538\t0.358202\n+chr2L\t275000\t280000\t0.207538\t0.064762\n+chr2L\t280000\t285000\t-0.234167\t-0.045664\n+chr2L\t285000\t290000\t0.176728\t0.057060\n+chr2L\t290000\t295000\t0.176728\t0.206234\n+chr2L\t295000\t300000\t-0.234167\t-0.040754\n+chr2L\t300000\t305000\t-0.234167\t-0.040754\n+chr2L\t305000\t310000\t0.587622\t0.164693\n+chr2L\t310000\t315000\t0.587622\t0.164693\n+chr2L\t315000\t320000\t0.038826\t0.011046\n+chr2L\t320000\t325000\t0.449720\t0.113770\n+chr2L\t325000\t330000\t0.707634\t0.045522\n+chr2L\t330000\t335000\t-0.234167\t-0.057202\n+chr2L\t335000\t340000\t-0.234167\t-0.057202\n+chr2L\t340000\t345000\t-0.234167\t-0.189929\n+chr2L\t345000\t350000\t-0.234167\t-0.189929\n+chr2L\t350000\t355000\t-0.234167\t-0.025196\n+chr2L\t355000\t360000\t-0.234167\t-0.025196\n+chr2L\t360000\t365000\t-0.234167\t-0.025196\n+chr2L\t365000\t370000\t-0.234167\t-0.025196\n+chr2L\t370000\t375000\t0.176728\t-0.087205\n+chr2L\t375000\t380000\t0.176728\t-0.087205\n+chr2L\t380000\t385000\t0.176728\t-0.087205\n+chr2L\t385000\t390000\t0.618432\t0.023221\n+chr2L\t390000\t395000\t0.207538\t-0.079502\n+chr2L\t395000\t400000\t0.207538\t-0.079502\n+chr2L\t400000\t405000\t-0.234167\t-0.057202\n+chr2L\t405000\t410000\t0.038826\t0.011046\n+chr2L\t410000\t415000\t0.738444\t0.197489\n+chr2L\t415000\t420000\t0.207538\t0.197489\n+chr2L\t420000\t425000\t0.207538\t0.197489\n+chr2L\t425000\t430000\t0.480531\t0.299615\n+chr2L\t430000\t435000\t0.207538\t0.352112\n+chr2L\t435000\t440000\t0.690520\t0.352112\n+chr2L\t440000\t445000\t0.248816\t-0.069183\n+chr2L\t445000\t450000\t-0.234167\t-0.069183\n+chr2L\t450000\t455000\t0.176728\t-0.087205\n+chr2L\t455000\t460000\t0.176728\t-0.087205\n+chr2L\t460000\t465000\t-0.234167\t-0.069183\n+chr2L\t465000\t470000\t0.248816\t0.097421\n+chr2L\t470000\t475000\t0.248816\t0.097421\n+chr2L\t475000\t480000\t0.038826\t0.165669\n+chr2L\t480000\t485000\t0.618432\t0.023221\n+chr2L\t485000\t490000\t0.618432\t0.023221\n+chr2L\t490000\t495000\t1.026516\t0.125242\n+chr2L\t495000\t500000\t-0.234167'..b'36915\t-0.109242\n+chrX\t21985000\t21990000\t-0.136915\t-0.109242\n+chrX\t21990000\t21995000\t-0.136915\t-0.109242\n+chrX\t21995000\t22000000\t-0.136915\t-0.109242\n+chrX\t22000000\t22005000\t-0.136915\t-0.109242\n+chrX\t22005000\t22010000\t-0.136915\t-0.109242\n+chrX\t22010000\t22015000\t-0.136915\t-0.109242\n+chrX\t22015000\t22020000\t-0.136915\t-0.109242\n+chrX\t22020000\t22025000\t-0.136915\t-0.109242\n+chrX\t22025000\t22030000\t-0.136915\t-0.109242\n+chrX\t22030000\t22035000\t-0.13691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diff -r 000000000000 -r c852ad97ba28 test-data/find_TADs/multiFDR_zscore_matrix.h5
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diff -r 000000000000 -r c852ad97ba28 test-data/hicAggregateContacts/test_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAggregateContacts/test_regions.bed Tue Mar 16 21:17:26 2021 +0000
b
@@ -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
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+3L 3903421 3903422 msl2_peak_2958 4.32242
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+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
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+X 692287 692288 msl2_peak_22698 15.96065
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+X 1112721 1112722 msl2_peak_22727 26.81313
+X 1268823 1268824 msl2_peak_22735 29.73846
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+X 1819545 1819546 msl2_peak_22777 11.21560
+X 1918989 1918990 msl2_peak_22793 74.48118
+X 1956476 1956477 msl2_peak_22794 32.73601
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+X 2007235 2007236 msl2_peak_22798 11.21560
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+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 c852ad97ba28 test-data/hicAggregateContacts_results1.png
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diff -r 000000000000 -r c852ad97ba28 test-data/hicAverageRegions/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAverageRegions/regions.bed Tue Mar 16 21:17:26 2021 +0000
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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 c852ad97ba28 test-data/hicAverageRegions/result.npz
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diff -r 000000000000 -r c852ad97ba28 test-data/hicAverageRegions/result_rangeInBins_100.npz
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diff -r 000000000000 -r c852ad97ba28 test-data/hicAverageRegions/result_range_100000.npz
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCompartmentsPolarization/pca1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicCompartmentsPolarization/pca1.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
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diff -r 000000000000 -r c852ad97ba28 test-data/hicConvertFormat/small_test_matrix_chr4.cool
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Binary file test-data/hicConvertFormat/small_test_matrix_chr4.cool has changed
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diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
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b
diff -r 000000000000 -r c852ad97ba28 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 c852ad97ba28 test-data/hicConvertFormat/test_matrix.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/test_matrix.bed Tue Mar 16 21:17:26 2021 +0000
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCorrectMatrix/diagnostic_plot.png
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5
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Binary file test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCorrelate_heatmap_result1.png
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Binary file test-data/hicCorrelate_heatmap_result1.png has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/hicCorrelate_scatter_result1.png
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Binary file test-data/hicCorrelate_scatter_result1.png has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/hicDifferentialTAD/accepted.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,4 @@
+# Created with HiCExplorer's hicDifferentialTAD version 3.6
+# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.
+# Accepted regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one 
+# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicDifferentialTAD/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/multiNone_domains.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,1402 @@\n+chr3L\t165000\t260000\tID_0.01_1\t-0.103166750000\t.\t165000\t260000\t31,120,180\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655000000\t.\t260000\t335000\t51,160,44\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848000000\t.\t335000\t360000\t31,120,180\n+chr3L\t360000\t485000\tID_0.01_4\t-0.058081500000\t.\t360000\t485000\t51,160,44\n+chr3L\t485000\t525000\tID_0.01_5\t-0.071697750000\t.\t485000\t525000\t31,120,180\n+chr3L\t525000\t680000\tID_0.01_6\t-0.106040500000\t.\t525000\t680000\t51,160,44\n+chr3L\t680000\t705000\tID_0.01_7\t-0.014885500000\t.\t680000\t705000\t31,120,180\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784000000\t.\t705000\t740000\t51,160,44\n+chr3L\t740000\t870000\tID_0.01_9\t0.009499750000\t.\t740000\t870000\t31,120,180\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.095469750000\t.\t870000\t1010000\t51,160,44\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.051821750000\t.\t1010000\t1040000\t31,120,180\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.058748750000\t.\t1040000\t1110000\t51,160,44\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349000000\t.\t1110000\t1210000\t31,120,180\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.056756500000\t.\t1210000\t1245000\t51,160,44\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.064143500000\t.\t1245000\t1300000\t31,120,180\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379000000\t.\t1300000\t1465000\t51,160,44\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.013072250000\t.\t1465000\t1535000\t31,120,180\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.087115250000\t.\t1535000\t1580000\t51,160,44\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.082358750000\t.\t1580000\t1640000\t31,120,180\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.062875500000\t.\t1640000\t1670000\t51,160,44\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945000000\t.\t1670000\t1735000\t31,120,180\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313000000\t.\t1735000\t1815000\t51,160,44\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.017235250000\t.\t1815000\t1850000\t31,120,180\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.025997500000\t.\t1850000\t1925000\t51,160,44\n+chr3L\t1925000\t2155000\tID_0.01_25\t0.000083250000\t.\t1925000\t2155000\t31,120,180\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.040196500000\t.\t2155000\t2260000\t51,160,44\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.075185750000\t.\t2260000\t2390000\t31,120,180\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071000000\t.\t2390000\t2460000\t51,160,44\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.091323250000\t.\t2460000\t2560000\t31,120,180\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.091796750000\t.\t2560000\t2600000\t51,160,44\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.093485500000\t.\t2600000\t2740000\t31,120,180\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.089278750000\t.\t2740000\t2885000\t51,160,44\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.089725750000\t.\t2885000\t2945000\t31,120,180\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899000000\t.\t2945000\t2960000\t51,160,44\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.035686500000\t.\t2960000\t3045000\t31,120,180\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.004668750000\t.\t3045000\t3135000\t51,160,44\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702000000\t.\t3135000\t3220000\t31,120,180\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463000000\t.\t3220000\t3255000\t51,160,44\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796000000\t.\t3255000\t3315000\t31,120,180\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.054998750000\t.\t3315000\t3345000\t51,160,44\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.042340750000\t.\t3345000\t3475000\t31,120,180\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.050976750000\t.\t3475000\t3515000\t51,160,44\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488000000\t.\t3515000\t3545000\t31,120,180\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.024579250000\t.\t3545000\t3615000\t51,160,44\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683000000\t.\t3615000\t3670000\t31,120,180\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.099453250000\t.\t3670000\t3765000\t51,160,44\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454000000\t.\t3765000\t3785000\t31,120,180\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084000000\t.\t3785000\t3825000\t51,160,44\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.061011750000\t.\t3825000\t3900000\t31,120,180\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.068453500000\t.\t3900000\t4000000\t51,160,44\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.030078750000\t.\t4000000\t4120000\t31,120,180\n+chr3L\t4120000\t4165000\tID_0.01_5'..b'.\t22780000\t22885000\t31,120,180\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.056834750000\t.\t22885000\t22985000\t51,160,44\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.023781500000\t.\t22985000\t23110000\t31,120,180\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625000000\t.