Mercurial > repos > bgruening > hicexplorer_hiccorrelate

changeset 21:2786a931cad2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:38:07 +0000
parents 2b4d6a8dab36
children cd40ca76865a
files hicCorrelate.xml macros.xml test-data/cHi-C/chicExportData/aggregate.tar.gz 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/plots.tar.gz test-data/cHi-C/target_list.bed test-data/hicAggregateContacts_results1.png test-data/hicCorrectMatrix/diagnostic_plot.png test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicDifferentialTAD/accepted.txt test-data/hicDifferentialTAD/rejected.txt test-data/hicHyperoptDetectLoops/loops.bedgraph test-data/hicInfo/hicInfo_output.txt test-data/hicInterIntraTAD/matrix.cool test-data/hicInterIntraTAD/output.txt test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf 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/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/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 test-data/hicValidateLocations/overlap_smc3_statistics test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/small_test_matrix_result_sorted.bam
diffstat 38 files changed, 667 insertions(+), 668 deletions(-) [+]
line wrap: on
line diff
--- a/hicCorrelate.xml	Wed Oct 18 10:30:15 2023 +0000
+++ b/hicCorrelate.xml	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCorrelate</token>
--- a/macros.xml	Wed Oct 18 10:30:15 2023 +0000
+++ b/macros.xml	Mon Jul 01 19:38:07 2024 +0000
@@ -1,7 +1,8 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@TOOL_VERSION@">3.7.2</token>
+    <token name="@TOOL_VERSION@">3.7.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -248,7 +249,7 @@
         #set $matrices = []
         #set $mlabels = []
         #for $counter, $i in enumerate($input_files):
-            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 
+            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
             #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter,  $i.matrix.ext))
 
             #if str($i.mlabel.value) != "":
Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed
Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.7.2
+# Created with chicQualityControl version 3.7.5
 # 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
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.7.2
+# Created with chicQualityControl version 3.7.5
 # QC report for matrices: 0_matrix.cool 1_matrix.cool 
 #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
 
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
Binary file test-data/cHi-C/plots.tar.gz has changed
--- a/test-data/cHi-C/target_list.bed	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/cHi-C/target_list.bed	Mon Jul 01 19:38:07 2024 +0000
@@ -1,8 +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
+chr1	4480000	4549000
+chr1	4555000	4688000
+chr1	14274000	14279000
+chr1	14290000	14439000
+chr1	14444000	14467000
+chr1	14476000	14501000
+chr1	19077000	19118000
+chr1	19120000	19274000
Binary file test-data/hicAggregateContacts_results1.png has changed
Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed
Binary file test-data/hicCorrelate_heatmap_result1.png has changed
Binary file test-data/hicCorrelate_scatter_result1.png has changed
--- a/test-data/hicDifferentialTAD/accepted.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.7.2
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.5
 # 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	W left-inter-TAD	W right-inter-TAD	W intra-TAD
--- a/test-data/hicDifferentialTAD/rejected.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.7.2
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.5
 # 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.
 # Rejected 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	W left-inter-TAD	W right-inter-TAD	W intra-TAD
--- a/test-data/hicHyperoptDetectLoops/loops.bedgraph	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph	Mon Jul 01 19:38:07 2024 +0000
@@ -1,3 +1,3 @@
-# Created by HiCExplorer hicHyperoptDetectLoops 3.6
+# Created by HiCExplorer hicHyperoptDetectLoops 3.7.3
 
