| Previous changeset 15:41dbf4d162a2 (2023-01-10) Next changeset 17:c3e5e2cf12b7 (2024-07-01) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 |
|
modified:
hicPCA.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 41dbf4d162a2 -r 77919cc3618e hicPCA.xml --- a/hicPCA.xml Tue Jan 10 18:56:55 2023 +0000 +++ b/hicPCA.xml Wed Oct 18 10:39:52 2023 +0000 |
| [ |
| b'@@ -7,11 +7,17 @@\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n ln -s \'$matrix_h5_cooler\' \'matrix.$matrix_h5_cooler.ext\' &&\n+ mkdir output &&\n @BINARY@ --matrix \'matrix.$matrix_h5_cooler.ext\'\n \n @CHROMOSOME_LIST@\n \n- --outputFileName pca1.$outputFormat pca2.$outputFormat\n+ #set $eigenvectors = \' \'.join([ \'\\\'%s\\\'\' % $eigenvector for $eigenvector in str($whichEigenvectors).split(\' \') ])\n+ --whichEigenvectors $eigenvectors\n+ \n+ #set $eigenvectors_output = \' \'.join([ \'\\\'output/pca%s.%s\\\'\' % ($eigenvector, $outputFormat) for $eigenvector in str($whichEigenvectors).split(\' \') ])\n+\n+ --outputFileName $eigenvectors_output\n --format $outputFormat\n \n #if $ligation_factor:\n@@ -37,8 +43,6 @@\n --obsexpMatrix obsexp.$matrix_h5_cooler.ext\n #end if\n \n- && mv pca1.$outputFormat pca1\n- && mv pca2.$outputFormat pca2\n #if $pearsonMatrix:\n && mv pearson.$matrix_h5_cooler.ext pearson\n #end if\n@@ -50,48 +54,45 @@\n ]]>\n </command>\n <inputs>\n- <expand macro=\'matrix_h5_cooler_macro\' />\n- <param name=\'outputFormat\' type=\'select\' label="Output file format">\n- <option value=\'bigwig\' selected="true">bigwig</option>\n+ <expand macro="matrix_h5_cooler_macro" />\n+ <param name="outputFormat" type="select" label="Output file format">\n+ <option value="bigwig" selected="true">bigwig</option>\n <option value="bedgraph">bedgraph</option>\n </param>\n \n <expand macro="chromosome_list" />\n+ <param argument="--whichEigenvectors" optional="true" type="text" value="1 2" label="Eigenvectors to compute" help= "Define the eigenvectors that should be computed as a list. For example 1 2 5 to compute the first, second and fifth eigenvetor." />\n \n- <param name=\'ligation_factor\' type=\'boolean\' truevalue=\'--ligation_factor\' label=\'Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation\' />\n- <param name=\'ignoreMaskedBins\' type=\'boolean\' truevalue=\'--ignoreMaskedBins\' label=\'This option removes the masked bins before the PCA is computed\' />\n+ <param name="ligation_factor" type="boolean" truevalue="--ligation_factor" label="Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation" />\n+ <param name="ignoreMaskedBins" type="boolean" truevalue="--ignoreMaskedBins" label="This option removes the masked bins before the PCA is computed" />\n \n <conditional name="extra_track_conditional">\n- <param name=\'extra_track_selection\' label=\'Extra track type\' type=\'select\'>\n- <option value=\'\' selected=\'true\'>No track</option>\n- <option value=\'gene_density\'>Gene density</option>\n- <option value=\'histon_mark\'>Histon mark coverage</option>\n+ <param name="extra_track_selection" label="Extra track type" type="select">\n+ <option value="" selected="true">No track</option>\n+ <option value="gene_density">Gene density</option>\n+ <option value="histon_mark">Histon mark coverage</option>\n </param>\n- <when value=\'gene_density\' >\n- <param name=\'extraTrack\' type=\'data\' format=\'bed\' label=\'Correlate PCA with e.g. gene density or histon marks to flip sign\' />\n+ <when value="gene_density" >\n+ <param name="extraTrack" type="data" format="bed" label="Correlate PCA with e.g. gene density or histon marks to flip sign" />\n </when>\n- <when value=\'histon_mark\'>\n- <param name=\'extraTrack\' type=\'data\' format=\'bed,bigwig\' label=\'Correlate PCA with e.g. gene density or histon marks to flip sign\' />\n- <param name=\'histonMarkType\' type=\'select\' label="Histon mark type">\n- <option '..b' file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta=\'40000\' />\n+ <output name="pca">\n+ <discovered_dataset designation="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" />\n+ <discovered_dataset designation="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" />\n+ </output>\n </test>\n- <test>\n+ <test expect_num_outputs="3">\n <param name="matrix_h5_cooler" value="small_test_matrix.h5" />\n \n <param name="outputFormat" value="bigwig" />\n <conditional name="extra_track_conditional">\n <param name="extra_track_selection" value="" />\n </conditional>\n- <param name=\'pearsonMatrix\' value=\'True\' />\n- <param