\t23110000\t23185000\t51,160,44\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.002947250000\t.\t23185000\t23195000\t31,120,180\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.002757750000\t.\t23195000\t23415000\t51,160,44\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027000000\t.\t23415000\t23560000\t31,120,180\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602000000\t.\t23560000\t23770000\t51,160,44\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.111910500000\t.\t23770000\t23815000\t31,120,180\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.066076500000\t.\t23815000\t23920000\t51,160,44\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.042184750000\t.\t23920000\t24030000\t31,120,180\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.055795750000\t.\t24030000\t24160000\t51,160,44\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.015467250000\t.\t24160000\t24205000\t31,120,180\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.032601500000\t.\t24205000\t24345000\t51,160,44\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.062306500000\t.\t24345000\t24375000\t31,120,180\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.074939500000\t.\t24375000\t24450000\t51,160,44\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.098360750000\t.\t24450000\t24625000\t31,120,180\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.031713750000\t.\t24625000\t24745000\t51,160,44\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.085896250000\t.\t24745000\t24885000\t31,120,180\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.093237250000\t.\t24885000\t24995000\t51,160,44\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.058978500000\t.\t24995000\t25090000\t31,120,180\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.036742250000\t.\t25090000\t25165000\t51,160,44\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.046246500000\t.\t25165000\t25330000\t31,120,180\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.083033250000\t.\t25330000\t25405000\t51,160,44\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.005462250000\t.\t25405000\t25570000\t31,120,180\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.046540750000\t.\t25570000\t25580000\t51,160,44\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.018715750000\t.\t25580000\t25730000\t31,120,180\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.008588750000\t.\t25730000\t25880000\t51,160,44\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.105816250000\t.\t25880000\t25990000\t31,120,180\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403000000\t.\t25990000\t26050000\t51,160,44\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.093531500000\t.\t26050000\t26180000\t31,120,180\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.114692750000\t.\t26180000\t26275000\t51,160,44\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.100273500000\t.\t26275000\t26330000\t31,120,180\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304000000\t.\t26330000\t26490000\t51,160,44\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.062796500000\t.\t26490000\t26565000\t31,120,180\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.019744750000\t.\t26565000\t26640000\t51,160,44\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.074307250000\t.\t26640000\t26715000\t31,120,180\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789000000\t.\t26715000\t26870000\t51,160,44\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.024990500000\t.\t26870000\t27045000\t31,120,180\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189000000\t.\t27045000\t27155000\t51,160,44\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.006099250000\t.\t27155000\t27185000\t31,120,180\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.012810250000\t.\t27185000\t27250000\t51,160,44\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.049902750000\t.\t27250000\t27385000\t31,120,180\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305000000\t.\t27385000\t27420000\t51,160,44\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.049929500000\t.\t27420000\t27570000\t31,120,180\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.080943250000\t.\t27570000\t27700000\t51,160,44\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.015350000000\t.\t27700000\t27750000\t31,120,180\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.013577250000\t.\t27750000\t27770000\t51,160,44\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicDifferentialTAD/rejected.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt Tue Mar 16 21:17:26 2021 +0000
b
b"@@ -0,0 +1,1402 @@\n+# Created with HiCExplorer's hicDifferentialTAD version 3.6\n+# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.\n+# Rejected regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one \n+# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n+chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\tnan\t1.0\t1.0\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t1.0\t1.0\t1.0\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t1.0\t1.0\t1.0\n+chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t1.0\t1.0\t1.0\n+chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t1.0\t1.0\t1.0\n+chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t1.0\t1.0\t1.0\n+chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t1.0\t1.0\t1.0\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t1.0\t1.0\t1.0\n+chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t1.0\t1.0\t1.0\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t1.0\t1.0\t1.0\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1.0\t1.0\t1.0\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1.0\t1.0\t1.0\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1.0\t1.0\t1.0\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1.0\t1.0\t1.0\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1.0\t1.0\t1.0\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1.0\t1.0\t1.0\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1.0\t1.0\t1.0\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1.0\t1.0\t1.0\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1.0\t1.0\t1.0\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1.0\t1.0\t1.0\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1.0\t1.0\t1.0\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1.0\t1.0\t1.0\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1.0\t1.0\t1.0\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1.0\t1.0\t1.0\n+chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1.0\t1.0\t1.0\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t1.0\t1.0\t1.0\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t1.0\t1.0\t1.0\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t1.0\t1.0\t1.0\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t1.0\t1.0\t1.0\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t1.0\t1.0\t1.0\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t1.0\t1.0\t1.0\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t1.0\t1.0\t1.0\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t1.0\t1.0\t1.0\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t1.0\t1.0\t1.0\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t1.0\t1.0\t1.0\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t1.0\t1.0\t1.0\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t1.0\t1.0\t1.0\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t1.0\t1.0\t1.0\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t1.0\t1.0\t1.0\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t1.0\t1.0\t1.0\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t1.0\t1.0\t1.0\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t1.0\t1.0\t1.0\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t1.0\t1.0\t1.0\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t1.0\t1.0\t1.0\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t1.0\t1.0\t1.0\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t1.0\t1.0\t1.0\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t1.0\t1.0\t1.0\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t1.0\t1.0\t1.0\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t1.0\t1.0\t1.0\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t1.0\t1.0\t1.0\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t1.0\t1.0\t1.0\n+chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t1.0\t1.0\t1.0\n+chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t1.0\t1.0\t1.0\n+chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t1.0\t1.0\t1.0\n+chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t1.0\t1.0\t1.0\n+chr3L\t4270000\t4365000\tID_0.01_56\t-0.11633575\t.\t1.0\t1.0\t1.0\n+chr3L\t4365000\t4405000\tID_0.01_57\t-0.0944955\t.\t1.0\t1.0\t1.0\n+chr3L\t4405000\t4490000\tID_0.01_58\t-0.07463925\t.\t1.0\t1.0\t1.0\n+chr3L\t4490000\t4625000\tID_0.01_59\t0.00287075\t.\t1.0\t1.0\t1.0\n+chr3L\t4625000\t4650000\tID_0.01_60\t0.04064075\t.\t1.0\t1.0\t1.0\n+chr3L\t4650000\t4790000\tID_0.01_"..b'0.0932985\t.\t1.0\t1.0\t1.0\n+chr3R\t21615000\t21730000\tID_0.01_1340\t-0.081974\t.\t1.0\t1.0\t1.0\n+chr3R\t21730000\t21820000\tID_0.01_1341\t0.07025075\t.\t1.0\t1.0\t1.0\n+chr3R\t21820000\t21845000\tID_0.01_1342\t-0.00145975\t.\t1.0\t1.0\t1.0\n+chr3R\t21845000\t21950000\tID_0.01_1343\t0.0360515\t.\t1.0\t1.0\t1.0\n+chr3R\t21950000\t21990000\tID_0.01_1344\t0.002742\t.\t1.0\t1.0\t1.0\n+chr3R\t21990000\t22075000\tID_0.01_1345\t0.00713375\t.\t1.0\t1.0\t1.0\n+chr3R\t22075000\t22220000\tID_0.01_1346\t-0.087915\t.\t1.0\t1.0\t1.0\n+chr3R\t22220000\t22270000\tID_0.01_1347\t0.0614505\t.\t1.0\t1.0\t1.0\n+chr3R\t22270000\t22310000\tID_0.01_1348\t-0.02575325\t.\t1.0\t1.0\t1.0\n+chr3R\t22310000\t22380000\tID_0.01_1349\t-0.04946475\t.\t1.0\t1.0\t1.0\n+chr3R\t22380000\t22500000\tID_0.01_1350\t-0.055847\t.\t1.0\t1.0\t1.0\n+chr3R\t22500000\t22520000\tID_0.01_1351\t-0.0631105\t.\t1.0\t1.0\t1.0\n+chr3R\t22520000\t22605000\tID_0.01_1352\t-0.062648\t.\t1.0\t1.0\t1.0\n+chr3R\t22605000\t22695000\tID_0.01_1353\t-0.011252\t.\t1.0\t1.0\t1.0\n+chr3R\t22695000\t22780000\tID_0.01_1354\t-0.089033\t.\t1.0\t1.0\t1.0\n+chr3R\t22780000\t22885000\tID_0.01_1355\t-0.04050025\t.\t1.0\t1.0\t1.0\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.05683475\t.\t1.0\t1.0\t1.0\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.0237815\t.\t1.0\t1.0\t1.0\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625\t.\t1.0\t1.0\t1.0\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.00294725\t.\t1.0\t1.0\t1.0\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.00275775\t.\t1.0\t1.0\t1.0\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027\t.\t1.0\t1.0\t1.0\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602\t.\t1.0\t1.0\t1.0\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.1119105\t.\t1.0\t1.0\t1.0\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.0660765\t.\t1.0\t1.0\t1.0\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.04218475\t.\t1.0\t1.0\t1.0\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.05579575\t.\t1.0\t1.0\t1.0\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.01546725\t.\t1.0\t1.0\t1.0\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.0326015\t.\t1.0\t1.0\t1.0\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.0623065\t.\t1.0\t1.0\t1.0\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.0749395\t.\t1.0\t1.0\t1.0\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.09836075\t.\t1.0\t1.0\t1.0\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.03171375\t.\t1.0\t1.0\t1.0\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.08589625\t.\t1.0\t1.0\t1.0\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.09323725\t.\t1.0\t1.0\t1.0\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.0589785\t.\t1.0\t1.0\t1.0\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.03674225\t.