-{'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
+{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 2300000, 'maximumNumberOfLoops': 5, 'oet': 1.230889168935347, 'p': 0.048940366161874596, 'peakWidth': 6, 'pit': 22.88867979095296, 'pp': 0.13365961880597724, 'proteinFile': '/tmp/tmpjkr0wi60/files/6/a/7/dataset_6a78c4eb-7f74-459b-9ed8-08972cc0c5f4.dat', 'resolution': 2, 'threads': 1, 'windowSize': 6}
\ No newline at end of file
--- a/test-data/hicInfo/hicInfo_output.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5
 File:	matrix_name.h5
 Size:	33,754
 Bin_length:	5000
Binary file test-data/hicInterIntraTAD/matrix.cool has changed
--- a/test-data/hicInterIntraTAD/output.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicInterIntraTAD/output.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,22 +1,22 @@
-# Created with HiCExplorer's hicInterIntraTAD version 3.7.2
+# Created with HiCExplorer's hicInterIntraTAD version 3.7.5
 # 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
+chr2	17100000	18100000	ID_0.01_10	-0.230354	.	0	148.64979	0	1.0	0	90	0	90	289.00809	100	100	1.0	0.0	0.5143447368549441	0.5143447368549441
+chr2	18100000	19100000	ID_0.01_11	-0.5135365	.	162.11248	211.04027000000002	1.0	1.0	100	140	100	140	277.9356	100	100	1.0	0.5832735353081793	0.7593135604075189	1.3425870957156982
+chr2	19100000	20600000	ID_0.01_12	-0.4202525	.	223.14355000000003	150.01946	1.0	1.0	150	90	150	90	556.14405	225	225	1.0	0.4012333675061345	0.2697492852795962	0.6709826527857307
+chr2	20600000	21300000	ID_0.01_13	-0.9980865	.	171.34865000000002	274.46791	1.0	1.0	105	84	105	84	149.85761000000002	49	49	1.0	1.1434097340802378	1.8315246719869613	2.974934406067199
+chr2	21300000	22600000	ID_0.01_14	-0.859866	.	283.89281	768.8750100000001	1.0	1.0	91	208	91	208	24180.409890000003	169	169	1.0	0.01174061197851762	0.031797434927601224	0.043538046906118844
+chr2	22600000	24300000	ID_0.01_15	-0.281294	.	789.8040400000002	321.70053	1.0	1.0	221	238	221	238	659.9594400000001	289	289	1.0	1.1967463333807304	0.48745500178010936	1.6842013351608398
+chr2	24300000	25800000	ID_0.01_16	-1.0366175	.	340.44703	836.7906700000001	1.0	1.0	255	720	255	720	598.88844	225	225	1.0	0.5684648546564032	1.397239642828972	1.9657044974853752
+chr2	25800000	30700000	ID_0.01_17	-0.1471245	.	852.3657199999999	1593.09544	1.0	1.0	735	1421	735	1421	4153.28651	2401	2401	1.0	0.205226804832205	0.38357465495439663	0.5888014597866016
+chr2	30700000	33700000	ID_0.01_18	-1.0134455	.	1644.36207	315.02405	1.0	1.0	1470	240	1470	240	1873.0712400000002	900	900	1.0	0.877896171210231	0.16818583472564555	1.0460820059358766
+chr2	33700000	34600000	ID_0.01_19	-1.33809	.	351.38599999999997	204.32889000000003	1.0	1.0	270	153	270	153	245.00895	81	81	1.0	1.4341761800946453	0.8339650041355633	2.268141184230209
+chr2	34600000	36400000	ID_0.01_20	-0.6325015	.	213.88889999999998	379.5344099999999	1.0	1.0	162	288	162	288	770.63772	324	324	1.0	0.27754792485371726	0.4924939438469219	0.7700418687006392
+chr2	36400000	38100000	ID_0.01_21	-0.925006	.	399.4784	189.43412	1.0	1.0	306	136	306	136	635.96573	289	289	1.0	0.6281445385429809	0.2978684401752277	0.9260129787182088
+chr2	38100000	39000000	ID_0.01_22	-0.911804	.	209.82147	74.59004	1.0	1.0	153	45	153	45	229.67774999999997	81	81	1.0	0.9135472199636231	0.3247595380919571	1.2383067580555802
+chr2	39000000	39600000	ID_0.01_23	-0.474157	.	87.22966	120.04826999999999	1.0	1.0	54	72	54	72	114.23772	36	36	1.0	0.7635801905010009	1.05086367269935	1.8144438632003508
+chr2	39600000	40900000	ID_0.01_24	-0.483398	.	127.68592	348.8071999999999	1.0	1.0	78	247	78	247	447.58727999999996	169	169	1.0	0.28527602482358305	0.7793054351321154	1.0645814599556984
+chr2	40900000	42900000	ID_0.01_25	-0.7016145	.	363.61542999999995	330.73137999999994	1.0	1.0	260	240	260	240	912.1014799999999	400	400	1.0	0.3986567700778207	0.362603709403037	0.7612604794808577
+chr2	42900000	44200000	ID_0.01_26	-0.6584895	.	353.76149	305.35633	1.0	1.0	260	208	260	208	434.01493999999997	169	169	1.0	0.8150905819048533	0.7035617944396109	1.5186523763444641
+chr2	44200000	45900000	ID_0.01_27	-1.4067435	.	321.38521000000003	309.73695	1.0	1.0	221	221	221	221	667.4121100000001	289	289	1.0	0.4815393745252839	0.46408649971904153	0.9456258742443254
+chr2	45900000	47300000	ID_0.01_28	-0.656308	.	330.14417000000003	330.30287	1.0	1.0	238	238	238	238	509.86028	196	196	1.0	0.6475189045908814	0.647830166334981	1.2953490709258624
+chr2	47300000	49100000	ID_0.01_29	-0.0033885	.	330.30287	0	1.0	0	238	0	238	0	737.44951	324	324	1.0	0.4478989619235085	0.0	0.4478989619235085
Binary file test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf has changed
Binary file test-data/hicPlotAverageRegions/defaults.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log1p.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png has changed
Binary file test-data/hicPlotMatrix/plot1.png has changed
Binary file test-data/hicPlotMatrix/plot2.pdf has changed
--- a/test-data/hicPlotMatrix/plot3_pca.svg	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg	Mon Jul 01 19:38:07 2024 +0000
@@ -1,24 +1,23 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
   "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Created with matplotlib (https://matplotlib.org/) -->
-<svg height="540pt" version="1.1" viewBox="0 0 612 540" width="612pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg xmlns:xlink="http://www.w3.org/1999/xlink" width="612pt" height="540pt" viewBox="0 0 612 540" xmlns="http://www.w3.org/2000/svg" version="1.1">
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--- a/test-data/hicPlotSVL/p_values.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicPlotSVL/p_values.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.7.2
+# Created with HiCExplorer's hicPlotSVL 3.7.5
 # 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
Binary file test-data/hicPlotSVL/plot.png has changed
--- a/test-data/hicPlotSVL/ratios.txt	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicPlotSVL/ratios.txt	Mon Jul 01 19:38:07 2024 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.7.2
+# Created with HiCExplorer's hicPlotSVL 3.7.5
 # Short range vs long range contacts per chromosome: raw data
 # Short range contacts: <= 2000000
 #	0_small_test_matrix.h5			1_small_test_matrix.h5
--- a/test-data/hicQuickQC/QC.log	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicQuickQC/QC.log	Mon Jul 01 19:38:07 2024 +0000
@@ -1,5 +1,5 @@
 