name=\'obsexpMatrix\' value=\'True\' />\n+ <param name="pearsonMatrix" value="True" />\n+ <param name="obsexpMatrix" value="True" />\n \n <repeat name="chromosome_list">\n <param name="chromosomes" value="chrX" />\n@@ -178,17 +187,19 @@\n <param name="chromosomes" value="chrXHet" />\n </repeat>\n \n- <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta=\'40000\' />\n- <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta=\'40000\' />\n+ <output name="pca">\n+ <discovered_dataset designation="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" />\n+ <discovered_dataset designation="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" />\n+ </output>\n \n <output name="pearson_outfile" ftype="h5">\n <assert_contents>\n- <has_h5_keys keys=\'intervals,matrix\' />\n+ <has_h5_keys keys="intervals,matrix" />\n </assert_contents>\n </output>\n <output name="obsexp_outfile" ftype="h5">\n <assert_contents>\n- <has_h5_keys keys=\'intervals,matrix\' />\n+ <has_h5_keys keys="intervals,matrix" />\n </assert_contents>\n </output>\n </test>\n@@ -201,7 +212,7 @@\n `Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments.\n \n **hicPCA** computes two eigenvector files based on the input matrix for an A / B compartment analysis following the computation steps detailed by `Lieberman-Aiden et al. (2009)`_: the transformation of the contact matrix\n-into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the Pearson correlation matrix gives the eigenvectors\n+into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the obs/exp matrix gives the eigenvectors\n and Lieberman-Aiden shows that the values of the eigenvectors correspond to the distribution of genes and with features of open and closed chromatin. In some cases the first principal component corresponds to the two\n chromosomes arms and the second eigenvector to the plaid pattern. Therefore always the first two principal components needs to be returned and investigated.\n \n@@ -228,7 +239,7 @@\n | For more information about HiCExplorer please consider our documentation on readthedocs.io_\n \n .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html\n-.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369\n+.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/\n ]]> </help>\n <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e macros.xml --- a/macros.xml Tue Jan 10 18:56:55 2023 +0000 +++ b/macros.xml Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/aggregate.tar.gz |
| b |
| Binary file test-data/cHi-C/aggregate.tar.gz has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 |
| b |
| Binary file test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicDifferentialTest/differential.hdf5 |
| b |
| Binary file test-data/cHi-C/chicDifferentialTest/differential.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicExportData/aggregate.tar.gz |
| b |
| Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig |
| b |
| Binary file test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig |
| b |
| Binary file test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig |
| b |
| Binary file test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig |
| b |
| Binary file test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicQualityControl/histogram.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:39:52 2023 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:39:52 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. |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicQualityControl/sparsity.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/chicViewpoint/two_matrices.hdf5 |
| b |
| Binary file test-data/cHi-C/chicViewpoint/two_matrices.hdf5 has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 2023 +0000 |
| b |
| @@ -0,0 +1,93 @@ +chr1 249250621 +chr2 243199373 +chr3 198022430 +chr4 191154276 +chr5 180915260 +chr6 171115067 +chr7 159138663 +chrX 155270560 +chr8 146364022 +chr9 141213431 +chr10 135534747 +chr11 135006516 +chr12 133851895 +chr13 115169878 +chr14 107349540 +chr15 102531392 +chr16 90354753 +chr17 81195210 +chr18 78077248 +chr20 63025520 +chrY 59373566 +chr19 59128983 +chr22 51304566 +chr21 48129895 +chr6_ssto_hap7 4928567 +chr6_mcf_hap5 4833398 +chr6_cox_hap2 4795371 +chr6_mann_hap4 4683263 +chr6_apd_hap1 4622290 +chr6_qbl_hap6 4611984 +chr6_dbb_hap3 4610396 +chr17_ctg5_hap1 1680828 +chr4_ctg9_hap1 590426 +chr1_gl000192_random 547496 +chrUn_gl000225 211173 +chr4_gl000194_random 191469 +chr4_gl000193_random 