\t1.0\t1.0\t1.0\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.0462465\t.\t1.0\t1.0\t1.0\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.08303325\t.\t1.0\t1.0\t1.0\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.00546225\t.\t1.0\t1.0\t1.0\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.04654075\t.\t1.0\t1.0\t1.0\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.01871575\t.\t1.0\t1.0\t1.0\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.00858875\t.\t1.0\t1.0\t1.0\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.10581625\t.\t1.0\t1.0\t1.0\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403\t.\t1.0\t1.0\t1.0\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.0935315\t.\t1.0\t1.0\t1.0\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.11469275\t.\t1.0\t1.0\t1.0\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.1002735\t.\t1.0\t1.0\t1.0\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304\t.\t1.0\t1.0\t1.0\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.0627965\t.\t1.0\t1.0\t1.0\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.01974475\t.\t1.0\t1.0\t1.0\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.07430725\t.\t1.0\t1.0\t1.0\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789\t.\t1.0\t1.0\t1.0\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.0249905\t.\t1.0\t1.0\t1.0\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189\t.\t1.0\t1.0\t1.0\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.00609925\t.\t1.0\t1.0\t1.0\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.01281025\t.\t1.0\t1.0\t1.0\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.04990275\t.\t1.0\t1.0\t1.0\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305\t.\t1.0\t1.0\t1.0\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.0499295\t.\t1.0\t1.0\t1.0\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.08094325\t.\t1.0\t1.0\t1.0\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.01535\t.\t1.0\tnan\t1.0\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.01357725\t.\t1.0\tnan\t1.0\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicFindRestrictionSites/reference_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/reference_genome.fasta Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,2 @@
+>chr1
+CTACGGTACGAACGTACGGTACGcgtaCGNAGTCATG
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicFindRestrictionSites/restriction_sites.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/restriction_sites.bed Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/hicHyperoptDetectLoops/loops.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,3 @@
+# Created by HiCExplorer hicHyperoptDetectLoops 3.6
+
+{'matrixFile': 'matrix.cool', 'maxLoopDistance': 2600000, 'maximumNumberOfLoops': 5, 'oet': 4.594451600287669, 'p': 0.07561093779253786, 'peakWidth': 2, 'pit': 68.07931954714506, 'pp': 0.021875258449572325, 'proteinFile': 'hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak', 'resolution': 2, 'threads': 1, 'windowSize': 10}
\ No newline at end of file
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicInfo/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,10 @@
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.4
+File: matrix_name.h5
+Size: 33,754
+Bin_length: 5000
+Sum of matrix: 35778.0
+Chromosomes:length: chr2L: 23011544 bp; chr2LHet: 368872 bp; chr2R: 21146708 bp; chr2RHet: 3288761 bp; chr3L: 24543557 bp; chr3LHet: 2555491 bp; chr3R: 27905053 bp; chr3RHet: 2517507 bp; chr4: 1351857 bp; chrM: 19517 bp; chrUextra: 29004656 bp; chrU: 10049037 bp; chrX: 22422827 bp; chrXHet: 204112 bp; chrYHet: 347038 bp; 
+Non-zero elements: 69,213
+Minimum (non zero): 1
+Maximum: 8
+NaN bins: 0
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo_output.txt Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/hicMergeDomains/100kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/100kbtad_domains.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,179 @@\n+1\t2600000\t3800000\tID_0.01_1\t-1.141686912309\t.\t2600000\t3800000\t31,120,180\n+1\t3800000\t6000000\tID_0.01_2\t-1.059483103498\t.\t3800000\t6000000\t51,160,44\n+1\t6000000\t7800000\tID_0.01_3\t-0.984430873493\t.\t6000000\t7800000\t31,120,180\n+1\t7800000\t8900000\tID_0.01_4\t-0.399067786162\t.\t7800000\t8900000\t51,160,44\n+1\t8900000\t9700000\tID_0.01_5\t-0.117593287650\t.\t8900000\t9700000\t31,120,180\n+1\t9700000\t10500000\tID_0.01_6\t-0.185496017524\t.\t9700000\t10500000\t51,160,44\n+1\t10500000\t11100000\tID_0.01_7\t-0.201392985635\t.\t10500000\t11100000\t31,120,180\n+1\t11100000\t12100000\tID_0.01_8\t-0.354700283296\t.\t11100000\t12100000\t51,160,44\n+1\t12100000\t13000000\tID_0.01_9\t-0.799256699715\t.\t12100000\t13000000\t31,120,180\n+1\t13000000\t13700000\tID_0.01_10\t-1.402270586960\t.\t13000000\t13700000\t51,160,44\n+1\t13700000\t15800000\tID_0.01_11\t-1.386012674902\t.\t13700000\t15800000\t31,120,180\n+1\t15800000\t16900000\tID_0.01_12\t-0.616324727763\t.\t15800000\t16900000\t51,160,44\n+1\t16900000\t18000000\tID_0.01_13\t-0.790309360336\t.\t16900000\t18000000\t31,120,180\n+1\t18000000\t19200000\tID_0.01_14\t-0.743221612017\t.\t18000000\t19200000\t51,160,44\n+1\t19200000\t20000000\tID_0.01_15\t-0.771014287578\t.\t19200000\t20000000\t31,120,180\n+1\t20000000\t21000000\tID_0.01_16\t-0.197406966417\t.\t20000000\t21000000\t51,160,44\n+1\t21000000\t23300000\tID_0.01_17\t-0.246857948260\t.\t21000000\t23300000\t31,120,180\n+1\t23300000\t24100000\tID_0.01_18\t-0.073204223258\t.\t23300000\t24100000\t51,160,44\n+1\t24100000\t25600000\tID_0.01_19\t-0.481483747078\t.\t24100000\t25600000\t31,120,180\n+1\t25600000\t26800000\tID_0.01_20\t-0.288019958082\t.\t25600000\t26800000\t51,160,44\n+1\t26800000\t27200000\tID_0.01_21\t-0.373426473072\t.\t26800000\t27200000\t31,120,180\n+1\t27200000\t28100000\tID_0.01_22\t-0.223857449717\t.\t27200000\t28100000\t51,160,44\n+1\t28100000\t29500000\tID_0.01_23\t-0.226553355171\t.\t28100000\t29500000\t31,120,180\n+1\t29500000\t31200000\tID_0.01_24\t-0.294342328563\t.\t29500000\t31200000\t51,160,44\n+1\t31200000\t32600000\tID_0.01_25\t-0.691915018713\t.\t31200000\t32600000\t31,120,180\n+1\t32600000\t34100000\tID_0.01_26\t-0.525120566221\t.\t32600000\t34100000\t51,160,44\n+1\t34100000\t35200000\tID_0.01_27\t-0.870691440603\t.\t34100000\t35200000\t31,120,180\n+1\t35200000\t36900000\tID_0.01_28\t-0.711717112535\t.\t35200000\t36900000\t51,160,44\n+1\t36900000\t37900000\tID_0.01_29\t-0.859237923761\t.\t36900000\t37900000\t31,120,180\n+1\t37900000\t39300000\tID_0.01_30\t-0.593840260031\t.\t37900000\t39300000\t51,160,44\n+1\t39300000\t40200000\tID_0.01_31\t-0.709231729337\t.\t39300000\t40200000\t31,120,180\n+1\t40200000\t40900000\tID_0.01_32\t-0.351235876672\t.\t40200000\t40900000\t51,160,44\n+1\t40900000\t41500000\tID_0.01_33\t-0.073064714746\t.\t40900000\t41500000\t31,120,180\n+1\t41500000\t43600000\tID_0.01_34\t-0.262432443657\t.\t41500000\t43600000\t51,160,44\n+1\t43600000\t44500000\tID_0.01_35\t0.149239103642\t.\t43600000\t44500000\t31,120,180\n+1\t44500000\t45200000\tID_0.01_36\t0.096413662017\t.\t44500000\t45200000\t51,160,44\n+1\t45200000\t46100000\tID_0.01_37\t-0.404853685700\t.\t45200000\t46100000\t31,120,180\n+1\t46100000\t46800000\tID_0.01_38\t-0.067313090808\t.\t46100000\t46800000\t51,160,44\n+1\t46800000\t47800000\tID_0.01_39\t-0.829091697703\t.\t46800000\t47800000\t31,120,180\n+1\t47800000\t49000000\tID_0.01_40\t-0.428048529291\t.\t47800000\t49000000\t51,160,44\n+1\t49000000\t50800000\tID_0.01_41\t-0.036098871211\t.\t49000000\t50800000\t31,120,180\n+1\t50800000\t51800000\tID_0.01_42\t-0.640230613455\t.\t50800000\t51800000\t51,160,44\n+1\t51800000\t52500000\tID_0.01_43\t-0.433531022931\t.\t51800000\t52500000\t31,120,180\n+1\t52500000\t53700000\tID_0.01_44\t-0.320908527204\t.\t52500000\t53700000\t51,160,44\n+1\t53700000\t55500000\tID_0.01_45\t-0.439064654323\t.\t53700000\t55500000\t31,120,180\n+1\t55500000\t57300000\tID_0.01_46\t-0.879707940385\t.\t55500000\t57300000\t51,160,44\n+1\t57300000\t59000000\tID_0.01_47\t-0.381026749753\t.\t57300000\t59000000\t31,120,180\n+1\t59000000\t60400000\tID_0.01_48\t-0.655963485561\t.\t59000000\t60400000\t51,160,44\n+1\t60400000\t61300000\tID_0.01_49\t-0.859845271814\t.\t60400000\t61300000\t31,120,180\n+1\t61300000\t62600000\tID_0.01_50\t-0.262470171293\t.\t61300000\t62600000\t51,160,44\n+1\t62600000\t63300000\tID_0.01_51\t-0.546928077555\t.\t62600000\t63300000\t31,120,180\n+1\t6330000'..b'.085993697651\t.\t183600000\t184700000\t51,160,44\n+1\t184700000\t186300000\tID_0.01_133\t-0.264326017277\t.\t184700000\t186300000\t31,120,180\n+1\t186300000\t187000000\tID_0.01_134\t-0.810844695593\t.\t186300000\t187000000\t51,160,44\n+1\t187000000\t189100000\tID_0.01_135\t-0.561032153453\t.\t187000000\t189100000\t31,120,180\n+1\t189100000\t190500000\tID_0.01_136\t-0.638786084967\t.\t189100000\t190500000\t51,160,44\n+1\t190500000\t192400000\tID_0.01_137\t-0.804987835576\t.\t190500000\t192400000\t31,120,180\n+1\t192400000\t193100000\tID_0.01_138\t-0.507139128164\t.\t192400000\t193100000\t51,160,44\n+1\t193100000\t196700000\tID_0.01_139\t-0.430679674288\t.\t193100000\t196700000\t31,120,180\n+1\t196700000\t197400000\tID_0.01_140\t-0.616769039323\t.\t196700000\t197400000\t51,160,44\n+1\t197400000\t198700000\tID_0.01_141\t-0.661933036585\t.\t197400000\t198700000\t31,120,180\n+1\t198700000\t199500000\tID_0.01_142\t-0.328622895529\t.\t198700000\t199500000\t51,160,44\n+1\t199500000\t200500000\tID_0.01_143\t-0.313487345050\t.\t199500000\t200500000\t31,120,180\n+1\t200500000\t201200000\tID_0.01_144\t-0.476811660882\t.\t200500000\t201200000\t51,160,44\n+1\t201200000\t202100000\tID_0.01_145\t-0.336680335423\t.\t201200000\t202100000\t31,120,180\n+1\t202100000\t203000000\tID_0.01_146\t-0.328206658579\t.\t202100000\t203000000\t51,160,44\n+1\t203000000\t204500000\tID_0.01_147\t-0.175368634940\t.\t203000000\t204500000\t31,120,180\n+1\t204500000\t205700000\tID_0.01_148\t-0.055292609383\t.\t204500000\t205700000\t51,160,44\n+1\t205700000\t206600000\tID_0.01_149\t-0.595915153530\t.\t205700000\t206600000\t31,120,180\n+1\t206600000\t208000000\tID_0.01_150\t-0.822116143046\t.\t206600000\t208000000\t51,160,44\n+1\t208000000\t210000000\tID_0.01_151\t-0.605461823805\t.\t208000000\t210000000\t31,120,180\n+1\t210000000\t211500000\tID_0.01_152\t-0.730355941393\t.\t210000000\t211500000\t51,160,44\n+1\t211500000\t213200000\tID_0.01_153\t-0.395995720491\t.\t211500000\t213200000\t31,120,180\n+1\t213200000\t214400000\tID_0.01_154\t-0.774652016856\t.\t213200000\t214400000\t51,160,44\n+1\t214400000\t215800000\tID_0.01_155\t-0.248691558239\t.\t214400000\t215800000\t31,120,180\n+1\t215800000\t218400000\tID_0.01_156\t-0.648407418733\t.\t215800000\t218400000\t51,160,44\n+1\t218400000\t220100000\tID_0.01_157\t-0.827592482183\t.\t218400000\t220100000\t31,120,180\n+1\t220100000\t221000000\tID_0.01_158\t-0.782329386852\t.\t220100000\t221000000\t51,160,44\n+1\t221000000\t222900000\tID_0.01_159\t-0.281723145889\t.\t221000000\t222900000\t31,120,180\n+1\t222900000\t223900000\tID_0.01_160\t-0.453846036859\t.\t222900000\t223900000\t51,160,44\n+1\t223900000\t225600000\tID_0.01_161\t-0.412075364480\t.\t223900000\t225600000\t31,120,180\n+1\t225600000\t226300000\tID_0.01_162\t-0.686074032274\t.\t225600000\t226300000\t51,160,44\n+1\t226300000\t227700000\tID_0.01_163\t-0.498861050155\t.\t226300000\t227700000\t31,120,180\n+1\t227700000\t228700000\tID_0.01_164\t-0.237089890217\t.\t227700000\t228700000\t51,160,44\n+1\t228700000\t229700000\tID_0.01_165\t-0.810630269570\t.\t228700000\t229700000\t31,120,180\n+1\t229700000\t230500000\tID_0.01_166\t-0.308673891608\t.\t229700000\t230500000\t51,160,44\n+1\t230500000\t231800000\tID_0.01_167\t-0.277432698909\t.\t230500000\t231800000\t31,120,180\n+1\t231800000\t233400000\tID_0.01_168\t-0.437570110362\t.