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

Changeset 13:f0216498a666 (2023-10-18)
Previous changeset 12:e30485c5e93b (2023-01-10)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
modified:
hicAggregateContacts.xml
macros.xml
test-data/cHi-C/chicQualityControl/histogram.png
test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
test-data/cHi-C/chicQualityControl/sparsity.png
test-data/cHi-C/referencePoints_chicViewpoint.bed
test-data/distVsCounts.txt
test-data/hicConvertFormat/small_test_matrix_chr4.homer
test-data/hicDifferentialTAD/accepted.txt
test-data/hicDifferentialTAD/rejected.txt
test-data/hicInfo/hicInfo_output.txt
test-data/hicMergeLoops/gm12878_all.bedgraph
test-data/hicPCA/pca1_test1.bw
test-data/hicPCA/pca1_test2.bw
test-data/hicPCA/pca1_test3.bw
test-data/hicPCA/pca2_test1.bw
test-data/hicPCA/pca2_test2.bw
test-data/hicPCA/pca2_test3.bw
test-data/hicPlotDistVsCounts_result1.png
test-data/hicPlotDistVsCounts_result2.png
test-data/hicPlotMatrix/plot2.pdf
test-data/hicPlotMatrix/plot3_pca.svg
test-data/hicPlotSVL/p_values.txt
test-data/hicPlotSVL/plot.png
test-data/hicPlotSVL/ratios.txt
test-data/hicQuickQC/QC.log
test-data/hicValidateLocations/overlap_smc3_matched_locations
test-data/hicValidateLocations/overlap_smc3_statistics
test-data/raw_qc_report
added:
test-data/cHi-C/aggregate.tar.gz
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt
test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt
test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5
test-data/cHi-C/chicDifferentialTest/differential.hdf5
test-data/cHi-C/chicExportData/aggregate.tar.gz
test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig
test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt
test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig
test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt
test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig
test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig
test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5
test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5
test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5
test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5
test-data/cHi-C/chicViewpoint/two_matrices.hdf5
test-data/cHi-C/hg19.chrom.sizes
test-data/cHi-C/plots.tar.gz
test-data/cHi-C/target_list.bed
test-data/hicCompartmentsPolarization/output_matrix.npz
test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt
test-data/hicConvertFormat/hg19.chrom.sizes
test-data/hicConvertFormat/small_test_matrix_chr4.bed
test-data/hicConvertFormat/small_test_matrix_chr4.hicpro
test-data/hicInterIntraTAD/matrix.cool
test-data/hicInterIntraTAD/output.txt
test-data/hicInterIntraTAD/plot.png
test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed
test-data/hicTADClassifier/predicted.txt
test-data/hicTADClassifier/predicted_second_classifier.txt
test-data/hicTADClassifier/unittest_classifier.BIN
test-data/hicTrainTADClassifier/model.BIN
test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed
test-data/hicTrainTADClassifier/small_test_matrix.cool
b
diff -r e30485c5e93b -r f0216498a666 hicAggregateContacts.xml
--- a/hicAggregateContacts.xml Tue Jan 10 19:13:28 2023 +0000
+++ b/hicAggregateContacts.xml Wed Oct 18 10:18:29 2023 +0000
[
@@ -66,7 +66,9 @@
     #if $vMax:
         --vMax $vMax
     #end if
-

+    $considerStrandDirection

     --outFileName plot.$image_file_format
     &&
     mv plot.$image_file_format plot
@@ -77,11 +79,11 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro="matrix_h5_cooler_macro" />
         <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
         <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />
 
-        <expand macro='range' />
+        <expand macro="range" />
         <param argument="--mode" type="select" label="Regions to consider.">
             <option value="inter-chr">inter-chr</option>
             <option value="intra-chr">intra-chr</option>
@@ -119,6 +121,7 @@
             <option value="mean">mean</option>
             <option value="sum">sum</option>
         </param>
+        <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />
 
         <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 
                            a bin of the input matrix, by default only the first bin 
@@ -189,14 +192,14 @@
             <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
         <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
-            <filter>'outFileObsExp' in outputs</filter>
+            <filter>outputs == 'outFileObsExp'</filter>
             <change_format>
                 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
             </change_format>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
             <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
             <param name="numberOfBins" value="30" />
b
diff -r e30485c5e93b -r f0216498a666 macros.xml
--- a/macros.xml Tue Jan 10 19:13:28 2023 +0000
+++ b/macros.xml Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,7 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">3.7.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -37,7 +37,8 @@
 
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.1133705</citation>
+            <citation type="doi">10.1093/nar/gkaa220</citation>
+            <citation type="doi">10.1093/nar/gky504</citation>
             <yield />
         </citations>
     </xml>
@@ -348,6 +349,10 @@
     <xml name='matrix_h5_cooler_multiple_macro'>
         <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
     </xml>
+
+    <xml name='matrix_cooler_multiple_macro'>
+        <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
+    </xml>
     <xml name='convertFormat_single_macro'>
         <conditional name="inputFormat_conditional">
             <param name="inputFormat_selector" type="select" label="Choose input file type">
@@ -356,6 +361,8 @@
                 <option value="optionHic">hic</option>
                 <option value="optionHomer">Homer</option>
                 <option value="optionHicpro">HiCPro</option>
+                <option value="option2Dtext">2D-text</option>
+
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_macro' />
@@ -377,9 +384,17 @@
                 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
             </when>
             <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' />
+                <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
                 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
             </when>
+            <when value="option2Dtext">
+                <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
+
+                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
+                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+                </param>
+                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
+            </when>
         </conditional>
     </xml>
 
@@ -390,6 +405,9 @@
                 <option value="optionH5">h5</option>
                 <option value="optionHomer">Homer</option>
                 <option value="optionHicpro">HiCPro</option>
+                <option value="option2Dtext">2D-text</option>
+
+
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_multiple_macro' />
@@ -408,6 +426,14 @@
                 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
                 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
             </when>
+            <when value="option2Dtext">
+                <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
+
+                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
+                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+                </param>
+                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
+            </when>
         </conditional>
     </xml>
     <xml name='convertFormat_single_output_macro'>
@@ -418,6 +444,8 @@
                 <option value="h5">h5</option>
                 <option value="homer">Homer</option>
                 <option value="ginteractions">ginteractions</option>
+                <option value="hicpro">hicpro</option>
+
             </param>
             <when value="cool">
                 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
@@ -426,6 +454,7 @@
             <when value='h5' />
             <when value='homer' />
             <when value='ginteractions' />
+            <when value='hicpro' />
         </conditional>
     </xml>
     <token name="@REFERENCES@">
b
diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate.tar.gz
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Binary file test-data/cHi-C/aggregate.tar.gz has changed
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 14274000 14278000 Eya1 673.000000000000 -23000 5.600000000000
+chr1 14295000 14298000 Eya1 673.000000000000 -3000 44.400000000000
+chr1 14314000 14319000 Eya1 673.000000000000 18000 24.200000000000
+chr1 14426000 14432000 Eya1 673.000000000000 131000 2.400000000000
+chr1 14447000 14455000 Eya1 673.000000000000 154000 4.400000000000