189789 +chr9_gl000200_random 187035 +chrUn_gl000222 186861 +chrUn_gl000212 186858 +chr7_gl000195_random 182896 +chrUn_gl000223 180455 +chrUn_gl000224 179693 +chrUn_gl000219 179198 +chr17_gl000205_random 174588 +chrUn_gl000215 172545 +chrUn_gl000216 172294 +chrUn_gl000217 172149 +chr9_gl000199_random 169874 +chrUn_gl000211 166566 +chrUn_gl000213 164239 +chrUn_gl000220 161802 +chrUn_gl000218 161147 +chr19_gl000209_random 159169 +chrUn_gl000221 155397 +chrUn_gl000214 137718 +chrUn_gl000228 129120 +chrUn_gl000227 128374 +chr1_gl000191_random 106433 +chr19_gl000208_random 92689 +chr9_gl000198_random 90085 +chr17_gl000204_random 81310 +chrUn_gl000233 45941 +chrUn_gl000237 45867 +chrUn_gl000230 43691 +chrUn_gl000242 43523 +chrUn_gl000243 43341 +chrUn_gl000241 42152 +chrUn_gl000236 41934 +chrUn_gl000240 41933 +chr17_gl000206_random 41001 +chrUn_gl000232 40652 +chrUn_gl000234 40531 +chr11_gl000202_random 40103 +chrUn_gl000238 39939 +chrUn_gl000244 39929 +chrUn_gl000248 39786 +chr8_gl000196_random 38914 +chrUn_gl000249 38502 +chrUn_gl000246 38154 +chr17_gl000203_random 37498 +chr8_gl000197_random 37175 +chrUn_gl000245 36651 +chrUn_gl000247 36422 +chr9_gl000201_random 36148 +chrUn_gl000235 34474 +chrUn_gl000239 33824 +chr21_gl000210_random 27682 +chrUn_gl000231 27386 +chrUn_gl000229 19913 +chrM 16571 +chrUn_gl000226 15008 +chr18_gl000207_random 4262 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/plots.tar.gz |
| b |
| Binary file test-data/cHi-C/plots.tar.gz has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/cHi-C/referencePoints_chicViewpoint.bed --- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:39:52 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 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 2023 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/distVsCounts.txt --- a/test-data/distVsCounts.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 10:39:52 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\t0.00014352350197344816\t27870\t1.0\n+551\tsmall_test_matrix_h5\tall\t2760000\t7.178235589692053e-05\t27862\t1.0\n+552\tsmall_test_matrix_h5\tall\t2765000\t0.00014360594528613484\t27854\t1.0\n+553\tsmall_test_matrix_h5\tall\t2770000\t0.00025138260432378077\t27846\t1.0\n+554\tsmall_test_matrix_h5\tall\t2775000\t0.00014368848336805806\t27838\t1.0\n+555\tsmall_test_matrix_h5\tall\t2780000\t0.00014372978799856272\t27830\t1.0\n+556\tsmall_test_matrix_h5\tall\t2785000\t0.0001437711163827187\t27822\t1.0\n+557\tsmall_test_matrix_h5\tall\t2790000\t0.00025167181994678936\t27814\t1.0\n+558\tsmall_test_matrix_h5\tall\t2795000\t0.0001438538444939941\t27806\t1.0\n+559\tsmall_test_matrix_h5\tall\t2800000\t0.00010792143319663285\t27798\t1.0\n+560\tsmall_test_matrix_h5\tall\t2805000\t0.00021590500179920834\t27790\t1.0\n+561\tsmall_test_matrix_h5\tall\t2810000\t0.00017997264415808796\t27782\t1.0\n+562\tsmall_test_matrix_h5\tall\t2815000\t3.600489666594657e-05\t27774\t1.0\n+563\tsmall_test_matrix_h5\tall\t2820000\t0.0002160916228480876\t27766\t1.0\n+564\tsmall_test_matrix_h5\tall\t2825000\t0.000144102601051949\t27758\t1.0\n+565\tsmall_test_matrix_h5\tall\t2830000\t0.00014414414414414415\t27750\t1.0\n+566\tsmall_test_matrix_h5\tall\t2835000\t0.0002523249945930358\t27742\t1.0\n+567\tsmall_test_matrix_h5\tall\t2840000\t0.00018028412778538978\t27734\t1.0\n+568\tsmall_test_matrix_h5\tall\t2845000\t0.00010820168794633196\t27726\t1.0\n+569\tsmall_test_matrix_h5\tall\t2850000\t0.00018038819539649325\t27718\t1.0\n+570\tsmall_test_matrix_h5\tall\t2855000\t7.217610970768675e-05\t27710\t1.0\n+571\tsmall_test_matrix_h5\tall\t2860000\t0.0003248862897985705\t27702\t1.0\n+572\tsmall_test_matrix_h5\tall\t2865000\t0.00018054452227919405\t27694\t1.0\n+573\tsmall_test_matrix_h5\tall\t2870000\t0.0002889547063497797\t27686\t1.0\n+574\tsmall_test_matrix_h5\tall\t2875000\t0.00036129778163162076\t27678\t1.0\n+575\tsmall_test_matrix_h5\tall\t2880000\t0.00014456089627755693\t27670\t1.0\n+576\tsmall_test_matrix_h5\tall\t2890000\t0.00021696680407897592\t27654\t1.0\n+577\tsmall_test_matrix_h5\tall\t2895000\t0.0001808579903060117\t27646\t1.0\n+578\tsmall_test_matrix_h5\tall\t2900000\t7.236413633403285e-05\t27638\t1.0\n+579\tsmall_test_matrix_h5\tall\t2905000\t0.0002533478103510677\t27630\t1.0\n+580\tsmall_test_matrix_h5\tall\t2910000\t0.00010860907971906451\t27622\t1.0\n+581\tsmall_test_matrix_h5\tall\t2915000\t0.00010864054465126386\t27614\t1.0\n+582\tsmall_test_matrix_h5\tall\t2920000\t0.00021734405564007825\t27606\t1.0\n+583