\t231800000\t233400000\t51,160,44\n+1\t233400000\t234600000\tID_0.01_169\t-0.414319513122\t.\t233400000\t234600000\t31,120,180\n+1\t234600000\t235600000\tID_0.01_170\t-0.141395263545\t.\t234600000\t235600000\t51,160,44\n+1\t235600000\t236200000\tID_0.01_171\t-0.323799017466\t.\t235600000\t236200000\t31,120,180\n+1\t236200000\t236800000\tID_0.01_172\t-0.554960355802\t.\t236200000\t236800000\t51,160,44\n+1\t236800000\t237800000\tID_0.01_173\t-0.428483691552\t.\t236800000\t237800000\t31,120,180\n+1\t237800000\t240200000\tID_0.01_174\t-0.753565268993\t.\t237800000\t240200000\t51,160,44\n+1\t240200000\t241600000\tID_0.01_175\t-0.875271039667\t.\t240200000\t241600000\t31,120,180\n+1\t241600000\t243400000\tID_0.01_176\t-0.260297744910\t.\t241600000\t243400000\t51,160,44\n+1\t243400000\t244700000\tID_0.01_177\t-0.933246847344\t.\t243400000\t244700000\t31,120,180\n+1\t244700000\t245200000\tID_0.01_178\t-0.507093336860\t.\t244700000\t245200000\t51,160,44\n+1\t245200000\t247000000\tID_0.01_179\t-0.500640827349\t.\t245200000\t247000000\t31,120,180\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/10kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/10kbtad_domains.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,769 @@\n+1\t710000\t1250000\tID_0.01_1\t-1.092317509315\t.\t710000\t1250000\t31,120,180\n+1\t1250000\t1480000\tID_0.01_2\t-0.447503916673\t.\t1250000\t1480000\t51,160,44\n+1\t1480000\t1680000\tID_0.01_3\t-0.604504964540\t.\t1480000\t1680000\t31,120,180\n+1\t1680000\t1850000\tID_0.01_4\t-0.732633171546\t.\t1680000\t1850000\t51,160,44\n+1\t1850000\t2110000\tID_0.01_5\t-0.629554185360\t.\t1850000\t2110000\t31,120,180\n+1\t2110000\t2330000\tID_0.01_6\t-0.599226178976\t.\t2110000\t2330000\t51,160,44\n+1\t2330000\t2580000\tID_0.01_7\t-0.502359023333\t.\t2330000\t2580000\t31,120,180\n+1\t2580000\t2690000\tID_0.01_8\t-0.877928092599\t.\t2580000\t2690000\t51,160,44\n+1\t2690000\t3330000\tID_0.01_9\t-0.876074031445\t.\t2690000\t3330000\t31,120,180\n+1\t3330000\t3540000\tID_0.01_10\t-0.865581452964\t.\t3330000\t3540000\t51,160,44\n+1\t3540000\t3830000\tID_0.01_11\t-0.175894888290\t.\t3540000\t3830000\t31,120,180\n+1\t3830000\t4050000\tID_0.01_12\t-0.788906681678\t.\t3830000\t4050000\t51,160,44\n+1\t4050000\t5240000\tID_0.01_13\t-0.632755573429\t.\t4050000\t5240000\t31,120,180\n+1\t5240000\t5500000\tID_0.01_14\t-0.503708327228\t.\t5240000\t5500000\t51,160,44\n+1\t5500000\t5890000\tID_0.01_15\t-0.535834764679\t.\t5500000\t5890000\t31,120,180\n+1\t5890000\t6050000\tID_0.01_16\t-0.441476370945\t.\t5890000\t6050000\t51,160,44\n+1\t6050000\t6300000\tID_0.01_17\t-0.559846730427\t.\t6050000\t6300000\t31,120,180\n+1\t6300000\t6410000\tID_0.01_18\t0.002675653077\t.\t6300000\t6410000\t51,160,44\n+1\t6410000\t6530000\tID_0.01_19\t0.238899723051\t.\t6410000\t6530000\t31,120,180\n+1\t6530000\t6750000\tID_0.01_20\t-0.092340076456\t.\t6530000\t6750000\t51,160,44\n+1\t6750000\t6970000\tID_0.01_21\t-0.342531967121\t.\t6750000\t6970000\t31,120,180\n+1\t6970000\t7090000\tID_0.01_22\t0.315970506814\t.\t6970000\t7090000\t51,160,44\n+1\t7090000\t7270000\tID_0.01_23\t0.316345600741\t.\t7090000\t7270000\t31,120,180\n+1\t7270000\t7710000\tID_0.01_24\t0.041072322941\t.\t7270000\t7710000\t51,160,44\n+1\t7710000\t7830000\tID_0.01_25\t-0.367257028586\t.\t7710000\t7830000\t31,120,180\n+1\t7830000\t8020000\tID_0.01_26\t-0.060901177985\t.\t7830000\t8020000\t51,160,44\n+1\t8020000\t8410000\tID_0.01_27\t-0.372407842081\t.\t8020000\t8410000\t31,120,180\n+1\t8410000\t8920000\tID_0.01_28\t-0.353886989897\t.\t8410000\t8920000\t51,160,44\n+1\t8920000\t9170000\tID_0.01_29\t-0.155898280238\t.\t8920000\t9170000\t31,120,180\n+1\t9170000\t9320000\tID_0.01_30\t0.172890208942\t.\t9170000\t9320000\t51,160,44\n+1\t9320000\t9650000\tID_0.01_31\t0.230612768882\t.\t9320000\t9650000\t31,120,180\n+1\t9650000\t10000000\tID_0.01_32\t-0.364293326660\t.\t9650000\t10000000\t51,160,44\n+1\t10000000\t10240000\tID_0.01_33\t0.125733381547\t.\t10000000\t10240000\t31,120,180\n+1\t10240000\t10430000\tID_0.01_34\t0.185519613694\t.\t10240000\t10430000\t51,160,44\n+1\t10430000\t10560000\tID_0.01_35\t-0.068211721541\t.\t10430000\t10560000\t31,120,180\n+1\t10560000\t11070000\tID_0.01_36\t-0.209526581188\t.\t10560000\t11070000\t51,160,44\n+1\t11070000\t11320000\tID_0.01_37\t-0.442016430124\t.\t11070000\t11320000\t31,120,180\n+1\t11320000\t11710000\tID_0.01_38\t-0.153236335699\t.\t11320000\t11710000\t51,160,44\n+1\t11710000\t12080000\tID_0.01_39\t-0.291811622494\t.\t11710000\t12080000\t31,120,180\n+1\t12080000\t12300000\tID_0.01_40\t-0.378333995495\t.\t12080000\t12300000\t51,160,44\n+1\t12300000\t13000000\tID_0.01_41\t-0.259805470041\t.\t12300000\t13000000\t31,120,180\n+1\t13000000\t13365000\tID_0.01_42\t-1.067953037504\t.\t13000000\t13365000\t51,160,44\n+1\t13365000\t13780000\tID_0.01_43\t-1.156490175521\t.\t13365000\t13780000\t31,120,180\n+1\t13780000\t14310000\tID_0.01_44\t-1.051207076369\t.\t13780000\t14310000\t51,160,44\n+1\t14310000\t14620000\tID_0.01_45\t-0.562478325837\t.\t14310000\t14620000\t31,120,180\n+1\t14620000\t14870000\tID_0.01_46\t0.011917497078\t.\t14620000\t14870000\t51,160,44\n+1\t14870000\t15240000\tID_0.01_47\t-0.175593305400\t.\t14870000\t15240000\t31,120,180\n+1\t15240000\t15430000\tID_0.01_48\t0.732843695067\t.\t15240000\t15430000\t51,160,44\n+1\t15430000\t15640000\tID_0.01_49\t-0.097096568114\t.\t15430000\t15640000\t31,120,180\n+1\t15640000\t15850000\tID_0.01_50\t0.126020671904\t.\t15640000\t15850000\t51,160,44\n+1\t15850000\t16090000\tID_0.01_51\t-0.368966352544\t.\t15850000\t16090000\t31,120,180\n+1\t16090000\t16390000\tID_0.01_52\t-0.250126706658\t.\t16090000\t16390000\t51,160,44\n+1\t16390000\t16570000\tID_0.01_53\t-0.167971774967\t'..b'\t233980000\t234230000\tID_0.01_722\t0.136798678827\t.\t233980000\t234230000\t51,160,44\n+1\t234230000\t234620000\tID_0.01_723\t-0.186433248117\t.\t234230000\t234620000\t31,120,180\n+1\t234620000\t234740000\tID_0.01_724\t-0.360480782180\t.\t234620000\t234740000\t51,160,44\n+1\t234740000\t234860000\tID_0.01_725\t0.252946330572\t.\t234740000\t234860000\t31,120,180\n+1\t234860000\t235260000\tID_0.01_726\t0.754861401185\t.\t234860000\t235260000\t51,160,44\n+1\t235260000\t235670000\tID_0.01_727\t-0.448130419649\t.\t2352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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/50kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/50kbtad_domains.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,355 @@\n+1\t1650000\t2600000\tID_0.01_1\t-0.941207732888\t.\t1650000\t2600000\t31,120,180\n+1\t2600000\t3300000\tID_0.01_2\t-1.237580853228\t.\t2600000\t3300000\t51,160,44\n+1\t3300000\t3800000\tID_0.01_3\t-1.151700420320\t.\t3300000\t3800000\t31,120,180\n+1\t3800000\t4550000\tID_0.01_4\t-1.041662687209\t.\t3800000\t4550000\t51,160,44\n+1\t4550000\t5500000\tID_0.01_5\t-0.688597101194\t.\t4550000\t5500000\t31,120,180\n+1\t5500000\t6050000\tID_0.01_6\t-0.628644578723\t.\t5500000\t6050000\t51,160,44\n+1\t6050000\t6750000\tID_0.01_7\t-0.895952939155\t.\t6050000\t6750000\t31,120,180\n+1\t6750000\t7250000\tID_0.01_8\t-0.511165876940\t.\t6750000\t7250000\t51,160,44\n+1\t7250000\t7700000\tID_0.01_9\t0.355926203340\t.\t7250000\t7700000\t31,120,180\n+1\t7700000\t8400000\tID_0.01_10\t-0.385973482757\t.\t7700000\t8400000\t51,160,44\n+1\t8400000\t8900000\tID_0.01_11\t-0.297633621417\t.\t8400000\t8900000\t31,120,180\n+1\t8900000\t9200000\tID_0.01_12\t-0.103062710178\t.\t8900000\t9200000\t51,160,44\n+1\t9200000\t9650000\tID_0.01_13\t0.381386755351\t.\t9200000\t9650000\t31,120,180\n+1\t9650000\t10500000\tID_0.01_14\t-0.447368843956\t.\t9650000\t10500000\t51,160,44\n+1\t10500000\t11100000\tID_0.01_15\t-0.359017600599\t.\t10500000\t11100000\t31,120,180\n+1\t11100000\t12050000\tID_0.01_16\t-0.555500948051\t.\t11100000\t12050000\t51,160,44\n+1\t12050000\t13200000\tID_0.01_17\t-0.558021048643\t.\t12050000\t13200000\t31,120,180\n+1\t13200000\t13700000\tID_0.01_18\t-1.424878334272\t.\t13200000\t13700000\t51,160,44\n+1\t13700000\t14350000\tID_0.01_19\t-1.417230081378\t.\t13700000\t14350000\t31,120,180\n+1\t14350000\t14900000\tID_0.01_20\t-0.674184421719\t.\t14350000\t14900000\t51,160,44\n+1\t14900000\t15400000\tID_0.01_21\t-0.120096103025\t.\t14900000\t15400000\t31,120,180\n+1\t15400000\t15850000\tID_0.01_22\t0.056591795677\t.\t15400000\t15850000\t51,160,44\n+1\t15850000\t16850000\tID_0.01_23\t-0.419813857869\t.\t15850000\t16850000\t31,120,180\n+1\t16850000\t17250000\tID_0.01_24\t-0.887068568084\t.\t16850000\t17250000\t51,160,44\n+1\t17250000\t18000000\tID_0.01_25\t-0.818151721874\t.\t17250000\t18000000\t31,120,180\n+1\t18000000\t18900000\tID_0.01_26\t-0.733730593234\t.\t18000000\t18900000\t51,160,44\n+1\t18900000\t19600000\tID_0.01_27\t-0.677565744037\t.\t18900000\t19600000\t31,120,180\n+1\t19600000\t20050000\tID_0.01_28\t-0.351217184289\t.\t19600000\t20050000\t51,160,44\n+1\t20050000\t21000000\tID_0.01_29\t-0.161369381439\t.\t20050000\t21000000\t31,120,180\n+1\t21000000\t21550000\tID_0.01_30\t-0.349470139952\t.\t21000000\t21550000\t51,160,44\n+1\t21550000\t22000000\tID_0.01_31\t-0.348222230703\t.\t21550000\t22000000\t31,120,180\n+1\t22000000\t22400000\tID_0.01_32\t-0.455156564539\t.\t22000000\t22400000\t51,160,44\n+1\t22400000\t23300000\tID_0.01_33\t-0.490329118409\t.\t22400000\t23300000\t31,120,180\n+1\t23300000\t24100000\tID_0.01_34\t-0.195454888302\t.\t23300000\t24100000\t51,160,44\n+1\t24100000\t24350000\tID_0.01_35\t-0.508833512761\t.\t24100000\t24350000\t31,120,180\n+1\t24350000\t25150000\tID_0.01_36\t-0.474766388632\t.\t24350000\t25150000\t51,160,44\n+1\t25150000\t25550000\tID_0.01_37\t0.009562997912\t.\t25150000\t25550000\t31,120,180\n+1\t25550000\t26150000\tID_0.01_38\t-0.725354576289\t.\t25550000\t26150000\t51,160,44\n+1\t26150000\t26800000\tID_0.01_39\t0.012086774053\t.\t26150000\t26800000\t31,120,180\n+1\t26800000\t27300000\tID_0.01_40\t-0.496773634611\t.\t26800000\t27300000\t51,160,44\n+1\t27300000\t28050000\tID_0.01_41\t-0.122171629693\t.\t27300000\t28050000\t31,120,180\n+1\t28050000\t28550000\tID_0.01_42\t-0.107449220090\t.\t28050000\t28550000\t51,160,44\n+1\t28550000\t28950000\tID_0.01_43\t-0.240858507387\t.\t28550000\t28950000\t31,120,180\n+1\t28950000\t29550000\tID_0.01_44\t-0.105648280303\t.\t28950000\t29550000\t51,160,44\n+1\t29550000\t30200000\tID_0.01_45\t-0.609240092390\t.\t29550000\t30200000\t31,120,180\n+1\t30200000\t30700000\tID_0.01_46\t0.199001543736\t.\t30200000\t30700000\t51,160,44\n+1\t30700000\t31200000\tID_0.01_47\t0.374849061907\t.\t30700000\t31200000\t31,120,180\n+1\t31200000\t32550000\tID_0.01_48\t-0.477190179719\t.\t31200000\t32550000\t51,160,44\n+1\t32550000\t32850000\tID_0.01_49\t-0.268222026026\t.\t32550000\t32850000\t31,120,180\n+1\t32850000\t33300000\tID_0.01_50\t-0.298708034680\t.\t32850000\t33300000\t51,160,44\n+1\t33300000\t34100000\tID_0.01_51\t-0.083861512239\t.\t33300000\t34100000\t31,120,180\n+1\t34100000\t35200000\tID_0.01_52\t-0.846782123854'..b'0.567164872602\t.\t216900000\t217550000\t51,160,44\n+1\t217550000\t217950000\tID_0.01_309\t-0.088531062983\t.\t217550000\t217950000\t31,120,180\n+1\t217950000\t218450000\tID_0.01_310\t-0.491793817527\t.\t217950000\t218450000\t51,160,44\n+1\t218450000\t219350000\tID_0.01_311\t-0.979772940001\t.\t218450000\t219350000\t31,120,180\n+1\t219350000\t220100000\tID_0.01_312\t-0.101493710653\t.\t219350000\t220100000\t51,160,44\n+1\t220100000\t221000000\tID_0.01_313\t-0.733308192699\t.\t220100000\t221000000\t31,120,180\n+1\t221000000\t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diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf
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Binary file test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf has changed