+chr1 14460000 14465000 Eya1 673.000000000000 164000 3.200000000000
+chr1 14480000 14488000 Eya1 673.000000000000 187000 7.600000000000
+chr1 14491000 14501000 Eya1 673.000000000000 200000 20.650000000000
b
diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 4481000 4488000 Sox17 810.000000000000 0 297.800000000000
+chr1 4499000 4502000 Sox17 810.000000000000 14000 20.400000000000
+chr1 4509000 4515000 Sox17 810.000000000000 27000 27.800000000000
+chr1 4561000 4567000 Sox17 810.000000000000 79000 11.600000000000
+chr1 4585000 4590000 Sox17 810.000000000000 102000 8.000000000000
+chr1 4652000 4658000 Sox17 810.000000000000 170000 6.000000000000
+chr1 4664000 4669000 Sox17 810.000000000000 181000 1.200000000000
+chr1 4674000 4679000 Sox17 810.000000000000 191000 1.600000000000
b
diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,10 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 19078000 19081000 Tfap2d 472.000000000000 -13000 0.000000000000
+chr1 19086000 19091000 Tfap2d 472.000000000000 -3000 32.800000000000
+chr1 19104000 19106000 Tfap2d 472.000000000000 12000 10.600000000000
+chr1 19109000 19114000 Tfap2d 472.000000000000 20000 18.600000000000
+chr1 19125000 19129000 Tfap2d 472.000000000000 35000 7.800000000000
+chr1 19133000 19139000 Tfap2d 472.000000000000 45000 10.000000000000
+chr1 19182000 19185000 Tfap2d 472.000000000000 91000 1.000000000000
+chr1 19189000 19238000 Tfap2d 472.000000000000 144000 25.800000000000
+chr1 19254000 19261000 Tfap2d 472.000000000000 167000 6.400000000000
b
diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 14274000 14278000 Eya1 832.000000000000 -23000 0.000000000000
+chr1 14295000 14298000 Eya1 832.000000000000 -3000 49.800000000000
+chr1 14314000 14319000 Eya1 832.000000000000 18000 23.400000000000
+chr1 14426000 14432000 Eya1 832.000000000000 131000 9.000000000000
+chr1 14447000 14455000 Eya1 832.000000000000 154000 12.400000000000
+chr1 14460000 14465000 Eya1 832.000000000000 164000 7.600000000000
+chr1 14480000 14488000 Eya1 832.000000000000 187000 3.200000000000
+chr1 14491000 14501000 Eya1 832.000000000000 200000 18.750000000000
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 4481000 4488000 Sox17 978.000000000000 0 400.400000000000
+chr1 4499000 4502000 Sox17 978.000000000000 14000 21.000000000000
+chr1 4509000 4515000 Sox17 978.000000000000 27000 13.200000000000
+chr1 4561000 4567000 Sox17 978.000000000000 79000 12.400000000000
+chr1 4585000 4590000 Sox17 978.000000000000 102000 2.400000000000
+chr1 4652000 4658000 Sox17 978.000000000000 170000 5.000000000000
+chr1 4664000 4669000 Sox17 978.000000000000 181000 5.400000000000
+chr1 4674000 4679000 Sox17 978.000000000000 191000 5.200000000000
b
diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,10 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 19078000 19081000 Tfap2d 800.000000000000 -13000 9.000000000000
+chr1 19086000 19091000 Tfap2d 800.000000000000 -3000 88.600000000000
+chr1 19104000 19106000 Tfap2d 800.000000000000 12000 14.800000000000
+chr1 19109000 19114000 Tfap2d 800.000000000000 20000 22.200000000000
+chr1 19125000 19129000 Tfap2d 800.000000000000 35000 8.800000000000
+chr1 19133000 19139000 Tfap2d 800.000000000000 45000 12.800000000000
+chr1 19182000 19185000 Tfap2d 800.000000000000 91000 5.000000000000
+chr1 19189000 19238000 Tfap2d 800.000000000000 144000 126.600000000000
+chr1 19254000 19261000 Tfap2d 800.000000000000 167000 1.400000000000
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicDifferentialTest/differential.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/aggregate.tar.gz
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 10:18:29 2023 +0000
b
b'@@ -0,0 +1,402 @@\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+chr1\t14100000\t14101000\tEya1\t673.000000000000\t-200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.000000000000\t-199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.000000000000\t-198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.000000000000\t-197000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.000000000000\t-196000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.000000000000\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.000000000000\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.000000000000\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.000000000000\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.000000000000\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.000000000000\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.000000000000\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.000000000000\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.000000000000\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.000000000000\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.000000000000\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.000000000000\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.000000000000\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.000000000000\t-182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.000000000000\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.000000000000\t-180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.000000000000\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.000000000000\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.000000000000\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.000000000000\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.000000000000\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.000000000000\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.000000000000\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.000000000000\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.000000000000\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.000000000000\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.000000000000\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.000000000000\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.000000000000\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.0000000000'..b'.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.000000000000\t166000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.000000000000\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.000000000000\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.000000000000\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.000000000000\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.000000000000\t171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.000000000000\t172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.000000000000\t173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.000000000000\t174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.000000000000\t175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.000000000000\t176000\t0.000297176820\t0.000000000000\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.000000000000\t177000\t0.000297176820\t0.000000000000\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.000000000000\t178000\t0.000594353640\t0.000000000000\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.000000000000\t179000\t0.000594353640\t0.000000000000\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.000000000000\t180000\t0.001485884101\t0.000000000000\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.000000000000\t181000\t0.001188707281\t0.000000000000\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.000000000000\t182000\t0.001188707281\t0.000000000000\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.000000000000\t183000\t0.001783060921\t0.000000000000\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.000000000000\t184000\t0.002080237741\t0.000000000000\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.000000000000\t185000\t0.001188707281\t0.000000000000\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.000000000000\t186000\t0.001188707281\t0.000000000000\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.000000000000\t187000\t0.001188707281\t0.000000000000\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.000000000000\t188000\t0.000594353640\t0.000000000000\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.000000000000\t189000\t0.000297176820\t0.000000000000\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.000000000000\t190000\t0.000297176820\t0.000000000000\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.000000000000\t191000\t0.002080237741\t0.000000000000\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.000000000000\t192000\t0.003268945022\t0.000000000000\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.000000000000\t193000\t0.002971768202\t0.000000000000\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.000000000000\t194000\t0.003268945022\t0.000000000000\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.000000000000\t195000\t0.003268945022\t0.000000000000\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.000000000000\t196000\t0.002971768202\t0.000000000000\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.000000000000\t197000\t0.002080237741\t0.000000000000\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.000000000000\t198000\t0.002971768202\t0.000000000000\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.000000000000\t199000\t0.003343239227\t0.000000000000\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.000000000000\t200000\t0.004457652303\t0.000000000000\t7.575723225668\t3.000000000000\n'