\tsmall_test_matrix_h5\tall\t2925000\t0.00010870352924124937\t27598\t1.0\n+584\tsmall_test_matrix_h5\tall\t2930000\t0.0001812250815512867\t27590\t1.0\n+585\tsmall_test_matrix_h5\tall\t2935000\t0.00010876658690450294\t27582\t1.0\n+586\tsmall_test_matrix_h5\tall\t2940000\t0.00014506419090447523\t27574\t1.0\n+587\tsmall_test_matrix_h5\tall\t2945000\t0.000290212580715374\t27566\t1.0\n+588\tsmall_test_matrix_h5\tall\t2950000\t0.0001451484142535743\t27558\t1.0\n+589\tsmall_test_matrix_h5\tall\t2955000\t0.00025408348457350274\t27550\t1.0\n+590\tsmall_test_matrix_h5\tall\t2960000\t0.00010892455159392927\t27542\t1.0\n+591\tsmall_test_matrix_h5\tall\t2965000\t7.263746640517178e-05\t27534\t1.0\n+592\tsmall_test_matrix_h5\tall\t2970000\t3.6329288672527794e-05\t27526\t1.0\n+593\tsmall_test_matrix_h5\tall\t2975000\t7.26797005596337e-05\t27518\t1.0\n+594\tsmall_test_matrix_h5\tall\t2980000\t0.00010905125408942203\t27510\t1.0\n+595\tsmall_test_matrix_h5\tall\t2985000\t0.00021816595156715876\t27502\t1.0\n+596\tsmall_test_matrix_h5\tall\t2990000\t0.00010911471593802284\t27494\t1.0\n+597\tsmall_test_matrix_h5\tall\t2995000\t0.00014552863275849522\t27486\t1.0\n+598\tsmall_test_matrix_h5\tall\t3000000\t0.00029114200451270107\t27478\t1.0\n' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicCompartmentsPolarization/output_matrix.npz |
| b |
| Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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\t229393754\t229394381\tchr1\t229617774\t229618119\t3.49385678131\n+chr12\t10162531\t10162752\tchr12\t10292561\t10293019\t2.43174030806666\n+chr7\t18391997\t18392287\tchr7\t18650001\t18650242\t2.08062031061257\n+chr1\t101985827\t101986200\tchr1\t103436139\t103436315\t2.59457710004122\n+chr1\t181448199\t181448775\tchr1\t181645361\t181645851\t4.01057379390341\n+chr1\t181448199\t181448775\tchr1\t181906059\t181906414\t3.65517514743069\n+chr17\t30580033\t30580393\tchr17\t30646486\t30646917\t3.56831556005795\n+chr17\t30580033\t30580393\tchr17\t30646066\t30646209\t3.70134276477366\n+chr3\t120137809\t120138037\tchr3\t120277636\t120278018\t2.27750826455946\n+chr12\t114418331\t114418691\tchr12\t114946270\t114946668\t2.14159004423436\n+chr5\t89735499\t89735803\tchr5\t89825737\t89826329\t2.44447108269179\n+chr11\t67033632\t67033889\tchr11\t67056444\t67056617\t2.24785515824013\n+chr5\t32489800\t32490359\tchr5\t32613087\t32613692\t3.27921037485541\n+chr5\t34958326\t34958497\tchr5\t35003486\t35003856\t3.60298680582628\n+chr1\t182993093\t182993280\tchr1\t183040545\t183040701\t2.95339357383931\n+chr15\t84403369\t84403769\tchr15\t84703999\t84704519\t2.95913116827052\n+chr2\t85618403\t85618856\tchr2\t85647720\t85648198\t2.09056716583535\n+chr2\t206640855\t206641052\tchr2\t206678315\t206678579\t2.37559022379089\n+chrX\t18409089\t18409518\tchrX\t19352148\t19352594\t4.22802523282061\n+chrX\t18409089\t18409518\tchrX\t19353159\t19353437\t4.07323113400888\n+chr11\t72542616\t72542834\tchr11\t72888997\t72889570\t2.70387692541757\n+chr4\t91340277\t91340624\tchr4\t93308662\t93308909\t2.28363584748403\n+chr17\t55935737\t55936099\tchr17\t56072822\t56073114\t2.95734118880821\n+chr17\t55935737\t55936099\tchr17\t56076925\t56077120\t2.9214419425273\n+chr12\t64943314\t64943798\tchr12\t65090199\t65090423\t3.23555574413297\n+chr22\t42092980\t42093866\tchr22\t42159132\t42159429\t2.10400066069958\n+chr17\t55935737\t55936099\tchr17\t56190365\t56190770\t2.88126072360434\n+chr12\t127593244\t127593484\tchr12\t128162137\t128162347\t3.7481808942314\n+chr16\t33963114\t33963487\tchr2\t133012624\t133012990\t2.13583221262673\n+chr1\t121484228\t121485221\tchr10\t42529551\t42529721\t-1.84581207064953\n+chr1\t121485244\t121485510\tchr12\t34846267\t34846471\t-0.053284227252058\n+chr6\t58778098\t58778474\tchr10\t103539709\t103539949\t-0.949127868852785\n+chr6\t58778098\t58778474\tchr10\t103540905\t103541164\t-0.987874581868838\n+chr19\t27739073\t27739440\tchr10\t42529793\t42529937\t-0.946696465553499\n+chr2\t133012624\t133012990\tchr21\t9825501\t9826596\t1.5886518541928\n+chr1\t121484228\t121485221\tchr12\t34846267\t34846471\t-0.181494465044725\n+chr1\t91852718\t91853144\tchr12\t34372527\t34372768\t2.76052969833544\n+chr16\t33964837\t33964977\tchr21\t9826742\t9827563\t1.3483824850377\n+chr1\t121485244\t121485510\tchr10\t42529793\t42529937\t-1.33390778053503\n+chr20\t26189870\t26190303\tchr21\t9825501\t9826596\t1.68049013972561\n+chr20\t26188844\t26189203\tchr21\t9826742\t9827563\t1.46477612725631\n+chr20\t26189870\t26190303\tchr21\t9826742\t9827563