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diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/ctcf_sorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/ctcf_sorted.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,3403 @@\n+chr1\t805186\t805436\t.\t0\t.\t59.5609057962358\t-1\t4.7429214225993\t125\n+chr1\t840030\t840280\t.\t0\t.\t83.6226028373057\t-1\t4.7429214225993\t125\n+chr1\t848233\t848483\t.\t0\t.\t21.7013707748217\t-1\t3.97409700379598\t125\n+chr1\t873538\t873788\t.\t0\t.\t19.5674784603862\t-1\t3.88351633069348\t125\n+chr1\t886823\t887073\t.\t0\t.\t22.5711320345953\t-1\t4.11312075496602\t125\n+chr1\t911486\t911736\t.\t0\t.\t31.509769734266\t-1\t4.27124510662348\t125\n+chr1\t919601\t919851\t.\t0\t.\t33.1859544183338\t-1\t4.7429214225993\t125\n+chr1\t937269\t937519\t.\t0\t.\t48.2208573550132\t-1\t4.7429214225993\t125\n+chr1\t950804\t951054\t.\t0\t.\t27.7376222191221\t-1\t4.296482367922\t125\n+chr1\t954689\t954939\t.\t0\t.\t19.1922365041399\t-1\t3.79979779059073\t125\n+chr1\t968355\t968605\t.\t0\t.\t27.9104706029461\t-1\t4.29525180136426\t125\n+chr1\t999239\t999489\t.\t0\t.\t67.3973204081303\t-1\t4.7429214225993\t125\n+chr1\t1057530\t1057780\t.\t0\t.\t88.0665088853952\t-1\t4.7429214225993\t125\n+chr1\t1166148\t1166398\t.\t0\t.\t27.9814352288374\t-1\t4.29482615193429\t125\n+chr1\t1200463\t1200713\t.\t0\t.\t33.5952614512378\t-1\t4.7429214225993\t125\n+chr1\t1225610\t1225860\t.\t0\t.\t73.9102584682168\t-1\t4.7429214225993\t125\n+chr1\t1227292\t1227542\t.\t0\t.\t69.7040984837778\t-1\t4.7429214225993\t125\n+chr1\t1235462\t1235712\t.\t0\t.\t45.538363572806\t-1\t4.7429214225993\t125\n+chr1\t1237377\t1237627\t.\t0\t.\t19.9924023420945\t-1\t3.87966283949506\t125\n+chr1\t1280051\t1280301\t.\t0\t.\t52.5126590486595\t-1\t4.7429214225993\t125\n+chr1\t1284662\t1284912\t.\t0\t.\t26.3007670733988\t-1\t4.30716073872335\t125\n+chr1\t1285194\t1285444\t.\t0\t.\t19.6869777946214\t-1\t3.882480265106\t125\n+chr1\t1307585\t1307668\t.\t0\t.\t98.4512721959962\t-1\t4.7429214225993\t33\n+chr1\t1334834\t1335084\t.\t0\t.\t45.7165675131359\t-1\t4.7429214225993\t125\n+chr1\t1337531\t1337625\t.\t0\t.\t129.568164313081\t-1\t4.7429214225993\t15\n+chr1\t1376405\t1376551\t.\t0\t.\t112.104098738192\t-1\t4.7429214225993\t78\n+chr1\t1440337\t1440587\t.\t0\t.\t50.3693879296427\t-1\t4.7429214225993\t125\n+chr1\t1486555\t1486805\t.\t0\t.\t23.5386437775045\t-1\t4.32716132803452\t125\n+chr1\t1509199\t1509449\t.\t0\t.\t24.0579975291309\t-1\t4.32323146812351\t125\n+chr1\t1533113\t1533363\t.\t0\t.\t28.1831148336541\t-1\t4.29344358599487\t125\n+chr1\t1597192\t1597442\t.\t0\t.\t40.4396667960704\t-1\t4.7429214225993\t125\n+chr1\t1610383\t1610633\t.\t0\t.\t18.8867819454862\t-1\t3.80287941044449\t125\n+chr1\t1720538\t1720788\t.\t0\t.\t20.2783981866113\t-1\t3.87717290488528\t125\n+chr1\t1790091\t1790341\t.\t0\t.\t20.1334751599979\t-1\t3.87840050291318\t125\n+chr1\t1837789\t1837915\t.\t0\t.\t147.268012144206\t-1\t4.7429214225993\t74\n+chr1\t1840463\t1840713\t.\t0\t.\t26.3851329756002\t-1\t4.30646077049034\t125\n+chr1\t1875555\t1875662\t.\t0\t.\t106.834270840707\t-1\t4.7429214225993\t32\n+chr1\t1891605\t1891733\t.\t0\t.\t131.407645767539\t-1\t4.7429214225993\t63\n+chr1\t1976452\t1976520\t.\t0\t.\t87.5358082894933\t-1\t4.7429214225993\t11\n+chr1\t1977991\t1978241\t.\t0\t.\t73.4031161610917\t-1\t4.7429214225993\t125\n+chr1\t1980938\t1981188\t.\t0\t.\t61.7452349072252\t-1\t4.7429214225993\t125\n+chr1\t2040119\t2040369\t.\t0\t.\t23.8201211984674\t-1\t4.32501595101874\t125\n+chr1\t2063702\t2063952\t.\t0\t.\t21.9975491279828\t-1\t3.97170648286736\t125\n+chr1\t2071507\t2071645\t.\t0\t.\t114.969306459524\t-1\t4.7429214225993\t67\n+chr1\t2105852\t2105978\t.\t0\t.\t122.600087913384\t-1\t4.7429214225993\t61\n+chr1\t2126654\t2126904\t.\t0\t.\t86.7497585482926\t-1\t4.7429214225993\t125\n+chr1\t2144503\t2144753\t.\t0\t.\t20.0994558159811\t-1\t3.87871962123126\t125\n+chr1\t2246665\t2246915\t.\t0\t.\t20.7731784135031\t-1\t3.9821096350928\t125\n+chr1\t2313240\t2313490\t.\t0\t.\t84.2342744659508\t-1\t4.7429214225993\t125\n+chr1\t2314098\t2314348\t.\t0\t.\t62.0405584533353\t-1\t4.7429214225993\t125\n+chr1\t2345876\t2346126\t.\t0\t.\t87.6097808292363\t-1\t4.7429214225993\t125\n+chr1\t2361551\t2361801\t.\t0\t.\t80.0672677773095\t-1\t4.7429214225993\t125\n+chr1\t2470816\t2471066\t.\t0\t.\t28.4737352542628\t-1\t4.29140585420779\t125\n+chr1\t2479588\t2479691\t.\t0\t.\t108.435096866948\t-1\t4.7429214225993\t75\n+chr1\t2493400\t2493650\t.\t0\t.\t34.0043068331574\t-1\t4.7429214225993\t125\n+chr1\t3236597\t3236847\t.\t0\t.\t26.8900011644677\t-1\t4.30265555395945\t125\n+chr1\t3333725\t3333975\t.\t0\t.\t31.1329672384982\t-1\t4.27373412851497\t125\n+chr1\t3341315\t3341565\t.\t0\t.\t74.7245302958789\t-1\t4.7429214225993\t125\n+chr1\t3369726\t3369976\t.\t0\t.\t106.444209601322\t-1\t4.74'..b'-1\t4.7429214225993\t125\n+chr1\t242161899\t242162149\t.\t0\t.\t44.297888867722\t-1\t4.7429214225993\t125\n+chr1\t242180997\t242181247\t.\t0\t.\t78.3741983761816\t-1\t4.7429214225993\t125\n+chr1\t242183188\t242183438\t.\t0\t.\t66.679819217778\t-1\t4.7429214225993\t125\n+chr1\t242292490\t242292740\t.\t0\t.\t32.4950929799733\t-1\t4.7429214225993\t125\n+chr1\t242588613\t242588863\t.\t0\t.\t21.7470007916771\t-1\t3.97378078432702\t125\n+chr1\t242618161\t242618411\t.\t0\t.\t78.5029082464728\t-1\t4.7429214225993\t125\n+chr1\t242630897\t242631147\t.\t0\t.\t102.227246099934\t-1\t4.7429214225993\t125\n+chr1\t242687307\t242687557\t.\t0\t.\t22.7287067377493\t-1\t4.11180672135341\t125\n+chr1\t242815149\t242815399\t.\t0\t.\t35.7768576072339\t-1\t4.7429214225993\t125\n+chr1\t243488683\t243488933\t.\t0\t.\t90.1078055184278\t-1\t4.7429214225993\t125\n+chr1\t243507297\t243507547\t.\t0\t.\t26.9963883881902\t-1\t4.30181824820205\t125\n+chr1\t243599201\t243599451\t.\t0\t.\t18.8414344411906\t-1\t3.80332673324125\t125\n+chr1\t243912162\t243912226\t.\t0\t.\t87.857332864143\t-1\t4.7429214225993\t51\n+chr1\t244110436\t244110686\t.\t0\t.\t46.3085476394558\t-1\t4.7429214225993\t125\n+chr1\t244374493\t244374743\t.\t0\t.\t25.7700067096386\t-1\t4.3108702504201\t125\n+chr1\t244436420\t244436627\t.\t0\t.\t283.127937666882\t-1\t4.7429214225993\t95\n+chr1\t244462883\t244463009\t.\t0\t.\t147.278221747753\t-1\t4.7429214225993\t70\n+chr1\t244577886\t244578136\t.\t0\t.\t32.9862979478918\t-1\t4.7429214225993\t125\n+chr1\t244615509\t244615759\t.\t0\t.\t33.1173735732974\t-1\t4.7429214225993\t125\n+chr1\t244766862\t244766927\t.\t0\t.\t97.0255477829226\t-1\t4.7429214225993\t47\n+chr1\t244960248\t244960356\t.\t0\t.\t129.583735802963\t-1\t4.7429214225993\t60\n+chr1\t244964535\t244964785\t.\t0\t.\t84.8099516070166\t-1\t4.7429214225993\t125\n+chr1\t244997073\t244997323\t.\t0\t.\t22.335859434006\t-1\t4.11501773629396\t125\n+chr1\t245206072\t245206218\t.\t0\t.\t123.855729926098\t-1\t4.7429214225993\t94\n+chr1\t245242471\t245242584\t.\t0\t.\t98.1825295407773\t-1\t4.7429214225993\t47\n+chr1\t245316353\t245316603\t.\t0\t.\t47.5885191255838\t-1\t4.7429214225993\t125\n+chr1\t245319815\t245320065\t.\t0\t.\t55.2508551342203\t-1\t4.7429214225993\t125\n+chr1\t245960970\t245961220\t.\t0\t.\t32.5771666146799\t-1\t4.7429214225993\t125\n+chr1\t246052206\t246052456\t.\t0\t.\t24.5061272930621\t-1\t4.31976515886242\t125\n+chr1\t246166517\t246166767\t.\t0\t.\t92.0980997998447\t-1\t4.7429214225993\t125\n+chr1\t246175619\t246175869\t.\t0\t.\t51.4488542084578\t-1\t4.7429214225993\t125\n+chr1\t246280539\t246280789\t.\t0\t.\t21.6377563313938\t-1\t3.97462352512303\t125\n+chr1\t246614163\t246614413\t.\t0\t.\t81.518747690178\t-1\t4.7429214225993\t125\n+chr1\t246655996\t246656246\t.\t0\t.\t109.37604786956\t-1\t4.7429214225993\t125\n+chr1\t246660775\t246660850\t.\t0\t.\t82.9851636747842\t-1\t4.7429214225993\t22\n+chr1\t246695891\t246696141\t.\t0\t.\t25.0855614617435\t-1\t4.31573949961708\t125\n+chr1\t246852894\t246853036\t.\t0\t.\t124.192301187883\t-1\t4.7429214225993\t82\n+chr1\t246859830\t246860080\t.\t0\t.\t30.9781608987903\t-1\t4.27498099617164\t125\n+chr1\t246862512\t246862762\t.\t0\t.\t68.6201993339489\t-1\t4.7429214225993\t125\n+chr1\t246917344\t246917412\t.\t0\t.\t91.59542672781\t-1\t4.7429214225993\t58\n+chr1\t247134742\t247134992\t.\t0\t.\t38.4463313194636\t-1\t4.7429214225993\t125\n+chr1\t247536155\t247536254\t.\t0\t.\t102.859260815154\t-1\t4.7429214225993\t38\n+chr1\t247537236\t247537486\t.\t0\t.\t44.0355783173363\t-1\t4.7429214225993\t125\n+chr1\t247553517\t247553579\t.\t0\t.\t95.9419919672686\t-1\t4.7429214225993\t59\n+chr1\t247844634\t247844884\t.\t0\t.\t59.3259049794319\t-1\t4.7429214225993\t125\n+chr1\t248100255\t248100505\t.\t0\t.\t80.4098611245686\t-1\t4.7429214225993\t125\n+chr1\t248406472\t248406722\t.\t0\t.\t90.7185193033561\t-1\t4.7429214225993\t125\n+chr1\t248782263\t248782513\t.\t0\t.\t63.6214662074559\t-1\t4.7429214225993\t125\n+chr1\t248785834\t248786084\t.\t0\t.\t39.8323966052336\t-1\t4.7429214225993\t125\n+chr1\t249101416\t249101666\t.\t0\t.\t67.566711609504\t-1\t4.7429214225993\t125\n+chr1\t249120786\t249121036\t.\t0\t.\t52.442416642201\t-1\t4.7429214225993\t125\n+chr1\t249135979\t249136229\t.\t0\t.\t49.8223747632579\t-1\t4.7429214225993\t125\n+chr1\t249152776\t249153026\t.\t0\t.\t29.3016121090888\t-1\t4.28584974050218\t125\n+chr1\t249200566\t249200816\t.\t0\t.\t63.5123370035645\t-1\t4.7429214225993\t125\n+chr1\t249218992\t249219242\t.\t0\t.\t83.8506766777808\t-1\t4.7429214225993\t125\n\\ No newline at end of file\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/merged_list.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/merged_list.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,1287 @@\n+1\t710000\t1250000\tID_1\t-1.092317509315\t.\t710000\t1250000\t31,120,180\n+1\t1250000\t1480000\tID_2\t-0.447503916673\t.\t1250000\t1480000\t51,160,44\n+1\t1480000\t1680000\tID_3\t-0.604504964540\t.\t1480000\t1680000\t31,120,180\n+1\t1650000\t2600000\tID_4\t-0.941207732888\t.\t1650000\t2600000\t31,120,180\n+1\t1680000\t1850000\tID_5\t-0.732633171546\t.\t1680000\t1850000\t51,160,44\n+1\t1850000\t2110000\tID_6\t-0.629554185360\t.\t1850000\t2110000\t31,120,180\n+1\t2110000\t2330000\tID_7\t-0.599226178976\t.\t2110000\t2330000\t51,160,44\n+1\t2330000\t2580000\tID_8\t-0.502359023333\t.\t2330000\t2580000\t31,120,180\n+1\t2580000\t2690000\tID_9\t-0.877928092599\t.\t2580000\t2690000\t51,160,44\n+1\t2600000\t3300000\tID_10\t-1.237580853228\t.\t2600000\t3300000\t51,160,44\n+1\t2600000\t3800000\tID_11\t-1.141686912309\t.\t2600000\t3800000\t31,120,180\n+1\t2690000\t3330000\tID_12\t-0.876074031445\t.\t2690000\t3330000\t31,120,180\n+1\t3300000\t3800000\tID_13\t-1.151700420320\t.\t3300000\t3800000\t31,120,180\n+1\t3330000\t3540000\tID_14\t-0.865581452964\t.\t3330000\t3540000\t51,160,44\n+1\t3540000\t3830000\tID_15\t-0.175894888290\t.\t3540000\t3830000\t31,120,180\n+1\t3800000\t4550000\tID_16\t-1.041662687209\t.\t3800000\t4550000\t51,160,44\n+1\t3800000\t6000000\tID_17\t-1.059483103498\t.\t3800000\t6000000\t51,160,44\n+1\t3830000\t4050000\tID_18\t-0.788906681678\t.\t3830000\t4050000\t51,160,44\n+1\t4050000\t5240000\tID_19\t-0.632755573429\t.\t4050000\t5240000\t31,120,180\n+1\t4550000\t5500000\tID_20\t-0.688597101194\t.\t4550000\t5500000\t31,120,180\n+1\t5240000\t5500000\tID_21\t-0.503708327228\t.\t5240000\t5500000\t51,160,44\n+1\t5500000\t5890000\tID_22\t-0.535834764679\t.\t5500000\t5890000\t31,120,180\n+1\t5500000\t6050000\tID_23\t-0.628644578723\t.\t5500000\t6050000\t51,160,44\n+1\t5890000\t6050000\tID_24\t-0.441476370945\t.\t5890000\t6050000\t51,160,44\n+1\t6000000\t7800000\tID_25\t-0.984430873493\t.\t6000000\t7800000\t31,120,180\n+1\t6050000\t6300000\tID_26\t-0.559846730427\t.\t6050000\t6300000\t31,120,180\n+1\t6050000\t6750000\tID_27\t-0.895952939155\t.\t6050000\t6750000\t31,120,180\n+1\t6300000\t6410000\tID_28\t0.002675653077\t.\t6300000\t6410000\t51,160,44\n+1\t6410000\t6530000\tID_29\t0.238899723051\t.\t6410000\t6530000\t31,120,180\n+1\t6530000\t6750000\tID_30\t-0.092340076456\t.\t6530000\t6750000\t51,160,44\n+1\t6750000\t6970000\tID_31\t-0.342531967121\t.