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig
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Binary file test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig has changed
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 10:18:29 2023 +0000
b
b'@@ -0,0 +1,402 @@\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+chr1\t14100000\t14101000\tEya1\t832.000000000000\t-200000\t0.000400641026\t0.028365821799\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.000000000000\t-199000\t0.000300480769\t0.036748857670\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.000000000000\t-198000\t0.000240384615\t0.042850447268\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.000000000000\t-197000\t0.000240384615\t0.042850447268\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.000000000000\t-196000\t0.000240384615\t0.042850447268\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.000000000000\t-195000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.000000000000\t-194000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.000000000000\t-193000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.000000000000\t-192000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.000000000000\t-191000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.000000000000\t-190000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.000000000000\t-189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.000000000000\t-188000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.000000000000\t-187000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.000000000000\t-186000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.000000000000\t-185000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.000000000000\t-184000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.000000000000\t-183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.000000000000\t-182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.000000000000\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.000000000000\t-180000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.000000000000\t-179000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.000000000000\t-178000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.000000000000\t-177000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.000000000000\t-176000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.000000000000\t-175000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.000000000000\t-174000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.000000000000\t-173000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.000000000000\t-172000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.000000000000\t-171000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.000000000000\t-170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.000000000000\t-169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.000000000000\t-168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.000000000000\t-167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.0000000000'..b'.000000000000\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.000000000000\t166000\t0.000240384615\t0.000000000000\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.000000000000\t167000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.000000000000\t168000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.000000000000\t169000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.000000000000\t170000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.000000000000\t171000\t0.000480769231\t0.000000000000\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.000000000000\t172000\t0.000480769231\t0.000000000000\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.000000000000\t173000\t0.000480769231\t0.000000000000\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.000000000000\t174000\t0.000480769231\t0.000000000000\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.000000000000\t175000\t0.000480769231\t0.000000000000\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.000000000000\t176000\t0.000240384615\t0.000000000000\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.000000000000\t177000\t0.000480769231\t0.000000000000\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.000000000000\t178000\t0.000480769231\t0.000000000000\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.000000000000\t179000\t0.000480769231\t0.000000000000\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.000000000000\t180000\t0.000480769231\t0.000000000000\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.000000000000\t181000\t0.000240384615\t0.000000000000\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.000000000000\t182000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.000000000000\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.000000000000\t184000\t0.000240384615\t0.000000000000\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.000000000000\t185000\t0.000961538462\t0.000000000000\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.000000000000\t186000\t0.000961538462\t0.000000000000\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.000000000000\t187000\t0.000961538462\t0.000000000000\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.000000000000\t188000\t0.001201923077\t0.000000000000\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.000000000000\t189000\t0.001442307692\t0.000000000000\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.000000000000\t190000\t0.000721153846\t0.000000000000\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.000000000000\t191000\t0.001442307692\t0.000000000000\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.000000000000\t192000\t0.002403846154\t0.000000000000\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.000000000000\t193000\t0.002163461538\t0.000000000000\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.000000000000\t194000\t0.001682692308\t0.000000000000\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.000000000000\t195000\t0.002163461538\t0.000000000000\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.000000000000\t196000\t0.001682692308\t0.000000000000\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.000000000000\t197000\t0.001442307692\t0.000000000000\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.000000000000\t198000\t0.002644230769\t0.000000000000\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.000000000000\t199000\t0.003305288462\t0.000000000000\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.000000000000\t200000\t0.003605769231\t0.000000000000\t6.127958811148\t3.000000000000\n'
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicQualityControl/histogram.png
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:18:29 2023 +0000
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@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.6
+# Created with chicQualityControl version 3.7.2
 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
 # Used Matrices 0_matrix.cool 1_matrix.cool
 # Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.6
+# Created with chicQualityControl version 3.7.2
 # QC report for matrices: 0_matrix.cool 1_matrix.cool 
 #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
 
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicQualityControl/sparsity.png
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/chicViewpoint/two_matrices.hdf5
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/hg19.chrom.sizes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/hg19.chrom.sizes Wed Oct 18 10:18:29 2023 +0000
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@@ -0,0 +1,93 @@
+chr1 249250621
+chr2 243199373
+chr3 198022430
+chr4 191154276
+chr5 180915260
+chr6 171115067
+chr7 159138663
+chrX 155270560
+chr8 146364022
+chr9 141213431
+chr10 135534747
+chr11 135006516
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr18 78077248
+chr20 63025520
+chrY 59373566
+chr19 59128983
+chr22 51304566
+chr21 48129895
+chr6_ssto_hap7 4928567
+chr6_mcf_hap5 4833398
+chr6_cox_hap2 4795371
+chr6_mann_hap4 4683263
+chr6_apd_hap1 4622290
+chr6_qbl_hap6 4611984
+chr6_dbb_hap3 4610396
+chr17_ctg5_hap1 1680828
+chr4_ctg9_hap1 590426
+chr1_gl000192_random 547496
+chrUn_gl000225 211173
+chr4_gl000194_random 191469
+chr4_gl000193_random 189789
+chr9_gl000200_random 187035
+chrUn_gl000222 186861
+chrUn_gl000212 186858
+chr7_gl000195_random 182896
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000219 179198
+chr17_gl000205_random 174588
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chr9_gl000199_random 169874
+chrUn_gl000211 166566
+chrUn_gl000213 164239
+chrUn_gl000220 161802
+chrUn_gl000218 161147
+chr19_gl000209_random 159169
+chrUn_gl000221 155397
+chrUn_gl000214 137718
+chrUn_gl000228 129120
+chrUn_gl000227 128374