\t1.58116976947492\n+chr16\t33964837\t33964977\tchr21\t9825501\t9826596\t1.44770285528839\n+chr20\t26188844\t26189203\tchr21\t9825501\t9826596\t1.564096497507\n+chr1\t91852718\t91853144\tchr12\t34371447\t34371686\t2.81678518546069\n+chr2\t133012624\t133012990\tchr21\t9826742\t9827563\t1.48933148394211\n+chr16\t33963114\t33963487\tchr21\t9826742\t9827563\t1.51813092113023\n+chr16\t33963114\t33963487\tchr21\t9825501\t9826596\t1.61745129138092\n+chr19\t27739073\t27739440\tchr10\t42529551\t42529721\t-0.856324383087355\n+chr1\t121485244\t121485510\tchr10\t42529551\t42529721\t-1.24353569806889\n+chr2\t91815114\t91815304\tchr4\t9764754\t9765075\t1.5316452618788\n+chr19\t27739073\t27739440\tchr1\t121485244\t121485510\t0.665658949132087\n+chr19\t27739073\t27739440\tchr1\t121484228\t121485221\t0.420403755247875\n' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 2023 +0000 |
| b |
| @@ -0,0 +1,93 @@ +chr1 249250621 +chr2 243199373 +chr3 198022430 +chr4 191154276 +chr5 180915260 +chr6 171115067 +chr7 159138663 +chrX 155270560 +chr8 146364022 +chr9 141213431 +chr10 135534747 +chr11 135006516 +chr12 133851895 +chr13 115169878 +chr14 107349540 +chr15 102531392 +chr16 90354753 +chr17 81195210 +chr18 78077248 +chr20 63025520 +chrY 59373566 +chr19 59128983 +chr22 51304566 +chr21 48129895 +chr6_ssto_hap7 4928567 +chr6_mcf_hap5 4833398 +chr6_cox_hap2 4795371 +chr6_mann_hap4 4683263 +chr6_apd_hap1 4622290 +chr6_qbl_hap6 4611984 +chr6_dbb_hap3 4610396 +chr17_ctg5_hap1 1680828 +chr4_ctg9_hap1 590426 +chr1_gl000192_random 547496 +chrUn_gl000225 211173 +chr4_gl000194_random 191469 +chr4_gl000193_random 189789 +chr9_gl000200_random 187035 +chrUn_gl000222 186861 +chrUn_gl000212 186858 +chr7_gl000195_random 182896 +chrUn_gl000223 180455 +chrUn_gl000224 179693 +chrUn_gl000219 179198 +chr17_gl000205_random 174588 +chrUn_gl000215 172545 +chrUn_gl000216 172294 +chrUn_gl000217 172149 +chr9_gl000199_random 169874 +chrUn_gl000211 166566 +chrUn_gl000213 164239 +chrUn_gl000220 161802 +chrUn_gl000218 161147 +chr19_gl000209_random 159169 +chrUn_gl000221 155397 +chrUn_gl000214 137718 +chrUn_gl000228 129120 +chrUn_gl000227 128374 +chr1_gl000191_random 106433 +chr19_gl000208_random 92689 +chr9_gl000198_random 90085 +chr17_gl000204_random 81310 +chrUn_gl000233 45941 +chrUn_gl000237 45867 +chrUn_gl000230 43691 +chrUn_gl000242 43523 +chrUn_gl000243 43341 +chrUn_gl000241 42152 +chrUn_gl000236 41934 +chrUn_gl000240 41933 +chr17_gl000206_random 41001 +chrUn_gl000232 40652 +chrUn_gl000234 40531 +chr11_gl000202_random 40103 +chrUn_gl000238 39939 +chrUn_gl000244 39929 +chrUn_gl000248 39786 +chr8_gl000196_random 38914 +chrUn_gl000249 38502 +chrUn_gl000246 38154 +chr17_gl000203_random 37498 +chr8_gl000197_random 37175 +chrUn_gl000245 36651 +chrUn_gl000247 36422 +chr9_gl000201_random 36148 +chrUn_gl000235 34474 +chrUn_gl000239 33824 +chr21_gl000210_random 27682 +chrUn_gl000231 27386 +chrUn_gl000229 19913 +chrM 16571 +chrUn_gl000226 15008 +chr18_gl000207_random 4262 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 2023 +0000 |
| b |
| @@ -0,0 +1,271 @@ +chr4 0 5000 1 +chr4 5000 10000 2 +chr4 10000 15000 3 +chr4 15000 20000 4 +chr4 20000 25000 5 +chr4 25000 30000 6 +chr4 30000 35000 7 +chr4 35000 40000 8 +chr4 40000 45000 9 +chr4 45000 50000 10 +chr4 50000 55000 11 +chr4 55000 60000 12 +chr4 60000 65000 13 +chr4 65000 70000 14 +chr4 70000 75000 15 +chr4 75000 80000 16 +chr4 80000 85000 17 +chr4 85000 90000 18 +chr4 90000 95000 19 +chr4 95000 100000 20 +chr4 100000 105000 21 +chr4 105000 110000 22 +chr4 110000 115000 23 +chr4 115000 120000 24 +chr4 120000 125000 25 +chr4 125000 130000 26 +chr4 130000 135000 27 +chr4 135000 140000 28 +chr4 140000 145000 29 +chr4 145000 150000 30 +chr4 150000 155000 31 +chr4 155000 160000 32 +chr4 160000 165000 33 +chr4 165000 170000 34 +chr4 170000 175000 35 +chr4 175000 180000 36 +chr4 180000 185000 37 +chr4 185000 190000 38 +chr4 190000 195000 39 +chr4 195000 200000 40 +chr4 200000 205000 41 +chr4 205000 210000 42 +chr4 210000 215000 43 +chr4 215000 220000 44 +chr4 220000 225000 45 +chr4 225000 230000 46 +chr4 230000 235000 47 +chr4 235000 240000 48 +chr4 240000 245000 49 +chr4 245000 250000 50 +chr4 250000 255000 51 +chr4 255000 260000 52 +chr4 260000 265000 53 +chr4 265000 270000 54 +chr4 270000 275000 55 +chr4 275000 280000 56 +chr4 280000 285000 57 +chr4 285000 290000 58 +chr4 290000 295000 59 +chr4 295000 300000 60 +chr4 300000 305000 61 +chr4 305000 310000 62 +chr4 310000 315000 63 +chr4 315000 320000 64 +chr4 320000 325000 