\t6750000\t6970000\t31,120,180\n+1\t6750000\t7250000\tID_32\t-0.511165876940\t.\t6750000\t7250000\t51,160,44\n+1\t6970000\t7090000\tID_33\t0.315970506814\t.\t6970000\t7090000\t51,160,44\n+1\t7090000\t7270000\tID_34\t0.316345600741\t.\t7090000\t7270000\t31,120,180\n+1\t7250000\t7700000\tID_35\t0.355926203340\t.\t7250000\t7700000\t31,120,180\n+1\t7270000\t7710000\tID_36\t0.041072322941\t.\t7270000\t7710000\t51,160,44\n+1\t7700000\t8400000\tID_37\t-0.385973482757\t.\t7700000\t8400000\t51,160,44\n+1\t7710000\t7830000\tID_38\t-0.367257028586\t.\t7710000\t7830000\t31,120,180\n+1\t7800000\t8900000\tID_39\t-0.399067786162\t.\t7800000\t8900000\t51,160,44\n+1\t7830000\t8020000\tID_40\t-0.060901177985\t.\t7830000\t8020000\t51,160,44\n+1\t8020000\t8410000\tID_41\t-0.372407842081\t.\t8020000\t8410000\t31,120,180\n+1\t8400000\t8900000\tID_42\t-0.297633621417\t.\t8400000\t8900000\t31,120,180\n+1\t8410000\t8920000\tID_43\t-0.353886989897\t.\t8410000\t8920000\t51,160,44\n+1\t8900000\t9200000\tID_44\t-0.103062710178\t.\t8900000\t9200000\t51,160,44\n+1\t8900000\t9700000\tID_45\t-0.117593287650\t.\t8900000\t9700000\t31,120,180\n+1\t8920000\t9170000\tID_46\t-0.155898280238\t.\t8920000\t9170000\t31,120,180\n+1\t9170000\t9320000\tID_47\t0.172890208942\t.\t9170000\t9320000\t51,160,44\n+1\t9200000\t9650000\tID_48\t0.381386755351\t.\t9200000\t9650000\t31,120,180\n+1\t9320000\t9650000\tID_49\t0.230612768882\t.\t9320000\t9650000\t31,120,180\n+1\t9650000\t10000000\tID_50\t-0.364293326660\t.\t9650000\t10000000\t51,160,44\n+1\t9650000\t10500000\tID_51\t-0.447368843956\t.\t9650000\t10500000\t51,160,44\n+1\t9700000\t10500000\tID_52\t-0.185496017524\t.\t9700000\t10500000\t51,160,44\n+1\t10000000\t10240000\tID_53\t0.125733381547\t.\t10000000\t10240000\t31,120,180\n+1\t10240000\t10430000\tID_54\t0.185519613694\t.\t10240000\t10430000\t51,160,44\n+1\t10430000\t10560000\tID_55\t-0.068211721541\t.\t10430000\t10560000\t31,120,180\n+1\t10500000\t11100000\tID_56\t-0.201392985635\t.\t10500000\t11100000\t31,120,180\n+1\t10560000\t11070000\tID_57\t-0.209526581188\t.\t10560000\t11070000\t51,160,44\n+1\t11070000\t11'..b'50000\t239150000\t51,160,44\n+1\t238620000\t239150000\tID_1238\t-0.183581653147\t.\t238620000\t239150000\t31,120,180\n+1\t239150000\t239580000\tID_1239\t-0.390241779515\t.\t239150000\t239580000\t51,160,44\n+1\t239150000\t239600000\tID_1240\t-0.387270948386\t.\t239150000\t239600000\t31,120,180\n+1\t239580000\t240150000\tID_1241\t-0.484242138670\t.\t239580000\t240150000\t31,120,180\n+1\t239600000\t240150000\tID_1242\t-0.583270038512\t.\t239600000\t240150000\t51,160,44\n+1\t24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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/relationship.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/relationship.txt Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,1456 @@\n+1\tID_4\tID_5\n+1\tID_4\tID_6\n+1\tID_4\tID_7\n+1\tID_4\tID_8\n+1\tID_10\tID_9\n+1\tID_11\tID_9\n+1\tID_11\tID_10\n+1\tID_11\tID_12\n+1\tID_11\tID_13\n+1\tID_11\tID_14\n+1\tID_13\tID_14\n+1\tID_17\tID_16\n+1\tID_16\tID_18\n+1\tID_17\tID_18\n+1\tID_17\tID_19\n+1\tID_17\tID_20\n+1\tID_17\tID_21\n+1\tID_17\tID_22\n+1\tID_20\tID_21\n+1\tID_23\tID_24\n+1\tID_25\tID_26\n+1\tID_25\tID_27\n+1\tID_25\tID_28\n+1\tID_25\tID_29\n+1\tID_25\tID_30\n+1\tID_25\tID_31\n+1\tID_25\tID_32\n+1\tID_25\tID_33\n+1\tID_25\tID_34\n+1\tID_25\tID_35\n+1\tID_25\tID_36\n+1\tID_27\tID_26\n+1\tID_27\tID_28\n+1\tID_27\tID_29\n+1\tID_27\tID_30\n+1\tID_32\tID_31\n+1\tID_32\tID_33\n+1\tID_37\tID_38\n+1\tID_37\tID_40\n+1\tID_39\tID_37\n+1\tID_39\tID_40\n+1\tID_39\tID_41\n+1\tID_39\tID_42\n+1\tID_45\tID_44\n+1\tID_44\tID_46\n+1\tID_45\tID_46\n+1\tID_45\tID_47\n+1\tID_45\tID_48\n+1\tID_45\tID_49\n+1\tID_48\tID_47\n+1\tID_48\tID_49\n+1\tID_51\tID_50\n+1\tID_51\tID_52\n+1\tID_51\tID_53\n+1\tID_51\tID_54\n+1\tID_52\tID_50\n+1\tID_52\tID_53\n+1\tID_52\tID_54\n+1\tID_56\tID_57\n+1\tID_59\tID_58\n+1\tID_59\tID_61\n+1\tID_60\tID_58\n+1\tID_60\tID_61\n+1\tID_60\tID_62\n+1\tID_63\tID_64\n+1\tID_63\tID_65\n+1\tID_63\tID_66\n+1\tID_65\tID_64\n+1\tID_65\tID_66\n+1\tID_68\tID_67\n+1\tID_68\tID_69\n+1\tID_72\tID_71\n+1\tID_71\tID_73\n+1\tID_72\tID_73\n+1\tID_72\tID_74\n+1\tID_72\tID_75\n+1\tID_72\tID_76\n+1\tID_72\tID_77\n+1\tID_72\tID_78\n+1\tID_72\tID_79\n+1\tID_72\tID_81\n+1\tID_75\tID_74\n+1\tID_75\tID_76\n+1\tID_80\tID_81\n+1\tID_80\tID_82\n+1\tID_83\tID_84\n+1\tID_83\tID_85\n+1\tID_83\tID_86\n+1\tID_83\tID_87\n+1\tID_83\tID_88\n+1\tID_83\tID_89\n+1\tID_85\tID_84\n+1\tID_85\tID_86\n+1\tID_85\tID_87\n+1\tID_85\tID_88\n+1\tID_90\tID_91\n+1\tID_90\tID_93\n+1\tID_92\tID_90\n+1\tID_92\tID_91\n+1\tID_92\tID_93\n+1\tID_92\tID_94\n+1\tID_92\tID_95\n+1\tID_92\tID_96\n+1\tID_92\tID_97\n+1\tID_92\tID_98\n+1\tID_95\tID_94\n+1\tID_95\tID_96\n+1\tID_95\tID_97\n+1\tID_95\tID_98\n+1\tID_101\tID_102\n+1\tID_103\tID_102\n+1\tID_103\tID_104\n+1\tID_103\tID_106\n+1\tID_105\tID_104\n+1\tID_105\tID_106\n+1\tID_105\tID_107\n+1\tID_110\tID_109\n+1\tID_110\tID_111\n+1\tID_110\tID_112\n+1\tID_110\tID_113\n+1\tID_110\tID_114\n+1\tID_111\tID_109\n+1\tID_111\tID_112\n+1\tID_111\tID_113\n+1\tID_111\tID_114\n+1\tID_117\tID_115\n+1\tID_117\tID_116\n+1\tID_117\tID_118\n+1\tID_117\tID_119\n+1\tID_117\tID_120\n+1\tID_117\tID_121\n+1\tID_117\tID_122\n+1\tID_117\tID_123\n+1\tID_117\tID_124\n+1\tID_117\tID_125\n+1\tID_117\tID_126\n+1\tID_117\tID_127\n+1\tID_119\tID_118\n+1\tID_119\tID_120\n+1\tID_119\tID_121\n+1\tID_122\tID_123\n+1\tID_124\tID_125\n+1\tID_124\tID_126\n+1\tID_124\tID_127\n+1\tID_129\tID_128\n+1\tID_129\tID_130\n+1\tID_129\tID_131\n+1\tID_134\tID_132\n+1\tID_134\tID_133\n+1\tID_134\tID_135\n+1\tID_134\tID_136\n+1\tID_134\tID_137\n+1\tID_134\tID_138\n+1\tID_134\tID_139\n+1\tID_134\tID_140\n+1\tID_134\tID_141\n+1\tID_136\tID_137\n+1\tID_136\tID_138\n+1\tID_142\tID_143\n+1\tID_144\tID_142\n+1\tID_144\tID_143\n+1\tID_144\tID_145\n+1\tID_144\tID_146\n+1\tID_144\tID_147\n+1\tID_146\tID_145\n+1\tID_146\tID_147\n+1\tID_148\tID_149\n+1\tID_148\tID_150\n+1\tID_149\tID_150\n+1\tID_151\tID_152\n+1\tID_151\tID_153\n+1\tID_151\tID_154\n+1\tID_151\tID_155\n+1\tID_151\tID_156\n+1\tID_151\tID_157\n+1\tID_152\tID_153\n+1\tID_152\tID_154\n+1\tID_152\tID_155\n+1\tID_152\tID_156\n+1\tID_158\tID_159\n+1\tID_158\tID_161\n+1\tID_160\tID_158\n+1\tID_160\tID_161\n+1\tID_160\tID_162\n+1\tID_160\tID_163\n+1\tID_160\tID_164\n+1\tID_160\tID_165\n+1\tID_160\tID_167\n+1\tID_163\tID_164\n+1\tID_166\tID_167\n+1\tID_166\tID_168\n+1\tID_169\tID_170\n+1\tID_169\tID_171\n+1\tID_169\tID_172\n+1\tID_169\tID_173\n+1\tID_169\tID_174\n+1\tID_169\tID_175\n+1\tID_169\tID_176\n+1\tID_169\tID_177\n+1\tID_171\tID_170\n+1\tID_171\tID_172\n+1\tID_176\tID_177\n+1\tID_179\tID_178\n+1\tID_179\tID_181\n+1\tID_179\tID_182\n+1\tID_179\tID_183\n+1\tID_179\tID_184\n+1\tID_179\tID_185\n+1\tID_180\tID_178\n+1\tID_180\tID_181\n+1\tID_180\tID_182\n+1\tID_180\tID_183\n+1\tID_180\tID_184\n+1\tID_180\tID_185\n+1\tID_187\tID_186\n+1\tID_188\tID_187\n+1\tID_188\tID_189\n+1\tID_188\tID_190\n+1\tID_188\tID_191\n+1\tID_188\tID_192\n+1\tID_188\tID_193\n+1\tID_188\tID_194\n+1\tID_188\tID_195\n+1\tID_190\tID_191\n+1\tID_193\tID_194\n+1\tID_193\tID_195\n+1\tID_199\tID_201\n+1\tID_199\tID_202\n+1\tID_199\tID_203\n+1\tID_199\tID_204\n+1\tID_199\tID_205\n+1\tID_200\tID_201\n+1\tID_200\tID_202\n+1\tID_200\tID_203\n+1\tID_200\tID_204\n+1\tID_200\tID_205\n+1\tID_200\tID_206\n+1\tID_200\tID_208\n+1\tID_207\tID_206\n+1\tID_207\tID_208\n+1\tID_210\tID_211\n+1\tID_210\tID_212\n+1\tID_211\tID_212\n+1\tID_214\tID_213\n+1\tID_214\tID_216\n+1\tID_214\tID_217\n+1\tID_215\tID_213\n+1\tID_215'..b'\tID_1086\n+1\tID_1085\tID_1087\n+1\tID_1085\tID_1088\n+1\tID_1085\tID_1089\n+1\tID_1085\tID_1090\n+1\tID_1085\tID_1092\n+1\tID_1085\tID_1093\n+1\tID_1087\tID_1088\n+1\tID_1091\tID_1092\n+1\tID_1091\tID_1093\n+1\tID_1091\tID_1094\n+1\tID_1095\tID_1096\n+1\tID_1095\tID_1097\n+1\tID_1095\tID_1098\n+1\tID_1095\tID_1099\n+1\tID_1097\tID_1096\n+1\tID_1097\tID_1098\n+1\tID_1097\tID_1099\n+1\tID_1101\tID_1100\n+1\tID_1102\tID_1100\n+1\tID_1102\tID_1101\n+1\tID_1102\tID_1103\n+1\tID_1102\tID_1104\n+1\tID_1102\tID_1105\n+1\tID_1102\tID_1106\n+1\tID_1102\tID_1107\n+1\tID_1104\tID_1105\n+1\tID_1106\tID_1107\n+1\tID_1110\tID_1108\n+1\tID_1110\tID_1109\n+1\tID_1110\tID_1111\n+1\tID_1110\tID_1112\n+1\tID_1110\tID_1113\n+1\tID_1110\tID_1114\n+1\tID_1110\tID_1115\n+1\tID_1110\tID_1116\n+1\tID_1110\tID_1117\n+1\tID_1114\tID_1115\n+1\tID_1118\tID_1119\n+1\tID_1120\tID_1121\n+1\tID_1120\tID_1122\n+1\tID_1120\tID_1123\n+1\tID_1120\tID_1124\n+1\tID_1120\tID_1125\n+1\tID_1120\tID_1126\n+1\tID_1120\tID_1127\n+1\tID_1120\tID_1128\n+1\tID_1120\tID_1129\n+1\tID_1121\tID_1122\n+1\tID_1121\tID_1123\n+1\tID_1121\tID_1124\n+1\tID_1126\tID_1127\n+1\tID_1126\tID_1128\n+1\tID_1126\tID_1129\n+1\tID_1131\tID_1132\n+1\tID_1131\tID_1133\n+1\tID_1136\tID_1134\n+1\tID_1136\tID_1135\n+1\tID_1136\tID_1137\n+1\tID_1136\tID_1138\n+1\tID_1136\tID_1139\n+1\tID_1136\tID_1140\n+1\tID_1136\tID_1141\n+1\tID_1136\tID_1142\n+1\tID_1138\tID_1139\n+1\tID_1138\tID_1140\n+1\tID_1138\tID_1141\n+1\tID_1143\tID_1144\n+1\tID_1145\tID_1143\n+1\tID_1145\tID_1144\n+1\tID_1145\tID_1146\n+1\tID_1145\tID_1148\n+1\tID_1145\tID_1149\n+1\tID_1147\tID_1146\n+1\tID_1147\tID_1148\n+1\tID_1147\tID_1149\n+1\tID_1151\tID_1150\n+1\tID_1151\tID_1152\n+1\tID_1151\tID_1153\n+1\tID_1151\tID_1154\n+1\tID_1151\tID_1155\n+1\tID_1151\tID_1156\n+1\tID_1151\tID_1157\n+1\tID_1151\tID_1158\n+1\tID_1151\tID_1159\n+1\tID_1151\tID_1160\n+1\tID_1152\tID_1153\n+1\tID_1152\tID_1154\n+1\tID_1156\tID_1157\n+1\tID_1156\tID_1158\n+1\tID_1162\tID_1164\n+1\tID_1162\tID_1165\n+1\tID_1162\tID_1166\n+1\tID_1162\tID_1167\n+1\tID_1163\tID_1164\n+1\tID_1163\tID_1165\n+1\tID_1163\tID_1166\n+1\tID_1163\tID_1167\n+1\tID_1169\tID_1168\n+1\tID_1169\tID_1171\n+1\tID_1169\tID_1172\n+1\tID_1170\tID_1168\n+1\tID_1170\tID_1171\n+1\tID_1170\tID_1172\n+1\tID_1170\tID_1173\n+1\tID_1170\tID_1174\n+1\tID_1173\tID_1174\n+1\tID_1176\tID_1175\n+1\tID_1176\tID_1178\n+1\tID_1177\tID_1175\n+1\tID_1177\tID_1176\n+1\tID_1177\tID_1178\n+1\tID_1177\tID_1179\n+1\tID_1182\tID_1183\n+1\tID_1182\tID_1184\n+1\tID_1182\tID_1186\n+1\tID_1185\tID_1186\n+1\tID_1188\tID_1189\n+1\tID_1188\tID_1190\n+1\tID_1188\tID_1191\n+1\tID_1189\tID_1190\n+1\tID_1192\tID_1193\n+1\tID_1192\tID_1195\n+1\tID_1192\tID_1196\n+1\tID_1194\tID_1193\n+1\tID_1194\tID_1195\n+1\tID_1194\tID_1196\n+1\tID_1194\tID_1197\n+1\tID_1200\tID_1199\n+1\tID_1200\tID_1201\n+1\tID_1200\tID_1202\n+1\tID_1200\tID_1204\n+1\tID_1203\tID_1204\n+1\tID_1203\tID_1205\n+1\tID_1206\tID_1207\n+1\tID_1206\tID_1208\n+1\tID_1206\tID_1209\n+1\tID_1206\tID_1211\n+1\tID_1208\tID_1209\n+1\tID_1210\tID_1211\n+1\tID_1212\tID_1214\n+1\tID_1212\tID_1215\n+1\tID_1213\tID_1214\n+1\tID_1213\tID_1215\n+1\tID_1213\tID_1216\n+1\tID_1219\tID_1221\n+1\tID_1220\tID_1221\n+1\tID_1223\tID_1224\n+1\tID_1223\tID_1225\n+1\tID_1226\tID_1227\n+1\tID_1228\tID_1226\n+1\tID_1228\tID_1227\n+1\tID_1228\tID_1229\n+1\tID_1228\tID_1231\n+1\tID_1230\tID_1231\n+1\tID_1233\tID_1232\n+1\tID_1233\tID_1234\n+1\tID_1233\tID_1235\n+1\tID_1233\tID_1236\n+1\tID_1233\tID_1237\n+1\tID_1233\tID_1238\n+1\tID_1233\tID_1239\n+1\tID_1233\tID_1240\n+1\tID_1233\tID_1241\n+1\tID_1233\tID_1242\n+1\tID_1234\tID_1235\n+1\tID_1237\tID_1236\n+1\tID_1237\tID_1238\n+1\tID_1241\tID_1242\n+1\tID_1244\tID_1243\n+1\tID_1245\tID_1244\n+1\tID_1245\tID_1246\n+1\tID_1245\tID_1248\n+1\tID_1245\tID_1249\n+1\tID_1247\tID_1248\n+1\tID_1247\tID_1249\n+1\tID_1251\tID_1252\n+1\tID_1251\tID_1253\n+1\tID_1251\tID_1254\n+1\tID_1251\tID_1255\n+1\tID_1251\tID_1256\n+1\tID_1251\tID_1257\n+1\tID_1251\tID_1258\n+1\tID_1251\tID_1259\n+1\tID_1252\tID_1253\n+1\tID_1252\tID_1254\n+1\tID_1256\tID_1255\n+1\tID_1256\tID_1257\n+1\tID_1261\tID_1263\n+1\tID_1261\tID_1264\n+1\tID_1261\tID_1265\n+1\tID_1262\tID_1263\n+1\tID_1262\tID_1264\n+1\tID_1262\tID_1265\n+1\tID_1262\tID_1266\n+1\tID_1267\tID_1268\n+1\tID_1267\tID_1269\n+1\tID_1267\tID_1270\n+1\tID_1271\tID_1272\n+1\tID_1271\tID_1273\n+1\tID_1271\tID_1274\n+1\tID_1271\tID_1275\n+1\tID_1271\tID_1276\n+1\tID_1271\tID_1277\n+1\tID_1271\tID_1278\n+1\tID_1275\tID_1276\n+1\tID_1275\tID_1277\n+1\tID_1280\tID_1279\n+1\tID_1280\tID_1281\n+1\tID_1280\tID_1282\n+1\tID_1280\tID_1283\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeDomains/two_files_relation_ctcf.