+chr1_gl000191_random 106433
+chr19_gl000208_random 92689
+chr9_gl000198_random 90085
+chr17_gl000204_random 81310
+chrUn_gl000233 45941
+chrUn_gl000237 45867
+chrUn_gl000230 43691
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000241 42152
+chrUn_gl000236 41934
+chrUn_gl000240 41933
+chr17_gl000206_random 41001
+chrUn_gl000232 40652
+chrUn_gl000234 40531
+chr11_gl000202_random 40103
+chrUn_gl000238 39939
+chrUn_gl000244 39929
+chrUn_gl000248 39786
+chr8_gl000196_random 38914
+chrUn_gl000249 38502
+chrUn_gl000246 38154
+chr17_gl000203_random 37498
+chr8_gl000197_random 37175
+chrUn_gl000245 36651
+chrUn_gl000247 36422
+chr9_gl000201_random 36148
+chrUn_gl000235 34474
+chrUn_gl000239 33824
+chr21_gl000210_random 27682
+chrUn_gl000231 27386
+chrUn_gl000229 19913
+chrM 16571
+chrUn_gl000226 15008
+chr18_gl000207_random 4262
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/plots.tar.gz
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/referencePoints_chicViewpoint.bed
--- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,4 +1,3 @@
 chr1 4487435 4487435 Sox17
 chr1 14300280 14300280 Eya1
-chr1 19093103 19093103 Tfap2d
-
+chr1 19093103 19093103 Tfap2d
\ No newline at end of file
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diff -r e30485c5e93b -r f0216498a666 test-data/cHi-C/target_list.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/target_list.bed Wed Oct 18 10:18:29 2023 +0000
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@@ -0,0 +1,8 @@
+chr1    4480000 4549000
+chr1    4555000 4688000
+chr1    14274000    14279000
+chr1    14290000    14439000
+chr1    14444000    14467000
+chr1    14476000    14501000
+chr1    19077000    19118000
+chr1    19120000    19274000
\ No newline at end of file
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diff -r e30485c5e93b -r f0216498a666 test-data/distVsCounts.txt
--- a/test-data/distVsCounts.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/distVsCounts.txt Wed Oct 18 10:18:29 2023 +0000
b
b'@@ -1,600 +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'..b'_h5\tall\t2715000\t3.579866828953963e-05\t27934\t1.0\n+543\tsmall_test_matrix_h5\tall\t2720000\t0.0001432356943350283\t27926\t1.0\n+544\tsmall_test_matrix_h5\tall\t2725000\t3.581918475535497e-05\t27918\t1.0\n+545\tsmall_test_matrix_h5\tall\t2730000\t0.00014331780723754928\t27910\t1.0\n+546\tsmall_test_matrix_h5\tall\t2735000\t0.00021503834850548347\t27902\t1.0\n+547\tsmall_test_matrix_h5\tall\t2740000\t7.170000717000071e-05\t27894\t1.0\n+548\tsmall_test_matrix_h5\tall\t2745000\t0.0003586028831671807\t27886\t1.0\n+549\tsmall_test_matrix_h5\tall\t2750000\t0.00014348231580457708\t27878\t1.0\n+550\tsmall_test_matrix_h5\tall\t2755000\t0.0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b
diff -r e30485c5e93b -r f0216498a666 test-data/hicCompartmentsPolarization/output_matrix.npz
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Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed
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diff -r e30485c5e93b -r f0216498a666 test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt Wed Oct 18 10:18:29 2023 +0000
b
b'@@ -0,0 +1,8688 @@\n+chr1\t9070077\t9070377\tchr1\t9161597\t9161998\t3.56853872159199\n+chr1\t33399109\t33399580\tchr1\t33472896\t33473132\t2.96495534866551\n+chr10\t120183442\t120183650\tchr10\t120219172\t120219445\t2.16689086564101\n+chr9\t33403433\t33403622\tchr9\t33466643\t33466934\t2.93417411277434\n+chr4\t82327572\t82327718\tchr4\t82765776\t82766279\t2.88416992254615\n+chr11\t47955862\t47956393\tchr11\t48131363\t48131755\t3.71969802258679\n+chr4\t143048082\t143048416\tchr4\t143274226\t143274598\t2.16311707296887\n+chr4\t143048082\t143048416\tchr4\t143761698\t143761933\t2.07342264106225\n+chr1\t91044809\t91045231\tchr1\t91744387\t91744562\t3.51909273701034\n+chr19\t6048781\t6049288\tchr19\t6125453\t6126018\t3.29338221810951\n+chr3\t114009726\t114010117\tchr3\t114137465\t114137878\t2.12000329080928\n+chr12\t7868964\t7869440\tchr12\t7959290\t7959857\t3.68024514839981\n+chr10\t56851410\t56851806\tchr10\t57023805\t57024048\t3.96640886878941\n+chr1\t160696549\t160697302\tchr1\t160738047\t160738414\t2.89116414906993\n+chr2\t159757650\t159758122\tchr2\t159975035\t159975474\t2.84014226125512\n+chr14\t20795485\t20795828\tchr14\t21077391\t21078231\t3.35059271246836\n+chr18\t55626554\t55626864\tchr18\t55789041\t55789434\t2.07615790164526\n+chr11\t8027897\t8028270\tchr11\t8120758\t8121217\t2.87072283976098\n+chr10\t101320283\t101320703\tchr10\t101371750\t101372300\t2.73733184380342\n+chr1\t65701483\t65702020\tchr1\t66153191\t66153690\t2.61573957577398\n+chr1\t65701483\t65702020\tchr1\t65925119\t65925446\t2.25869832061824\n+chr18\t44741865\t44742274\tchr18\t45282830\t45283060\t2.7685492265079\n+chr3\t135455696\t135456016\tchr3\t135613877\t135614273\t3.29133394789726\n+chr17\t73760711\t73761015\tchr17\t73844506\t73844791\t3.4820704597128\n+chr2\t105730818\t105731366\tchr2\t105854509\t105854661\t2.88287222042225\n+chr19\t17981148\t17981381\tchr19\t18043214\t18043759\t3.21815814201589\n+chr1\t968258\t968673\tchr1\t999245\t999513\t2.0898677183691\n+chr9\t71199335\t71199796\tchr9\t71300679\t71301065\t2.23458079847566\n+chr12\t3994711\t3995172\tchr12\t4386015\t4386462\t2.19499330026023\n+chr20\t36701900\t36702234\tchr20\t36793685\t36793968\t2.30055286128984\n+chrX\t147131403\t147131551\tchrX\t148086517\t148086769\t2.9129047806096\n+chr17\t5100354\t5100573\tchr17\t5140760\t5141199\t3.22477799940794\n+chr2\t165871624\t165871837\tchr2\t166060441\t166060815\t3.05782403079738\n+chr11\t62803219\t62803536\tchr11\t62980249\t62980432\t3.31066817882777\n+chr2\t105730818\t105731366\tchr2\t105852101\t105852503\t3.39284066154419\n+chr3\t196950934\t196951241\tchr3\t197236979\t197237377\t2.10831673803741\n+chr10\t92511204\t92511767\tchr10\t92630992\t92631276\t2.84382635556987\n+chr10\t92511204\t92511767\tchr10\t92622747\t92623111\t2.14121699866678\n+chr22\t22014517\t22014657\tchr22\t22307203\t22307475\t3.11735429074791\n+chr1\t155035599\t155035764\tchr1\t155057164\t155057722\t4.01383813965872\n+chr2\t74166651\t74166813\tchr2\t74214690\t74214882\t2.18499945967747\n+chr10\t101390269\t101390620\tchr10\t101470925\t101471221\t2.09196763275484\n+chr14\t93153253\t93153511\tchr14\t93249926\t93250605\t3.11082122588192\n+chr12\t124286170\t124286558\tchr12\t124326530\t124326755\t2.05957032269325\n+chr2\t11833000\t11833389\tchr2\t11919277\t11919692\t3.40777668251184\n+chr12\t21850781\t21851091\tchr12\t22596139\t22596803\t2.39933098199018\n+chr13\t85470363\t85470647\tchr13\t86402304\t86402529\t3.24881322547825\n+chr15\t68545243\t68545659\tchr15\t68675747\t68676109\t2.58748776974932\n+chr7\t106300372\t106301094\tchr7\t106376909\t106377352\t2.16592746274802\n+chr11\t65652144\t65652550\tchr11\t65756399\t65756930\t2.85484000816946\n+chr14\t72570826\t72571066\tchr14\t72759126\t72759488\t2.30918808091351\n+chr8\t64303880\t64304269\tchr8\t65294690\t65295020\t2.88681946013737\n+chr14\t65630731\t65631320\tchr14\t66291299\t66291784\t2.46223005124185\n+chr11\t90021495\t90021783\tchr11\t90168091\t90168231\t2.61407133628162\n+chr10\t17649444\t17649945\tchr10\t18393260\t18393633\t2.99679427749225\n+chr18\t5879451\t5879774\tchr18\t6219125\t6219404\t2.81824425454522\n+chr18\t5879451\t5879774\tchr18\t6482480\t6482966\t2.0952333712136\n+chr21\t30536571\t30537300\tchr21\t30744473\t30745011\t2.35393256739323\n+chr1\t32327060\t32327325\tchr1\t32429713\t32430270\t2.40655486151582\n+chr1\t228659628\t228659835\tchr1\t228703049\t228703255\t2.25870598019961\n+chr14\t24834779\t24835158\tchr14\t24900961\t2490125'..b'94\t157736229\tchr6\t158088133\t158088594\t3.10243121339195\n+chr5\t78428845\t78429343\tchr5\t78760365\t78760882\t3.0748988318322\n+chr1\t47902153\t47902427\tchr1\t48176083\t48176585\t2.48522594874561\n+chr2\t4006947\t4007241\tchr2\t6913151\t6913688\t4.24747297541131\n+chr12\t12798457\t12798785\tchr12\t12857512\t12857957\t2.30590982249516\n+chr15\t38766371\t38766732\tchr15\t38991833\t38992274\t2.27457695371833\n+chr3\t39748783\t39749163\tchr3\t40032056\t40032363\t2.36788372331025\n+chr3\t52325469\t52325828\tchr3\t52373415\t52373987\t2.77505578922318\n+chr1\t2293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b
diff -r e30485c5e93b -r f0216498a666 test-data/hicConvertFormat/hg19.chrom.sizes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/hg19.chrom.sizes Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,93 @@
+chr1 249250621
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b
diff -r e30485c5e93b -r f0216498a666 test-data/hicConvertFormat/small_test_matrix_chr4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.bed Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,271 @@
+chr4 0 5000 1
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b
diff -r e30485c5e93b -r f0216498a666 test-data/hicConvertFormat/small_test_matrix_chr4.hicpro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.hicpro Wed Oct 18 10:18:29 2023 +0000
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diff -r e30485c5e93b -r f0216498a666 test-data/hicConvertFormat/small_test_matrix_chr4.homer
b
Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicDifferentialTAD/accepted.txt
--- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.6
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.2
 # H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.
 # Accepted regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one 
-# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD
+# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicDifferentialTAD/rejected.txt
--- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:18:29 2023 +0000
b
b"@@ -1,1402 +1,1406 @@\n-# Created with HiCExplorer's hicDifferentialTAD version 3.6\n+# Created with HiCExplorer's hicDifferentialTAD version 3.7.2\n # H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.\n # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one \n-# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n-chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\tnan\t1.0\t1.0\n-chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t1.0\t1.0\t1.0\n-chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t1.0\t1.0\t1.0\n-chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t1.0\t1.0\t1.0\n-chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t1.0\t1.0\t1.0\n-chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t1.0\t1.0\t1.0\n-chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t1.0\t1.0\t1.0\n-chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t1.0\t1.0\t1.0\n-chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t1.0\t1.0\t1.0\n-chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t1.0\t1.0\t1.0\n-chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1.0\t1.0\t1.0\n-chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1.0\t1.0\t1.0\n-chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1.0\t1.0\t1.0\n-chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1.0\t1.0\t1.0\n-chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1.0\t1.0\t1.0\n-chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1.0\t1.0\t1.0\n-chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1.0\t1.0\t1.0\n-chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1.0\t1.0\t1.0\n-chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1.0\t1.0\t1.0\n-chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1.0\t1.0\t1.0\n-chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1.0\t1.0\t1.0\n-chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1.0\t1.0\t1.0\n-chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1.0\t1.0\t1.0\n-chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1.0\t1.0\t1.0\n-chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1.0\t1.0\t1.0\n-chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t1.0\t1.0\t1.0\n-chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t1.0\t1.0\t1.0\n-chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t1.0\t1.0\t1.0\n-chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t1.0\t1.0\t1.0\n-chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t1.0\t1.0\t1.0\n-chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t1.0\t1.0\t1.0\n-chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t1.0\t1.0\t1.0\n-chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t1.0\t1.0\t1.0\n-chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t1.0\t1.0\t1.0\n-chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t1.0\t1.0\t1.0\n-chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t1.0\t1.0\t1.0\n-chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t1.0\t1.0\t1.0\n-chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t1.0\t1.0\t1.0\n-chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t1.0\t1.0\t1.0\n-chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t1.0\t1.0\t1.0\n-chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t1.0\t1.0\t1.0\n-chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t1.0\t1.0\t1.0\n-chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t1.0\t1.0\t1.0\n-chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t1.0\t1.0\t1.0\n-chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t1.0\t1.0\t1.0\n-chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t1.0\t1.0\t1.0\n-chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t1.0\t1.0\t1.0\n-chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t1.0\t1.0\t1.0\n-chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t1.0\t1.0\t1.0\n-chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t1.0\t1.0\t1.0\n-chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t1.0\t1.0\t1.0\n-chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t1.0\t1.0\t1.0\n-chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t1.0\t1.0\t1.0\n-chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t1.0\t1.0\t1.0\n-chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t1.0\t1.0\t1.0\n-chr3L\t4270000\t4365000\tID_0.01_56\t-0.11633575\t.\t1.0\t1.0\t1.0\n-chr3L\t4365000\t4405000\tID_0.01_57\t-0.0944955\t.\t1.0\t1.0\t1.0\n-chr3L\t4405000\t4490000\tID_0.01_58\t-0.07463925\t.\t1.0\t1.0\t1.0\n-chr3L\t4490000\t4625000\tID_0.01_59\t0.00287075\t.\t1.0\t1.0\t1.0\n-chr3L\t4625000\t4650000\tI"..b'.0\t0.0\t0.0\t0.0\n+chr3R\t22380000\t22500000\tID_0.01_1350\t-0.055847\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22500000\t22520000\tID_0.01_1351\t-0.0631105\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22520000\t22605000\tID_0.01_1352\t-0.062648\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22605000\t22695000\tID_0.01_1353\t-0.011252\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22695000\t22780000\tID_0.01_1354\t-0.089033\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22780000\t22885000\tID_0.01_1355\t-0.04050025\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.05683475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.0237815\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.00294725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.00275775\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.1119105\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.0660765\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.04218475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.05579575\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.01546725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.0326015\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.0623065\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.0749395\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.09836075\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.03171375\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.08589625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.09323725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.0589785\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.03674225\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.0462465\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.08303325\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.00546225\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.04654075\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.01871575\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.00858875\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.10581625\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.0935315\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.11469275\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.1002735\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.0627965\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.01974475\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.07430725\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.0249905\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.00609925\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.01281025\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.04990275\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.0499295\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.08094325\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.01535\t.\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.01357725\t.\t1.0\tnan\t1.0\t0.0\tnan\t0.0\n'