65 +chr4 325000 330000 66 +chr4 330000 335000 67 +chr4 335000 340000 68 +chr4 340000 345000 69 +chr4 345000 350000 70 +chr4 350000 355000 71 +chr4 355000 360000 72 +chr4 360000 365000 73 +chr4 365000 370000 74 +chr4 370000 375000 75 +chr4 375000 380000 76 +chr4 380000 385000 77 +chr4 385000 390000 78 +chr4 390000 395000 79 +chr4 395000 400000 80 +chr4 400000 405000 81 +chr4 405000 410000 82 +chr4 410000 415000 83 +chr4 415000 420000 84 +chr4 420000 425000 85 +chr4 425000 430000 86 +chr4 430000 435000 87 +chr4 435000 440000 88 +chr4 440000 445000 89 +chr4 445000 450000 90 +chr4 450000 455000 91 +chr4 455000 460000 92 +chr4 460000 465000 93 +chr4 465000 470000 94 +chr4 470000 475000 95 +chr4 475000 480000 96 +chr4 480000 485000 97 +chr4 485000 490000 98 +chr4 490000 495000 99 +chr4 495000 500000 100 +chr4 500000 505000 101 +chr4 505000 510000 102 +chr4 510000 515000 103 +chr4 515000 520000 104 +chr4 520000 525000 105 +chr4 525000 530000 106 +chr4 530000 535000 107 +chr4 535000 540000 108 +chr4 540000 545000 109 +chr4 545000 550000 110 +chr4 550000 555000 111 +chr4 555000 560000 112 +chr4 560000 565000 113 +chr4 565000 570000 114 +chr4 570000 575000 115 +chr4 575000 580000 116 +chr4 580000 585000 117 +chr4 585000 590000 118 +chr4 590000 595000 119 +chr4 595000 600000 120 +chr4 600000 605000 121 +chr4 605000 610000 122 +chr4 610000 615000 123 +chr4 615000 620000 124 +chr4 620000 625000 125 +chr4 625000 630000 126 +chr4 630000 635000 127 +chr4 635000 640000 128 +chr4 640000 645000 129 +chr4 645000 650000 130 +chr4 650000 655000 131 +chr4 655000 660000 132 +chr4 660000 665000 133 +chr4 665000 670000 134 +chr4 670000 675000 135 +chr4 675000 680000 136 +chr4 680000 685000 137 +chr4 685000 690000 138 +chr4 690000 695000 139 +chr4 695000 700000 140 +chr4 700000 705000 141 +chr4 705000 710000 142 +chr4 710000 715000 143 +chr4 715000 720000 144 +chr4 720000 725000 145 +chr4 725000 730000 146 +chr4 730000 735000 147 +chr4 735000 740000 148 +chr4 740000 745000 149 +chr4 745000 750000 150 +chr4 750000 755000 151 +chr4 755000 760000 152 +chr4 760000 765000 153 +chr4 765000 770000 154 +chr4 770000 775000 155 +chr4 775000 780000 156 +chr4 780000 785000 157 +chr4 785000 790000 158 +chr4 790000 795000 159 +chr4 795000 800000 160 +chr4 800000 805000 161 +chr4 805000 810000 162 +chr4 810000 815000 163 +chr4 815000 820000 164 +chr4 820000 825000 165 +chr4 825000 830000 166 +chr4 830000 835000 167 +chr4 835000 840000 168 +chr4 840000 845000 169 +chr4 845000 850000 170 +chr4 850000 855000 171 +chr4 855000 860000 172 +chr4 860000 865000 173 +chr4 865000 870000 174 +chr4 870000 875000 175 +chr4 875000 880000 176 +chr4 880000 885000 177 +chr4 885000 890000 178 +chr4 890000 895000 179 +chr4 895000 900000 180 +chr4 900000 905000 181 +chr4 905000 910000 182 +chr4 910000 915000 183 +chr4 915000 920000 184 +chr4 920000 925000 185 +chr4 925000 930000 186 +chr4 930000 935000 187 +chr4 935000 940000 188 +chr4 940000 945000 189 +chr4 945000 950000 190 +chr4 950000 955000 191 +chr4 955000 960000 192 +chr4 960000 965000 193 +chr4 965000 970000 194 +chr4 970000 975000 195 +chr4 975000 980000 196 +chr4 980000 985000 197 +chr4 985000 990000 198 +chr4 990000 995000 199 +chr4 995000 1000000 200 +chr4 1000000 1005000 201 +chr4 1005000 1010000 202 +chr4 1010000 1015000 203 +chr4 1015000 1020000 204 +chr4 1020000 1025000 205 +chr4 1025000 1030000 206 +chr4 1030000 1035000 207 +chr4 1035000 1040000 208 +chr4 1040000 1045000 209 +chr4 1045000 1050000 210 +chr4 1050000 1055000 211 +chr4 1055000 1060000 212 +chr4 1060000 1065000 213 +chr4 1065000 1070000 214 +chr4 1070000 1075000 215 +chr4 1075000 1080000 216 +chr4 1080000 1085000 217 +chr4 1085000 1090000 218 +chr4 1090000 1095000 219 +chr4 1095000 1100000 220 +chr4 1100000 1105000 221 +chr4 1105000 1110000 222 +chr4 1110000 1115000 223 +chr4 1115000 1120000 224 +chr4 1120000 1125000 225 +chr4 1125000 1130000 226 +chr4 1130000 1135000 227 +chr4 1135000 1140000 228 +chr4 1140000 1145000 229 +chr4 1145000 1150000 230 +chr4 1150000 1155000 231 +chr4 1155000 1160000 232 +chr4 1160000 1165000 233 +chr4 1165000 1170000 234 +chr4 1170000 1175000 235 +chr4 1175000 1180000 236 +chr4 1180000 1185000 237 +chr4 1185000 1190000 238 +chr4 1190000 1195000 239 +chr4 1195000 1200000 240 +chr4 1200000 1205000 241 +chr4 1205000 1210000 242 +chr4 1210000 1215000 243 +chr4 1215000 1220000 244 +chr4 1220000 1225000 245 +chr4 1225000 1230000 246 +chr4 1230000 1235000 247 +chr4 1235000 1240000 248 +chr4 1240000 1245000 249 +chr4 1245000 1250000 250 +chr4 1250000 1255000 251 +chr4 1255000 1260000 252 +chr4 1260000 1265000 253 +chr4 1265000 1270000 254 +chr4 1270000 1275000 255 +chr4 1275000 1280000 256 +chr4 1280000 1285000 257 +chr4 1285000 1290000 258 +chr4 1290000 1295000 259 +chr4 1295000 1300000 260 +chr4 1300000 1305000 261 +chr4 1305000 1310000 262 +chr4 1310000 1315000 263 +chr4 1315000 1320000 264 +chr4 1320000 1325000 265 +chr4 1325000 1330000 266 +chr4 1330000 1335000 267 +chr4 1335000 1340000 268 +chr4 1340000 1345000 269 +chr4 1345000 1350000 270 +chr4 1350000 1351857 271 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 2023 +0000 |