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/two_files_relation_ctcf.txt Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,581 @@\n+1\tID_4\tID_5\n+1\tID_4\tID_6\n+1\tID_4\tID_7\n+1\tID_4\tID_8\n+1\tID_10\tID_9\n+1\tID_12\tID_13\n+1\tID_15\tID_16\n+1\tID_17\tID_15\n+1\tID_18\tID_19\n+1\tID_21\tID_22\n+1\tID_24\tID_23\n+1\tID_24\tID_25\n+1\tID_24\tID_26\n+1\tID_24\tID_27\n+1\tID_29\tID_28\n+1\tID_29\tID_30\n+1\tID_34\tID_35\n+1\tID_34\tID_36\n+1\tID_40\tID_41\n+1\tID_43\tID_42\n+1\tID_43\tID_44\n+1\tID_46\tID_45\n+1\tID_46\tID_47\n+1\tID_46\tID_48\n+1\tID_50\tID_51\n+1\tID_53\tID_52\n+1\tID_53\tID_54\n+1\tID_56\tID_57\n+1\tID_56\tID_58\n+1\tID_62\tID_63\n+1\tID_65\tID_64\n+1\tID_65\tID_66\n+1\tID_70\tID_71\n+1\tID_70\tID_72\n+1\tID_74\tID_73\n+1\tID_74\tID_75\n+1\tID_74\tID_76\n+1\tID_74\tID_77\n+1\tID_79\tID_78\n+1\tID_79\tID_80\n+1\tID_79\tID_81\n+1\tID_83\tID_82\n+1\tID_83\tID_84\n+1\tID_83\tID_85\n+1\tID_83\tID_86\n+1\tID_90\tID_89\n+1\tID_90\tID_91\n+1\tID_90\tID_92\n+1\tID_96\tID_95\n+1\tID_96\tID_97\n+1\tID_96\tID_98\n+1\tID_96\tID_99\n+1\tID_103\tID_102\n+1\tID_103\tID_104\n+1\tID_103\tID_105\n+1\tID_106\tID_107\n+1\tID_108\tID_109\n+1\tID_108\tID_110\n+1\tID_108\tID_111\n+1\tID_113\tID_112\n+1\tID_113\tID_114\n+1\tID_113\tID_115\n+1\tID_119\tID_120\n+1\tID_119\tID_121\n+1\tID_125\tID_126\n+1\tID_128\tID_127\n+1\tID_128\tID_129\n+1\tID_130\tID_131\n+1\tID_132\tID_133\n+1\tID_132\tID_134\n+1\tID_132\tID_135\n+1\tID_132\tID_136\n+1\tID_138\tID_139\n+1\tID_138\tID_140\n+1\tID_142\tID_143\n+1\tID_145\tID_146\n+1\tID_145\tID_147\n+1\tID_149\tID_148\n+1\tID_149\tID_150\n+1\tID_154\tID_153\n+1\tID_154\tID_155\n+1\tID_157\tID_156\n+1\tID_157\tID_158\n+1\tID_157\tID_159\n+1\tID_157\tID_160\n+1\tID_157\tID_161\n+1\tID_157\tID_162\n+1\tID_164\tID_163\n+1\tID_166\tID_167\n+1\tID_169\tID_170\n+1\tID_169\tID_171\n+1\tID_175\tID_176\n+1\tID_175\tID_177\n+1\tID_175\tID_178\n+1\tID_175\tID_179\n+1\tID_175\tID_180\n+1\tID_182\tID_181\n+1\tID_182\tID_183\n+1\tID_185\tID_186\n+1\tID_188\tID_187\n+1\tID_188\tID_189\n+1\tID_188\tID_190\n+1\tID_192\tID_191\n+1\tID_192\tID_193\n+1\tID_195\tID_194\n+1\tID_195\tID_196\n+1\tID_195\tID_197\n+1\tID_199\tID_200\n+1\tID_199\tID_201\n+1\tID_205\tID_206\n+1\tID_205\tID_207\n+1\tID_205\tID_208\n+1\tID_210\tID_211\n+1\tID_210\tID_212\n+1\tID_210\tID_213\n+1\tID_215\tID_214\n+1\tID_215\tID_216\n+1\tID_218\tID_219\n+1\tID_218\tID_220\n+1\tID_218\tID_221\n+1\tID_218\tID_222\n+1\tID_224\tID_223\n+1\tID_224\tID_225\n+1\tID_227\tID_228\n+1\tID_227\tID_229\n+1\tID_227\tID_230\n+1\tID_227\tID_231\n+1\tID_233\tID_232\n+1\tID_233\tID_234\n+1\tID_233\tID_235\n+1\tID_237\tID_236\n+1\tID_237\tID_238\n+1\tID_240\tID_239\n+1\tID_240\tID_241\n+1\tID_243\tID_242\n+1\tID_243\tID_244\n+1\tID_243\tID_245\n+1\tID_247\tID_248\n+1\tID_249\tID_250\n+1\tID_251\tID_252\n+1\tID_251\tID_253\n+1\tID_251\tID_254\n+1\tID_258\tID_259\n+1\tID_261\tID_262\n+1\tID_261\tID_263\n+1\tID_261\tID_264\n+1\tID_266\tID_265\n+1\tID_268\tID_269\n+1\tID_270\tID_271\n+1\tID_272\tID_273\n+1\tID_275\tID_274\n+1\tID_275\tID_276\n+1\tID_275\tID_277\n+1\tID_279\tID_278\n+1\tID_279\tID_280\n+1\tID_279\tID_281\n+1\tID_279\tID_282\n+1\tID_284\tID_285\n+1\tID_284\tID_286\n+1\tID_284\tID_287\n+1\tID_289\tID_290\n+1\tID_289\tID_291\n+1\tID_289\tID_292\n+1\tID_289\tID_293\n+1\tID_294\tID_295\n+1\tID_296\tID_297\n+1\tID_299\tID_300\n+1\tID_302\tID_303\n+1\tID_305\tID_304\n+1\tID_305\tID_306\n+1\tID_305\tID_307\n+1\tID_309\tID_308\n+1\tID_309\tID_310\n+1\tID_314\tID_315\n+1\tID_316\tID_317\n+1\tID_320\tID_321\n+1\tID_320\tID_322\n+1\tID_324\tID_325\n+1\tID_324\tID_326\n+1\tID_328\tID_327\n+1\tID_328\tID_329\n+1\tID_328\tID_330\n+1\tID_332\tID_333\n+1\tID_332\tID_334\n+1\tID_332\tID_335\n+1\tID_332\tID_336\n+1\tID_332\tID_337\n+1\tID_332\tID_338\n+1\tID_332\tID_339\n+1\tID_332\tID_340\n+1\tID_342\tID_343\n+1\tID_342\tID_344\n+1\tID_348\tID_347\n+1\tID_348\tID_349\n+1\tID_351\tID_352\n+1\tID_355\tID_356\n+1\tID_357\tID_358\n+1\tID_359\tID_360\n+1\tID_361\tID_362\n+1\tID_361\tID_363\n+1\tID_361\tID_364\n+1\tID_361\tID_365\n+1\tID_367\tID_368\n+1\tID_370\tID_371\n+1\tID_379\tID_380\n+1\tID_382\tID_381\n+1\tID_382\tID_383\n+1\tID_382\tID_384\n+1\tID_386\tID_387\n+1\tID_389\tID_388\n+1\tID_389\tID_390\n+1\tID_392\tID_393\n+1\tID_397\tID_398\n+1\tID_400\tID_401\n+1\tID_403\tID_404\n+1\tID_410\tID_409\n+1\tID_410\tID_411\n+1\tID_410\tID_412\n+1\tID_410\tID_413\n+1\tID_415\tID_416\n+1\tID_418\tID_417\n+1\tID_418\tID_419\n+1\tID_421\tID_422\n+1\tID_426\tID_425\n+1\tID_426\tID_427\n+1\tID_426\tID_428\n+1\tID_426\tID_429\n+1\tID_433\tID_434\n+1\tID_438\tID_437\n+1\tID_438\tID_439\n+1\tID_441\tID_442\n+1\tID_444\tID_445\n+1\tID_444\tID_446\n+1\tID_448\tID_447\n+1\tID_452\tID_453\n+1\tID_455\tID_454\n+1\tID_455\tID_456\n+1\tID_458\tID_457\n+1\tID_458\tID_459\n+1\tID_458\tID_460\n+1\tID_458\tID_4'..b'\tID_663\tID_664\n+1\tID_663\tID_665\n+1\tID_667\tID_668\n+1\tID_667\tID_669\n+1\tID_667\tID_670\n+1\tID_672\tID_671\n+1\tID_672\tID_673\n+1\tID_672\tID_674\n+1\tID_676\tID_675\n+1\tID_676\tID_677\n+1\tID_681\tID_680\n+1\tID_681\tID_682\n+1\tID_684\tID_683\n+1\tID_684\tID_685\n+1\tID_684\tID_686\n+1\tID_684\tID_687\n+1\tID_689\tID_690\n+1\tID_692\tID_691\n+1\tID_692\tID_693\n+1\tID_692\tID_694\n+1\tID_692\tID_695\n+1\tID_699\tID_698\n+1\tID_699\tID_700\n+1\tID_702\tID_703\n+1\tID_705\tID_706\n+1\tID_705\tID_707\n+1\tID_708\tID_709\n+1\tID_711\tID_710\n+1\tID_711\tID_712\n+1\tID_713\tID_714\n+1\tID_716\tID_715\n+1\tID_716\tID_717\n+1\tID_719\tID_720\n+1\tID_719\tID_721\n+1\tID_719\tID_722\n+1\tID_724\tID_723\n+1\tID_724\tID_725\n+1\tID_724\tID_726\n+1\tID_724\tID_727\n+1\tID_729\tID_728\n+1\tID_731\tID_732\n+1\tID_731\tID_733\n+1\tID_731\tID_734\n+1\tID_736\tID_737\n+1\tID_736\tID_738\n+1\tID_740\tID_741\n+1\tID_740\tID_742\n+1\tID_740\tID_743\n+1\tID_747\tID_746\n+1\tID_749\tID_750\n+1\tID_752\tID_751\n+1\tID_752\tID_753\n+1\tID_755\tID_756\n+1\tID_757\tID_758\n+1\tID_760\tID_759\n+1\tID_760\tID_761\n+1\tID_765\tID_766\n+1\tID_765\tID_767\n+1\tID_769\tID_770\n+1\tID_769\tID_771\n+1\tID_769\tID_772\n+1\tID_774\tID_775\n+1\tID_774\tID_776\n+1\tID_778\tID_777\n+1\tID_778\tID_779\n+1\tID_780\tID_781\n+1\tID_782\tID_783\n+1\tID_789\tID_790\n+1\tID_789\tID_791\n+1\tID_792\tID_793\n+1\tID_797\tID_796\n+1\tID_799\tID_800\n+1\tID_802\tID_801\n+1\tID_802\tID_803\n+1\tID_805\tID_804\n+1\tID_805\tID_806\n+1\tID_808\tID_809\n+1\tID_811\tID_812\n+1\tID_811\tID_813\n+1\tID_815\tID_814\n+1\tID_815\tID_816\n+1\tID_822\tID_821\n+1\tID_822\tID_823\n+1\tID_824\tID_825\n+1\tID_826\tID_827\n+1\tID_831\tID_830\n+1\tID_831\tID_832\n+1\tID_834\tID_835\n+1\tID_836\tID_837\n+1\tID_839\tID_838\n+1\tID_839\tID_840\n+1\tID_839\tID_841\n+1\tID_842\tID_843\n+1\tID_842\tID_844\n+1\tID_842\tID_845\n+1\tID_842\tID_846\n+1\tID_848\tID_847\n+1\tID_848\tID_849\n+1\tID_850\tID_851\n+1\tID_853\tID_852\n+1\tID_853\tID_854\n+1\tID_858\tID_857\n+1\tID_858\tID_859\n+1\tID_861\tID_862\n+1\tID_864\tID_865\n+1\tID_867\tID_866\n+1\tID_867\tID_868\n+1\tID_867\tID_869\n+1\tID_871\tID_870\n+1\tID_873\tID_874\n+1\tID_873\tID_875\n+1\tID_877\tID_878\n+1\tID_880\tID_879\n+1\tID_880\tID_881\n+1\tID_880\tID_882\n+1\tID_884\tID_883\n+1\tID_884\tID_885\n+1\tID_884\tID_886\n+1\tID_884\tID_887\n+1\tID_884\tID_888\n+1\tID_890\tID_889\n+1\tID_890\tID_891\n+1\tID_890\tID_892\n+1\tID_895\tID_896\n+1\tID_897\tID_898\n+1\tID_902\tID_903\n+1\tID_905\tID_906\n+1\tID_905\tID_907\n+1\tID_909\tID_908\n+1\tID_909\tID_910\n+1\tID_912\tID_911\n+1\tID_912\tID_913\n+1\tID_912\tID_914\n+1\tID_912\tID_915\n+1\tID_912\tID_916\n+1\tID_920\tID_919\n+1\tID_922\tID_923\n+1\tID_925\tID_926\n+1\tID_925\tID_927\n+1\tID_931\tID_932\n+1\tID_934\tID_935\n+1\tID_934\tID_936\n+1\tID_934\tID_937\n+1\tID_939\tID_938\n+1\tID_939\tID_940\n+1\tID_942\tID_941\n+1\tID_942\tID_943\n+1\tID_942\tID_944\n+1\tID_945\tID_946\n+1\tID_949\tID_950\n+1\tID_949\tID_951\n+1\tID_949\tID_952\n+1\tID_954\tID_953\n+1\tID_954\tID_955\n+1\tID_954\tID_956\n+1\tID_958\tID_957\n+1\tID_960\tID_961\n+1\tID_962\tID_963\n+1\tID_965\tID_964\n+1\tID_969\tID_970\n+1\tID_973\tID_974\n+1\tID_975\tID_976\n+1\tID_975\tID_977\n+1\tID_975\tID_978\n+1\tID_980\tID_981\n+1\tID_980\tID_982\n+1\tID_980\tID_983\n+1\tID_985\tID_986\n+1\tID_985\tID_987\n+1\tID_991\tID_992\n+1\tID_991\tID_993\n+1\tID_991\tID_994\n+1\tID_996\tID_997\n+1\tID_999\tID_998\n+1\tID_999\tID_1000\n+1\tID_999\tID_1001\n+1\tID_1003\tID_1002\n+1\tID_1003\tID_1004\n+1\tID_1003\tID_1005\n+1\tID_1007\tID_1008\n+1\tID_1007\tID_1009\n+1\tID_1013\tID_1014\n+1\tID_1013\tID_1015\n+1\tID_1013\tID_1016\n+1\tID_1013\tID_1017\n+1\tID_1019\tID_1018\n+1\tID_1019\tID_1020\n+1\tID_1019\tID_1021\n+1\tID_1022\tID_1023\n+1\tID_1025\tID_1024\n+1\tID_1025\tID_1026\n+1\tID_1032\tID_1033\n+1\tID_1035\tID_1036\n+1\tID_1038\tID_1039\n+1\tID_1038\tID_1040\n+1\tID_1038\tID_1041\n+1\tID_1047\tID_1048\n+1\tID_1047\tID_1049\n+1\tID_1051\tID_1052\n+1\tID_1053\tID_1054\n+1\tID_1055\tID_1056\n+1\tID_1055\tID_1057\n+1\tID_1061\tID_1062\n+1\tID_1066\tID_1067\n+1\tID_1069\tID_1070\n+1\tID_1072\tID_1073\n+1\tID_1075\tID_1074\n+1\tID_1075\tID_1076\n+1\tID_1079\tID_1080\n+1\tID_1082\tID_1081\n+1\tID_1084\tID_1085\n+1\tID_1084\tID_1086\n+1\tID_1088\tID_1089\n+1\tID_1088\tID_1090\n+1\tID_1092\tID_1091\n+1\tID_1092\tID_1093\n+1\tID_1097\tID_1096\n+1\tID_1097\tID_1098\n+1\tID_1097\tID_1099\n+1\tID_1097\tID_1100\n+1\tID_1102\tID_1103\n+1\tID_1102\tID_1104\n+1\tID_1106\tID_1105\n+1\tID_1108\tID_1109\n+1\tID_1108\tID_1110\n+1\tID_1113\tID_1112\n+1\tID_1113\tID_1114\n+1\tID_1113\tID_1115\n+1\tID_1113\tID_1116\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeLoops/gm12878_10kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_10kb.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeLoops/gm12878_25kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_25kb.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeLoops/gm12878_5kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_5kb.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicMergeLoops/gm12878_all.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Mar 16 21:17:26 2021 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r c852ad97ba28 test-data/hicPlotSVL/p_values.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,4 @@
+# Created with HiCExplorer's hicPlotSVL 3.6
+# 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 c852ad97ba28 test-data/hicPlotSVL/plot.png
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diff -r 000000000000 -r c852ad97ba28 test-data/hicPlotSVL/ratios.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,8 @@
+# Created with HiCExplorer's hicPlotSVL 3.6
+# 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 c852ad97ba28 test-data/hicQuickQC/QC.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicQuickQC/QC.log Tue Mar 16 21:17:26 2021 +0000
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@@ -0,0 +1,29 @@
+
+File /tmp/tmp12xmnm2f.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 GATC 1 (0.33)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 84 (28.00)
+self circle 33 (11.00)
+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 c852ad97ba28 test-data/hicTransform/obs_exp_norm.h5
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diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicValidateLocations/loops_1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/loops_1.bedgraph Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/hicValidateLocations/overlap_smc3_statistics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,7 @@