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicInfo/hicInfo_output.txt
--- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,8 +1,8 @@
-# Matrix information file. Created with HiCExplorer's hicInfo version 3.4
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2
 File: matrix_name.h5
 Size: 33,754
 Bin_length: 5000
-Sum of matrix: 35778.0
+Sum of matrix: 37321.0
 Chromosomes:length: chr2L: 23011544 bp; chr2LHet: 368872 bp; chr2R: 21146708 bp; chr2RHet: 3288761 bp; chr3L: 24543557 bp; chr3LHet: 2555491 bp; chr3R: 27905053 bp; chr3RHet: 2517507 bp; chr4: 1351857 bp; chrM: 19517 bp; chrUextra: 29004656 bp; chrU: 10049037 bp; chrX: 22422827 bp; chrXHet: 204112 bp; chrYHet: 347038 bp; 
 Non-zero elements: 69,213
 Minimum (non zero): 1
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicInterIntraTAD/matrix.cool
b
Binary file test-data/hicInterIntraTAD/matrix.cool has changed
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicInterIntraTAD/output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,22 @@
+# Created with HiCExplorer's hicInterIntraTAD version 3.7.2
+# Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio
+chr2 17100000 18100000 region_0 0 + 0 148.64980341892507 0 1.0 0 90 0 90 289.00804022517053 100 100 1.0 0.0 0.5143448718696884 0.5143448718696884
+chr2 18100000 19100000 region_1 0 + 162.1124908492847 211.04026046280666 1.0 1.0 100 140 100 140 277.9356647725957 100 100 1.0 0.583273438412172 0.7593133491359512 1.3425867875481232
+chr2 19100000 20600000 region_2 0 + 223.14353637851622 150.01947633135822 1.0 1.0 150 90 150 90 556.143932925097 225 225 1.0 0.4012334274777925 0.269749371430369 0.6709827989081616
+chr2 20600000 21300000 region_3 0 + 171.34866125986417 274.4679914622871 1.0 1.0 105 84 105 84 149.85761183392816 49 49 1.0 1.1434097952244984 1.8315251931710472 2.9749349883955456
+chr2 21300000 22600000 region_4 0 + 283.89289960594425 768.874984677404 1.0 1.0 91 208 91 208 24180.36424789467 169 169 1.0 0.011740637845464306 0.03179749390021485 0.04353813174567915
+chr2 22600000 24300000 region_5 0 + 789.804014201572 321.70053830625835 1.0 1.0 221 238 221 238 659.9593561049022 289 289 1.0 1.1967464464221198 0.48745507633219043 1.6842015227543101
+chr2 24300000 25800000 region_6 0 + 340.44705127228065 836.790681935677 1.0 1.0 255 720 255 720 598.8884085354028 225 225 1.0 0.5684649200422041 1.3972397361673277 1.965704656209532
+chr2 25800000 30700000 region_7 0 + 852.3657188383157 1593.0953595672838 1.0 1.0 735 1421 735 1421 4153.286346671477 2401 2401 1.0 0.20522681262307327 0.3835746506724779 0.5888014632955512
+chr2 30700000 33700000 region_8 0 + 1644.3620053137968 315.02407146145276 1.0 1.0 1470 240 1470 240 1873.0714290428866 900 900 1.0 0.8778960480722525 0.16818582920910052 1.046081877281353
+chr2 33700000 34600000 region_9 0 + 351.38600814451206 204.32883091037917 1.0 1.0 270 153 270 153 245.00889544594847 81 81 1.0 1.434176532672184 0.8339649486541041 2.268141481326288
+chr2 34600000 36400000 region_10 0 + 213.88883777381795 379.5343566721307 1.0 1.0 162 288 162 288 770.6376988509402 324 324 1.0 0.27754785172427593 0.49249388816305717 0.7700417398873332
+chr2 36400000 38100000 region_11 0 + 399.4783208321819 189.4340956757372 1.0 1.0 306 136 306 136 635.9658356069232 289 289 1.0 0.6281443097504547 0.29786835246417603 0.9260126622146307
+chr2 38100000 39000000 region_12 0 + 209.82145375215833 74.59004956153072 1.0 1.0 153 45 153 45 229.67774089590498 81 81 1.0 0.9135471854334115 0.3247595925951596 1.2383067780285713
+chr2 39000000 39600000 region_13 0 + 87.2296637584025 120.04828267162685 1.0 1.0 54 72 54 72 114.2377217834551 36 36 1.0 0.7635802114799864 1.0508637672168046 1.814443978696791
+chr2 39600000 40900000 region_14 0 + 127.68593516818584 348.8073054441913 1.0 1.0 78 247 78 247 447.58733970743407 169 169 1.0 0.2852760206569915 0.7793055667575172 1.0645815874145086
+chr2 40900000 42900000 region_15 0 + 363.6155543954171 330.73139298156053 1.0 1.0 260 240 260 240 912.1015373488856 400 400 1.0 0.3986568813953566 0.3626037008367121 0.7612605822320687
+chr2 42900000 44200000 region_16 0 + 353.76150800590995 305.3562724757596 1.0 1.0 260 208 260 208 434.0150296605763 169 169 1.0 0.8150904550069866 0.7035615165552332 1.51865197156222
+chr2 44200000 45900000 region_17 0 + 321.3851510623236 309.7368872510572 1.0 1.0 221 221 221 221 667.4121186463332 289 289 1.0 0.4815392799791639 0.4640863996885097 0.9456256796676736
+chr2 45900000 47300000 region_18 0 + 330.1441180225245 330.3028710611577 1.0 1.0 238 238 238 238 509.86032585858186 196 196 1.0 0.6475187444062777 0.6478301101481911 1.2953488545544687
+chr2 47300000 49100000 region_19 0 + 330.3028710611577 0 1.0 0 238 0 238 0 737.4495555644096 324 324 1.0 0.44789893568836614 0.0 0.44789893568836614
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicInterIntraTAD/plot.png
b
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diff -r e30485c5e93b -r f0216498a666 test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,20 @@
+chr2 17100000 18100000 ID_0.01_10 -0.230354000000 . 17100000 18100000 51,160,44
+chr2 18100000 19100000 ID_0.01_11 -0.513536500000 . 18100000 19100000 31,120,180
+chr2 19100000 20600000 ID_0.01_12 -0.420252500000 . 19100000 20600000 51,160,44
+chr2 20600000 21300000 ID_0.01_13 -0.998086500000 . 20600000 21300000 31,120,180
+chr2 21300000 22600000 ID_0.01_14 -0.859866000000 . 21300000 22600000 51,160,44
+chr2 22600000 24300000 ID_0.01_15 -0.281294000000 . 22600000 24300000 31,120,180
+chr2 24300000 25800000 ID_0.01_16 -1.036617500000 . 24300000 25800000 51,160,44
+chr2 25800000 30700000 ID_0.01_17 -0.147124500000 . 25800000 30700000 31,120,180
+chr2 30700000 33700000 ID_0.01_18 -1.013445500000 . 30700000 33700000 51,160,44
+chr2 33700000 34600000 ID_0.01_19 -1.338090000000 . 33700000 34600000 31,120,180
+chr2 34600000 36400000 ID_0.01_20 -0.632501500000 . 34600000 36400000 51,160,44
+chr2 36400000 38100000 ID_0.01_21 -0.925006000000 . 36400000 38100000 31,120,180
+chr2 38100000 39000000 ID_0.01_22 -0.911804000000 . 38100000 39000000 51,160,44
+chr2 39000000 39600000 ID_0.01_23 -0.474157000000 . 39000000 39600000 31,120,180
+chr2 39600000 40900000 ID_0.01_24 -0.483398000000 . 39600000 40900000 51,160,44
+chr2 40900000 42900000 ID_0.01_25 -0.701614500000 . 40900000 42900000 31,120,180
+chr2 42900000 44200000 ID_0.01_26 -0.658489500000 . 42900000 44200000 51,160,44
+chr2 44200000 45900000 ID_0.01_27 -1.406743500000 . 44200000 45900000 31,120,180
+chr2 45900000 47300000 ID_0.01_28 -0.656308000000 . 45900000 47300000 51,160,44
+chr2 47300000 49100000 ID_0.01_29 -0.003388500000 . 47300000 49100000 31,120,180
\ No newline at end of file
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicMergeLoops/gm12878_all.bedgraph
--- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:18:29 2023 +0000
b