| b |
| @@ -0,0 +1,326 @@ +15 15 1 +15 38 1 +16 17 1 +17 17 2 +17 18 1 +17 38 1 +18 38 1 +18 151 1 +19 21 1 +19 52 1 +19 207 1 +20 57 1 +21 29 1 +22 23 2 +22 32 1 +22 41 1 +22 223 1 +23 26 1 +23 43 1 +25 39 1 +25 51 1 +26 36 1 +26 45 1 +26 67 1 +27 28 1 +27 31 1 +28 28 1 +28 30 1 +28 40 1 +29 31 1 +29 34 1 +30 30 1 +30 43 1 +31 31 1 +31 32 1 +31 35 2 +31 55 1 +31 78 1 +31 119 1 +31 188 1 +32 32 5 +32 36 1 +32 118 1 +33 45 1 +33 162 1 +35 38 1 +35 122 1 +36 36 1 +36 38 1 +36 41 1 +36 43 1 +36 57 1 +36 64 1 +37 53 1 +37 55 1 +37 130 1 +38 38 3 +38 129 1 +39 39 1 +40 42 1 +40 55 1 +40 192 1 +40 218 1 +41 52 1 +41 67 1 +41 79 1 +42 43 1 +42 49 1 +42 120 1 +43 45 1 +45 46 1 +45 71 1 +48 49 1 +48 51 1 +48 119 1 +50 84 1 +53 65 1 +54 54 1 +54 67 1 +55 55 1 +56 56 2 +56 57 1 +59 104 1 +61 64 1 +62 66 1 +62 89 1 +63 80 1 +65 68 1 +65 77 1 +65 118 1 +67 70 1 +68 68 1 +68 70 1 +70 142 1 +71 72 1 +71 74 1 +71 75 1 +75 80 1 +75 190 1 +77 168 1 +78 92 1 +80 83 1 +81 95 1 +82 103 1 +82 120 1 +87 126 1 +88 216 1 +89 89 1 +89 90 1 +90 113 1 +92 92 1 +93 96 1 +94 98 1 +95 97 1 +97 151 1 +104 104 1 +105 105 1 +106 198 1 +108 113 1 +109 109 1 +109 110 1 +109 119 1 +109 125 1 +109 159 1 +110 165 1 +110 189 1 +111 112 1 +111 128 1 +112 112 1 +112 194 1 +113 198 1 +114 114 1 +114 122 1 +114 123 1 +114 165 1 +114 196 1 +115 116 1 +116 121 1 +116 129 1 +116 155 1 +117 119 1 +117 128 1 +118 121 1 +118 189 1 +119 125 1 +119 132 1 +120 142 1 +120 149 1 +121 132 1 +121 236 1 +122 131 1 +122 138 1 +122 146 1 +124 125 1 +124 134 1 +125 125 1 +125 141 1 +127 174 1 +127 212 1 +128 130 1 +128 135 1 +129 129 1 +130 178 1 +130 191 1 +130 204 1 +130 213 1 +132 184 1 +132 208 1 +134 136 1 +134 190 1 +134 242 1 +135 177 1 +135 186 1 +136 180 1 +137 142 1 +137 147 1 +137 189 1 +138 143 1 +138 160 1 +141 142 1 +142 142 1 +142 143 1 +142 178 1 +143 143 1 +144 193 1 +145 145 1 +146 146 1 +146 155 1 +147 147 1 +148 149 1 +148 154 1 +149 149 1 +149 150 1 +149 153 1 +149 155 1 +149 169 1 +149 170 1 +149 176 1 +150 162 1 +151 153 1 +153 154 1 +153 186 1 +154 154 1 +154 199 1 +154 215 1 +155 155 1 +155 156 1 +155 159 1 +156 156 1 +160 161 1 +164 176 1 +165 171 1 +166 168 1 +168 168 1 +168 201 1 +169 178 1 +170 176 1 +170 195 1 +171 196 1 +174 178 2 +174 194 1 +175 232 1 +175 243 1 +176 176 1 +177 177 1 +177 209 1 +178 178 1 +179 231 1 +180 212 1 +182 198 1 +183 185 1 +183 186 1 +183 187 1 +188 188 2 +189 201 1 +190 201 1 +192 193 1 +192 242 1 +193 193 1 +193 196 1 +194 206 1 +194 220 1 +195 196 2 +195 221 1 +196 196 1 +196 215 1 +196 223 1 +197 199 1 +198 199 1 +198 201 1 +198 207 1 +198 210 1 +199 199 1 +199 200 1 +199 206 1 +199 212 1 +201 201 1 +201 222 1 +202 203 1 +202 205 1 +203 205 1 +203 209 1 +204 205 1 +204 206 1 +205 205 2 +205 206 2 +205 208 1 +205 217 1 +205 242 1 +207 208 4 +207 209 1 +207 213 1 +207 216 1 +208 224 1 +208 228 1 +208 235 1 +208 241 1 +211 232 1 +212 221 1 +212 222 1 +212 232 1 +213 213 2 +213 214 1 +213 240 1 +213 243 1 +215 218 1 +217 217 1 +217 220 1 +218 218 1 +218 241 1 +219 237 1 +219 238 1 +220 239 1 +221 221 1 +221 222 1 +222 225 1 +222 227 1 +223 229 1 +224 224 1 +226 227 1 +227 228 1 +227 236 1 +228 228 1 +228 231 2 +228 232 1 +228 237 1 +228 242 1 +229 230 1 +229 234 1 +229 237 1 +229 238 1 +230 233 2 +232 232 1 +234 234 3 +235 238 1 +235 243 1 +236 236 1 +236 239 1 +237 237 1 +238 241 1 +238 251 1 +239 243 1 +240 240 1 +241 242 1 +250 250 1 +250 251 1 |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicConvertFormat/small_test_matrix_chr4.homer |
| b |
| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicDifferentialTAD/accepted.txt --- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicDifferentialTAD/rejected.txt --- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicInfo/hicInfo_output.txt --- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicInterIntraTAD/matrix.cool |
| b |