+# HiCExplorer hicValidateLocations 3.6
+# Overlap of loop file /tmp/tmpd80q3k6g/files/a/4/0/dataset_a40f2565-c94b-4e73-9b47-ec233d99bda8.dat with protein file /tmp/tmpd80q3k6g/files/7/1/1/dataset_7116b645-b87b-49a2-a957-3ebe53aba250.dat
+#
+Protein peaks: 3097
+Matched Loops: 530
+Total Loops: 1007
+Loops match protein: 0.5263157894736842
b
diff -r 000000000000 -r c852ad97ba28 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 Tue Mar 16 21:17:26 2021 +0000
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 c852ad97ba28 test-data/li_viewpoint_32-33Mb.png
b
Binary file test-data/li_viewpoint_32-33Mb.png has changed
b
diff -r 000000000000 -r c852ad97ba28 test-data/li_viewpoint_32Mb.png
b
Binary file test-data/li_viewpoint_32Mb.png has changed
b
diff -r 000000000000 -r c852ad97ba28 test-data/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiNone_domains.bed Tue Mar 16 21:17:26 2021 +0000
b
b'@@ -0,0 +1,1402 @@\n+chr3L\t165000\t260000\tID_0.01_1\t-0.103166750000\t.\t165000\t260000\t31,120,180\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655000000\t.\t260000\t335000\t51,160,44\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848000000\t.\t335000\t360000\t31,120,180\n+chr3L\t360000\t485000\tID_0.01_4\t-0.058081500000\t.\t360000\t485000\t51,160,44\n+chr3L\t485000\t525000\tID_0.01_5\t-0.071697750000\t.\t485000\t525000\t31,120,180\n+chr3L\t525000\t680000\tID_0.01_6\t-0.106040500000\t.\t525000\t680000\t51,160,44\n+chr3L\t680000\t705000\tID_0.01_7\t-0.014885500000\t.\t680000\t705000\t31,120,180\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784000000\t.\t705000\t740000\t51,160,44\n+chr3L\t740000\t870000\tID_0.01_9\t0.009499750000\t.\t740000\t870000\t31,120,180\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.095469750000\t.\t870000\t1010000\t51,160,44\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.051821750000\t.\t1010000\t1040000\t31,120,180\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.058748750000\t.\t1040000\t1110000\t51,160,44\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349000000\t.\t1110000\t1210000\t31,120,180\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.056756500000\t.\t1210000\t1245000\t51,160,44\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.064143500000\t.\t1245000\t1300000\t31,120,180\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379000000\t.\t1300000\t1465000\t51,160,44\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.013072250000\t.\t1465000\t1535000\t31,120,180\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.087115250000\t.\t1535000\t1580000\t51,160,44\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.082358750000\t.\t1580000\t1640000\t31,120,180\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.062875500000\t.\t1640000\t1670000\t51,160,44\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945000000\t.\t1670000\t1735000\t31,120,180\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313000000\t.\t1735000\t1815000\t51,160,44\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.017235250000\t.\t1815000\t1850000\t31,120,180\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.025997500000\t.\t1850000\t1925000\t51,160,44\n+chr3L\t1925000\t2155000\tID_0.01_25\t0.000083250000\t.\t1925000\t2155000\t31,120,180\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.040196500000\t.\t2155000\t2260000\t51,160,44\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.075185750000\t.\t2260000\t2390000\t31,120,180\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071000000\t.\t2390000\t2460000\t51,160,44\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.091323250000\t.\t2460000\t2560000\t31,120,180\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.091796750000\t.\t2560000\t2600000\t51,160,44\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.093485500000\t.\t2600000\t2740000\t31,120,180\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.089278750000\t.\t2740000\t2885000\t51,160,44\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.089725750000\t.\t2885000\t2945000\t31,120,180\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899000000\t.\t2945000\t2960000\t51,160,44\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.035686500000\t.\t2960000\t3045000\t31,120,180\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.004668750000\t.\t3045000\t3135000\t51,160,44\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702000000\t.\t3135000\t3220000\t31,120,180\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463000000\t.\t3220000\t3255000\t51,160,44\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796000000\t.\t3255000\t3315000\t31,120,180\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.054998750000\t.\t3315000\t3345000\t51,160,44\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.042340750000\t.\t3345000\t3475000\t31,120,180\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.050976750000\t.\t3475000\t3515000\t51,160,44\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488000000\t.\t3515000\t3545000\t31,120,180\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.024579250000\t.\t3545000\t3615000\t51,160,44\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683000000\t.\t3615000\t3670000\t31,120,180\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.099453250000\t.\t3670000\t3765000\t51,160,44\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454000000\t.\t3765000\t3785000\t31,120,180\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084000000\t.\t3785000\t3825000\t51,160,44\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.061011750000\t.\t3825000\t3900000\t31,120,180\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.068453500000\t.\t3900000\t4000000\t51,160,44\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.030078750000\t.\t4000000\t4120000\t31,120,180\n+chr3L\t4120000\t4165000\tID_0.01_5'..b'.\t22780000\t22885000\t31,120,180\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.056834750000\t.\t22885000\t22985000\t51,160,44\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.023781500000\t.\t22985000\t23110000\t31,120,180\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625000000\t.\t23110000\t23185000\t51,160,44\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.002947250000\t.\t23185000\t23195000\t31,120,180\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.002757750000\t.\t23195000\t23415000\t51,160,44\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027000000\t.\t23415000\t23560000\t31,120,180\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602000000\t.\t23560000\t23770000\t51,160,44\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.111910500000\t.\t23770000\t23815000\t31,120,180\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.066076500000\t.\t23815000\t23920000\t51,160,44\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.042184750000\t.\t23920000\t24030000\t31,120,180\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.055795750000\t.\t24030000\t24160000\t51,160,44\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.015467250000\t.\t24160000\t24205000\t31,120,180\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.032601500000\t.\t24205000\t24345000\t51,160,44\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.062306500000\t.\t24345000\t24375000\t31,120,180\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.074939500000\t.\t24375000\t24450000\t51,160,44\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.098360750000\t.\t24450000\t24625000\t31,120,180\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.031713750000\t.\t24625000\t24745000\t51,160,44\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.085896250000\t.\t24745000\t24885000\t31,120,180\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.093237250000\t.\t24885000\t24995000\t51,160,44\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.058978500000\t.\t24995000\t25090000\t31,120,180\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.036742250000\t.\t25090000\t25165000\t51,160,44\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.046246500000\t.\t25165000\t25330000\t31,120,180\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.083033250000\t.\t25330000\t25405000\t51,160,44\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.005462250000\t.\t25405000\t25570000\t31,120,180\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.046540750000\t.\t25570000\t25580000\t51,160,44\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.018715750000\t.\t25580000\t25730000\t31,120,180\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.008588750000\t.\t25730000\t25880000\t51,160,44\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.105816250000\t.\t25880000\t25990000\t31,120,180\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403000000\t.\t25990000\t26050000\t51,160,44\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.093531500000\t.\t26050000\t26180000\t31,120,180\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.114692750000\t.\t26180000\t26275000\t51,160,44\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.100273500000\t.\t26275000\t26330000\t31,120,180\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304000000\t.\t26330000\t26490000\t51,160,44\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.062796500000\t.\t26490000\t26565000\t31,120,180\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.019744750000\t.\t26565000\t26640000\t51,160,44\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.074307250000\t.\t26640000\t26715000\t31,120,180\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789000000\t.\t26715000\t26870000\t51,160,44\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.024990500000\t.\t26870000\t27045000\t31,120,180\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189000000\t.\t27045000\t27155000\t51,160,44\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.006099250000\t.\t27155000\t27185000\t31,120,180\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.012810250000\t.\t27185000\t27250000\t51,160,44\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.049902750000\t.\t27250000\t27385000\t31,120,180\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305000000\t.\t27385000\t27420000\t51,160,44\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.049929500000\t.\t27420000\t27570000\t31,120,180\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.080943250000\t.\t27570000\t27700000\t51,160,44\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.015350000000\t.\t27700000\t27750000\t31,120,180\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.013577250000\t.\t27750000\t27770000\t51,160,44\n'
b
diff -r 000000000000 -r c852ad97ba28 test-data/raw_qc_report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_qc_report Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,29 @@
+
+File matrix.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 GATC 1 (0.33)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 84 (28.00)
+self circle 33 (11.00)
+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 c852ad97ba28 test-data/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regions.bed Tue Mar 16 21:17:26 2021 +0000
b
@@ -0,0 +1,2 @@
+chrX 10000000 15000000
+chrX 18000000 22000000
b
diff -r 000000000000 -r c852ad97ba28 test-data/small_test_R1_unsorted.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_test_R1_unsorted.sam Tue Mar 16 21:17:26 2021 +0000
b
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b
diff -r 000000000000 -r c852ad97ba28 test-data/small_test_R2_unsorted.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_test_R2_unsorted.sam Tue Mar 16 21:17:26 2021 +0000
b
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