-File	/var/folders/nm/9sgmbhhj6gn_h8b308xvhm0w0000gt/T/tmp8sucpx99.h5		
+File	/tmp/tmpjkr0wi60/tmp/tmp8o_td4fd.h5		
 Sequenced reads	983		
 Min rest. site distance	300		
 Max library insert size	1000		
Binary file test-data/hicTADClassifier/unittest_classifier.BIN has changed
--- a/test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed	Wed Oct 18 10:30:15 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-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
Binary file test-data/hicTrainTADClassifier/small_test_matrix.cool has changed
--- a/test-data/hicValidateLocations/overlap_smc3_statistics	Wed Oct 18 10:30:15 2023 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics	Mon Jul 01 19:38:07 2024 +0000
@@ -1,5 +1,5 @@
-# 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
+# HiCExplorer hicValidateLocations 3.7.5
+# Overlap of loop file /tmp/tmpjkr0wi60/files/a/f/1/dataset_af1f91e3-b1bd-4c1c-8842-935caae86bf2.dat with protein file /tmp/tmpjkr0wi60/files/e/6/e/dataset_e6e4503d-c6a1-4370-bc34-70b2fae3fc95.dat
 #
 Protein peaks: 3097
 Matched Loops: 530
Binary file test-data/li_viewpoint_32-33Mb.png has changed
Binary file test-data/li_viewpoint_32Mb.png has changed
Binary file test-data/small_test_matrix_result_sorted.bam has changed