b'@@ -7,7 +7,7 @@\n 1\t1050000\t1075000\t1\t1175000\t1200000\t0.001\n 1\t1310000\t1320000\t1\t1410000\t1420000\t0.001\n 1\t1710000\t1720000\t1\t1830000\t1840000\t0.001\n-1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407133\n+1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407\n 1\t2080000\t2090000\t1\t3330000\t3340000\t0.001\n 1\t2110000\t2120000\t1\t2710000\t2720000\t0.001\n 1\t2120000\t2130000\t1\t2480000\t2490000\t0.001\n@@ -101,7 +101,7 @@\n 1\t13160000\t13170000\t1\t14520000\t14530000\t0.001\n 1\t13320000\t13330000\t1\t13440000\t13450000\t0.001\n 1\t13335000\t13340000\t1\t13540000\t13545000\t0.001\n-1\t13350000\t13360000\t1\t13630000\t13640000\t0.008992888101929171\n+1\t13350000\t13360000\t1\t13630000\t13640000\t0.0089928881019291\n 1\t13475000\t13500000\t1\t13700000\t13725000\t0.001\n 1\t13550000\t13575000\t1\t14325000\t14350000\t0.001\n 1\t13690000\t13700000\t1\t15390000\t15400000\t0.001\n@@ -151,7 +151,7 @@\n 1\t21100000\t21125000\t1\t22350000\t22375000\t0.001\n 1\t21310000\t21315000\t1\t21520000\t21525000\t0.001\n 1\t21360000\t21370000\t1\t21470000\t21480000\t0.001\n-1\t21575000\t21600000\t1\t21675000\t21700000\t0.0010553575253769206\n+1\t21575000\t21600000\t1\t21675000\t21700000\t0.0010553575253769\n 1\t21900000\t21910000\t1\t22900000\t22910000\t0.001\n 1\t21930000\t21940000\t1\t22690000\t22700000\t0.001\n 1\t22020000\t22030000\t1\t22280000\t22290000\t0.001\n@@ -203,11 +203,11 @@\n 1\t29550000\t29575000\t1\t31175000\t31200000\t0.001\n 1\t29560000\t29570000\t1\t30840000\t30850000\t0.001\n 1\t29560000\t29570000\t1\t30310000\t30320000\t0.001\n-1\t29560000\t29570000\t1\t30580000\t30590000\t0.00321287751564984\n+1\t29560000\t29570000\t1\t30580000\t30590000\t0.0032128775156498\n 1\t29780000\t29790000\t1\t30840000\t30850000\t0.001\n 1\t29870000\t29880000\t1\t30020000\t30030000\t0.001\n 1\t29870000\t29880000\t1\t31120000\t31130000\t0.001\n-1\t30030000\t30040000\t1\t31120000\t31130000\t0.001105560265853574\n+1\t30030000\t30040000\t1\t31120000\t31130000\t0.0011055602658535\n 1\t30260000\t30270000\t1\t30850000\t30860000\t0.001\n 1\t30260000\t30270000\t1\t31170000\t31180000\t0.001\n 1\t30425000\t30450000\t1\t30525000\t30550000\t0.001\n@@ -228,7 +228,7 @@\n 1\t34100000\t34125000\t1\t35200000\t35225000\t0.001\n 1\t34300000\t34325000\t1\t34400000\t34425000\t0.001\n 1\t34350000\t34360000\t1\t34450000\t34460000\t0.001\n-1\t34570000\t34580000\t1\t35070000\t35080000\t0.0026399240525339608\n+1\t34570000\t34580000\t1\t35070000\t35080000\t0.0026399240525339\n 1\t34925000\t34950000\t1\t35050000\t35075000\t0.001\n 1\t35320000\t35330000\t1\t35760000\t35770000\t0.001\n 1\t35650000\t35660000\t1\t36230000\t36240000\t0.001\n@@ -241,7 +241,7 @@\n 1\t36610000\t36620000\t1\t36750000\t36760000\t0.001\n 1\t36775000\t36800000\t1\t36875000\t36900000\t0.001\n 1\t37020000\t37030000\t1\t38100000\t38110000\t0.001\n-1\t37040000\t37050000\t1\t37780000\t37790000\t0.0030468037205961147\n+1\t37040000\t37050000\t1\t37780000\t37790000\t0.0030468037205961\n 1\t37060000\t37070000\t1\t37890000\t37900000\t0.001\n 1\t37160000\t37170000\t1\t37780000\t37790000\t0.001\n 1\t37190000\t37200000\t1\t37290000\t37300000\t0.001\n@@ -256,7 +256,7 @@\n 1\t38950000\t38960000\t1\t39050000\t39060000\t0.001\n 1\t39070000\t39080000\t1\t39290000\t39300000\t0.001\n 1\t39330000\t39340000\t1\t39450000\t39460000\t0.001\n-1\t39550000\t39575000\t1\t39650000\t39675000\t0.0012254650005710432\n+1\t39550000\t39575000\t1\t39650000\t39675000\t0.001225465000571\n 1\t39560000\t39570000\t1\t40000000\t40010000\t0.001\n 1\t39560000\t39570000\t1\t39720000\t39730000\t0.001\n 1\t39790000\t39800000\t1\t39910000\t39920000\t0.001\n@@ -338,7 +338,7 @@\n 1\t55125000\t55150000\t1\t55250000\t55275000\t0.001\n 1\t55600000\t55625000\t1\t55725000\t55750000\t0.001\n 1\t55600000\t55610000\t1\t57060000\t57070000\t0.001\n-1\t55600000\t55610000\t1\t57180000\t57190000\t0.004934547993800267\n+1\t55600000\t55610000\t1\t57180000\t57190000\t0.0049345479938002\n 1\t55825000\t55850000\t1\t57050000\t57075000\t0.001\n 1\t55940000\t55950000\t1\t56870000\t56880000\t0.001\n 1\t56025000\t56050000\t1\t57825000\t57850000\t0.001\n@@ -377,14 +377,14 @@\n 1\t64150000\t64160000\t1\t64600000\t64610000\t0.001\n 1\t64225000\t64250000\t1\t64325000\t64350000\t0.001\n 1\t64600000\t64610000\t1\t64700000\t64710000\t0.001\n-1\t64725000\t64750000\t1\t66150000\t66175000\t0.0036618652715747655\n+1\t64725000\t64750000\t1\t66150000\t66175000\t0.0036618652715747\n 1\t64730000\t64740000\t1\t65140000\t65150000\t0.001\n 1\t64730000\t64740000\t1\t65500000\t65510000\t0'..b'4803309559888334\n+1\t73380000\t73390000\t1\t74050000\t74060000\t0.0048033095598883\n 1\t74300000\t74310000\t1\t74930000\t74940000\t0.001\n 1\t74300000\t74325000\t1\t74450000\t74475000\t0.001\n 1\t74310000\t74320000\t1\t75150000\t75160000\t0.001\n@@ -426,7 +426,7 @@\n 1\t75230000\t75240000\t1\t75670000\t75680000\t0.001\n 1\t75240000\t75250000\t1\t76060000\t76070000\t0.001\n 1\t75720000\t75730000\t1\t76090000\t76100000\t0.001\n-1\t75725000\t75750000\t1\t75825000\t75850000\t0.0015043592556291366\n+1\t75725000\t75750000\t1\t75825000\t75850000\t0.0015043592556291\n 1\t76370000\t76380000\t1\t77190000\t77200000\t0.001\n 1\t76610000\t76620000\t1\t77590000\t77600000\t0.001\n 1\t76630000\t76640000\t1\t77360000\t77370000\t0.001\n@@ -481,7 +481,7 @@\n 1\t87590000\t87600000\t1\t88410000\t88420000\t0.001\n 1\t87750000\t87775000\t1\t89050000\t89075000\t0.001\n 1\t87750000\t87775000\t1\t88400000\t88425000\t0.001\n-1\t87800000\t87825000\t1\t87900000\t87925000\t0.003919529137873564\n+1\t87800000\t87825000\t1\t87900000\t87925000\t0.0039195291378735\n 1\t88260000\t88270000\t1\t88360000\t88370000\t0.001\n 1\t89125000\t89150000\t1\t89325000\t89350000\t0.001\n 1\t89450000\t89475000\t1\t89825000\t89850000\t0.001\n@@ -631,7 +631,7 @@\n 1\t120775000\t120800000\t1\t121075000\t121100000\t0.001\n 1\t121240000\t121250000\t1\t121340000\t121350000\t0.001\n 1\t121350000\t121375000\t1\t121450000\t121475000\t0.001\n-1\t142525000\t142550000\t1\t142625000\t142650000\t0.007224819791140677\n+1\t142525000\t142550000\t1\t142625000\t142650000\t0.0072248197911406\n 1\t142540000\t142550000\t1\t142960000\t142970000\t0.001\n 1\t142540000\t142550000\t1\t143540000\t143550000\t0.001\n 1\t142560000\t142570000\t1\t142730000\t142740000\t0.001\n@@ -655,7 +655,7 @@\n 1\t143880000\t143890000\t1\t144160000\t144170000\t0.0114591711614241\n 1\t144150000\t144175000\t1\t145325000\t145350000\t0.001\n 1\t144150000\t144175000\t1\t145775000\t145800000\t0.001\n-1\t144170000\t144180000\t1\t144510000\t144520000\t0.0010944871943884217\n+1\t144170000\t144180000\t1\t144510000\t144520000\t0.0010944871943884\n 1\t144180000\t144190000\t1\t145980000\t145990000\t0.001\n 1\t144210000\t144220000\t1\t145750000\t145760000\t0.001\n 1\t144210000\t144220000\t1\t144320000\t144330000\t0.001\n@@ -669,7 +669,7 @@\n 1\t144620000\t144630000\t1\t145300000\t145310000\t0.001\n 1\t144675000\t144700000\t1\t144950000\t144975000\t0.001\n 1\t144810000\t144820000\t1\t146230000\t146240000\t0.001\n-1\t144825000\t144850000\t1\t146450000\t146475000\t0.005463291888438761\n+1\t144825000\t144850000\t1\t146450000\t146475000\t0.0054632918884387\n 1\t144830000\t144840000\t1\t145370000\t145380000\t0.001\n 1\t144850000\t144860000\t1\t146020000\t146030000\t0.001\n 1\t144910000\t144920000\t1\t145050000\t145060000\t0.001\n@@ -789,7 +789,7 @@\n 1\t157550000\t157560000\t1\t157650000\t157660000\t0.001\n 1\t157730000\t157740000\t1\t157830000\t157840000\t0.001\n 1\t157930000\t157940000\t1\t158090000\t158100000\t0.001\n-1\t157950000\t157960000\t1\t159050000\t159060000\t0.026660483087000208\n+1\t157950000\t157960000\t1\t159050000\t159060000\t0.0266604830870002\n 1\t158150000\t158175000\t1\t158950000\t158975000\t0.001\n 1\t158170000\t158180000\t1\t158290000\t158300000\t0.001\n 1\t158170000\t158175000\t1\t158465000\t158470000\t0.001\n@@ -948,7 +948,7 @@\n 1\t185110000\t185120000\t1\t186330000\t186340000\t0.001\n 1\t185250000\t185275000\t1\t186275000\t186300000\t0.001\n 1\t185280000\t185290000\t1\t185560000\t185570000\t0.001\n-1\t185280000\t185290000\t1\t185380000\t185390000\t0.009307972819450458\n+1\t185280000\t185290000\t1\t185380000\t185390000\t0.0093079728194504\n 1\t185780000\t185790000\t1\t186180000\t186190000\t0.001\n 1\t186450000\t186460000\t1\t186950000\t186960000\t0.001\n 1\t186460000\t186470000\t1\t186560000\t186570000\t0.001\n@@ -1161,9 +1161,9 @@\n 1\t229850000\t229860000\t1\t230440000\t230450000\t0.001\n 1\t229860000\t229870000\t1\t229970000\t229980000\t0.001\n 1\t230225000\t230250000\t1\t230325000\t230350000\t0.001\n-1\t230770000\t230780000\t1\t231740000\t231750000\t0.03373828183610245\n+1\t230770000\t230780000\t1\t231740000\t231750000\t0.0337382818361024\n 1\t231050000\t231060000\t1\t231340000\t231350000\t0.001\n-1\t231050000\t231075000\t1\t231150000\t231175000\t0.001796188746513645\n+1\t231050000\t231075000\t1\t231150000\t231175000\t0.0017961887465136\n 1\t231060000\t231070000\t1\t231730000\t231740000\t0.001\n 1\t231475000\t231500000\t1\t231725000\t231750000\t0.001\n 1\t231990000\t232000000\t1\t233140000\t233150000\t0.001\n'
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diff -r e30485c5e93b -r f0216498a666 test-data/hicPlotMatrix/plot3_pca.svg
--- a/test-data/hicPlotMatrix/plot3_pca.svg Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg Wed Oct 18 10:18:29 2023 +0000
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b
diff -r e30485c5e93b -r f0216498a666 test-data/hicPlotSVL/p_values.txt
--- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.6
+# Created with HiCExplorer's hicPlotSVL 3.7.2
 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
 # Short range contacts: <= 2000000
 0_small_test_matrix.h5 1_small_test_matrix.h5 1.0
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicPlotSVL/plot.png
b
Binary file test-data/hicPlotSVL/plot.png has changed
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diff -r e30485c5e93b -r f0216498a666 test-data/hicPlotSVL/ratios.txt
--- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.6
+# Created with HiCExplorer's hicPlotSVL 3.7.2
 # Short range vs long range contacts per chromosome: raw data
 # Short range contacts: <= 2000000
 # 0_small_test_matrix.h5 1_small_test_matrix.h5
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicQuickQC/QC.log
--- a/test-data/hicQuickQC/QC.log Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,5 +1,5 @@
 
-File /tmp/tmp12xmnm2f.h5
+File /var/folders/nm/9sgmbhhj6gn_h8b308xvhm0w0000gt/T/tmp8sucpx99.h5
 Sequenced reads 983
 Min rest. site distance 300
 Max library insert size 1000
@@ -12,7 +12,7 @@
 Low mapping quality 164 (16.68)
 
 # count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end GATC 1 (0.33)
+dangling end GATC (restriction sequence GATC) 1 (0.33)
 self ligation (removed) 0 (0.00)
 One mate not close to rest site 0 (0.00)
 same fragment 84 (28.00)
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicTADClassifier/unittest_classifier.BIN
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Binary file test-data/hicTADClassifier/unittest_classifier.BIN has changed
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diff -r e30485c5e93b -r f0216498a666 test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed Wed Oct 18 10:18:29 2023 +0000
b
@@ -0,0 +1,26 @@
+chr2L 800001 1550001 ID_0.01_1 0.022884658057 . 800001 1550001 31,120,180
+chr2L 1550001 2100001 ID_0.01_2 -0.744086372037 . 1550001 2100001 51,160,44
+chr2L 2100001 2400001 ID_0.01_3 0.311391232701 . 2100001 2400001 31,120,180
+chr2L 2400001 2750001 ID_0.01_4 0.078149036231 . 2400001 2750001 51,160,44
+chr2L 2750001 3700001 ID_0.01_5 -0.648971714281 . 2750001 3700001 31,120,180
+chr2L 3700001 4200001 ID_0.01_6 -0.133385571846 . 3700001 4200001 51,160,44
+chr2L 4200001 5050001 ID_0.01_7 -0.598347187435 . 4200001 5050001 31,120,180
+chr2L 5050001 5450001 ID_0.01_8 -0.589296128895 . 5050001 5450001 51,160,44
+chr2L 5450001 6550001 ID_0.01_9 -0.463215188679 . 5450001 6550001 31,120,180
+chr2L 6550001 7250001 ID_0.01_10 -0.739312227247 . 6550001 7250001 51,160,44
+chr2L 7250001 7650001 ID_0.01_11 -0.558267533146 . 7250001 7650001 31,120,180
+chr2L 7650001 8100001 ID_0.01_12 -0.164474310036 . 7650001 8100001 51,160,44
+chr2L 8100001 8950001 ID_0.01_13 -0.618832592666 . 8100001 8950001 31,120,180
+chr2L 8950001 10450001 ID_0.01_14 -0.547147684409 . 8950001 10450001 51,160,44
+chr2L 10450001 10800001 ID_0.01_15 -0.938748995456 . 10450001 10800001 31,120,180
+chr2L 10800001 11600001 ID_0.01_16 -0.305174734420 . 10800001 11600001 51,160,44
+chr2L 11600001 12300001 ID_0.01_17 -0.941807294590 . 11600001 12300001 31,120,180
+chr2L 12300001 12650001 ID_0.01_18 -0.124089226194 . 12300001 12650001 51,160,44
+chr2L 12650001 13150001 ID_0.01_19 -0.535969778416 . 12650001 13150001 31,120,180
+chr2L 13150001 13800001 ID_0.01_20 -0.246694822549 . 13150001 13800001 51,160,44
+chr2L 13800001 14200001 ID_0.01_21 -0.220174816848 . 13800001 14200001 31,120,180
+chr2L 14200001 15650001 ID_0.01_22 -0.512329343230 . 14200001 15650001 51,160,44
+chr2L 15650001 16250001 ID_0.01_23 -0.711741883911 . 15650001 16250001 31,120,180
+chr2L 16250001 17550001 ID_0.01_24 -0.917923384534 . 16250001 17550001 51,160,44
+chr2L 17550001 17850001 ID_0.01_25 -0.423222465610 . 17550001 17850001 31,120,180
+chr2L 17850001 18550001 ID_0.01_26 -0.274143371604 . 17850001 18550001 51,160,44
\ No newline at end of file
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicTrainTADClassifier/small_test_matrix.cool
b
Binary file test-data/hicTrainTADClassifier/small_test_matrix.cool has changed
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicValidateLocations/overlap_smc3_matched_locations
--- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,6 +1,6 @@
 chr1 1050000 1060000 chr1 1180000 1190000 0.001
 chr1 1710000 1720000 chr1 1830000 1840000 0.001
-chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407133
+chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407
 chr1 2120000 2130000 chr1 2310000 2320000 0.001
 chr1 2120000 2130000 chr1 2480000 2490000 0.001
 chr1 2130000 2140000 chr1 3570000 3580000 0.001
@@ -79,7 +79,7 @@
 chr1 29200000 29210000 chr1 29520000 29530000 0.001
 chr1 29210000 29220000 chr1 29360000 29370000 0.001
 chr1 29560000 29570000 chr1 31180000 31190000 0.001
-chr1 29560000 29570000 chr1 30580000 30590000 0.00321287751564984
+chr1 29560000 29570000 chr1 30580000 30590000 0.0032128775156498
 chr1 30260000 30270000 chr1 30850000 30860000 0.001
 chr1 31270000 31280000 chr1 31380000 31390000 0.001
 chr1 31650000 31660000 chr1 32010000 32020000 0.001
@@ -96,7 +96,7 @@
 chr1 35910000 35920000 chr1 36190000 36200000 0.001
 chr1 36030000 36040000 chr1 36180000 36190000 0.001
 chr1 36610000 36620000 chr1 36750000 36760000 0.001
-chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961147
+chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961
 chr1 37160000 37170000 chr1 37780000 37790000 0.001
 chr1 38020000 38030000 chr1 38140000 38150000 0.001
 chr1 38490000 38500000 chr1 39050000 39060000 0.001
b
diff -r e30485c5e93b -r f0216498a666 test-data/hicValidateLocations/overlap_smc3_statistics
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,5 +1,5 @@
-# HiCExplorer hicValidateLocations 3.6
-# Overlap of loop file /tmp/tmpd80q3k6g/files/a/4/0/dataset_a40f2565-c94b-4e73-9b47-ec233d99bda8.dat with protein file /tmp/tmpd80q3k6g/files/7/1/1/dataset_7116b645-b87b-49a2-a957-3ebe53aba250.dat
+# HiCExplorer hicValidateLocations 3.7.2
+# Overlap of loop file /tmp/tmpjjk1hb59/files/a/8/9/dataset_a8916559-7d4d-42e7-b157-fdc26b57c5e2.dat with protein file /tmp/tmpjjk1hb59/files/e/5/a/dataset_e5ab267d-b489-4abc-88ce-c408eadfd25b.dat
 #
 Protein peaks: 3097
 Matched Loops: 530
b
diff -r e30485c5e93b -r f0216498a666 test-data/raw_qc_report
--- a/test-data/raw_qc_report Tue Jan 10 19:13:28 2023 +0000
+++ b/test-data/raw_qc_report Wed Oct 18 10:18:29 2023 +0000
b
@@ -1,5 +1,5 @@
 
-File matrix.h5
+File matrix.cool
 Sequenced reads 983
 Min rest. site distance 300
 Max library insert size 1000
@@ -12,7 +12,7 @@
 Low mapping quality 164 (16.68)
 
 # count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end GATC 1 (0.33)
+dangling end GATC (restriction sequence GATC) 1 (0.33)
 self ligation (removed) 0 (0.00)
 One mate not close to rest site 0 (0.00)
 same fragment 84 (28.00)