| Binary file test-data/hicInterIntraTAD/matrix.cool has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicInterIntraTAD/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicInterIntraTAD/plot.png |
| b |
| Binary file test-data/hicInterIntraTAD/plot.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicMergeLoops/gm12878_all.bedgraph --- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:39:52 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' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca1_test1.bw |
| b |
| Binary file test-data/hicPCA/pca1_test1.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca1_test2.bw |
| b |
| Binary file test-data/hicPCA/pca1_test2.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca1_test3.bw |
| b |
| Binary file test-data/hicPCA/pca1_test3.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca2_test1.bw |
| b |
| Binary file test-data/hicPCA/pca2_test1.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca2_test2.bw |
| b |
| Binary file test-data/hicPCA/pca2_test2.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPCA/pca2_test3.bw |
| b |
| Binary file test-data/hicPCA/pca2_test3.bw has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotDistVsCounts_result2.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result2.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotMatrix/plot2.pdf |
| b |
| Binary file test-data/hicPlotMatrix/plot2.pdf has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotMatrix/plot3_pca.svg --- a/test-data/hicPlotMatrix/plot3_pca.svg Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicPlotMatrix/plot3_pca.svg Wed Oct 18 10:39:52 2023 +0000 |
| b |
| b'@@ -7,7 +7,7 @@\n <rdf:RDF xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n <cc:Work>\n <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>\n- <dc:date>2021-02-14T19:28:28.926388</dc:date>\n+ <dc:date>2021-10-21T12:01:15.926583</dc:date>\n <dc:format>image/svg+xml</dc:format>\n <dc:creator>\n <cc:Agent>\n@@ -38,7 +38,7 @@\n z\n " style="fill:#ffffff;"/>\n </g>\n- <image height="410.4" id="image582374746f" transform="scale(1 -1)translate(0 -410.4)" width="453.6" x="72" xlink:href="data:image/png;base64,\n+ <image height="410.4" id="imagef9750a749d" transform="scale(1 -1)translate(0 -410.4)" width="453.6" x="72" xlink:href="data:image/png;base64,\n iVBORw0KGgoAAAANSUhEUgAAAD8AAAA5CAYAAACBBvPCAAABHElEQVR4nO2azRLCIAyEg1d9RHw7H5E7njrjT6kEQxKa/Y4OKtslG9OarkSVgnKx3oAlEB8ViD8LJfNeT0j7oEB8VE4lfi/YWmFHhMBbm1LHvWOLPzpGJtzT8FvZ4m+P4e8S518jUPMrUbJc6cH5qEC8J7Z61mipLPHcDY0I2FqpRktlieduaG+9xgXsBWmvRa+Lv9ahzwsg5jzHjc+1VsPSFOdL9jUAtcCxjwrEa3J02+l1XNUIQdc1Pzs4XYufDWpeEunBZdnBxvuPHRz7qCDtJXD3GKsDkWd1pVZWsHm5UCLH3nuqt3hzftSRFYUTIfDiAvFRgXjuf1bPQjPtV+3dHNDqPGBRYl/irercosRw7Ge53fO5lh0ltPNPhL1dYvY75GkAAAAASUVORK5CYII=" y="-36"/>\n <g id="matplotlib.axis_1">\n <g id="xtick_1">\n@@ -46,10 +46,10 @@\n <defs>\n <path d="M 0 0 \n L 0 -3.5 \n-" id="m7cb3fac755" style="stroke:#000000;stroke-width:0.8;"/>\n+" id="mb5ef7c54c4" style="stroke:#000000;stroke-width:0.8;"/>\n </defs>\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m7cb3fac755" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#mb5ef7c54c4" y="36.3125"/>\n </g>\n </g>\n <g id="text_1">\n@@ -128,7 +128,7 @@\n <g id="xtick_2">\n <g id="line2d_2">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="163.094318" xlink:href="#m7cb3fac755" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="163.094318" xlink:href="#mb5ef7c54c4" y="36.3125"/>\n </g>\n </g>\n <g id="text_2">\n@@ -160,7 +160,7 @@\n <g id="xtick_3">\n <g id="line2d_3">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="254.776136" xlink:href="#m7cb3fac755" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="254.776136" xlink:href="#mb5ef7c54c4" y="36.3125"/>\n </g>\n </g>\n <g id="text_3">\n@@ -203,7 +203,7 @@\n <g id="xtick_4">\n <g id="line2d_4">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="346.457955" xlink:href="#m7cb3fac755" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="346.457955" xlink:href="#mb5ef7c54c4" y="36.3125"/>\n </g>\n </g>\n <g id="text_4">\n@@ -220,7 +220,7 @@\n <g id="xtick_5">\n <g id="line2d_5">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="438.139773" xlink:href="#m7cb3fac755" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="438.139773" xlink:href="#mb5ef7c54c4" y="36.3125"/>\n </g>\n </g>\n <g id="text_5">\n@@ -406,10 +406,10 @@\n <defs>\n <path d="M 0 0 \n L -3.5 0 \n-" id="m646aa5daad" style="stroke:#000000;stroke-width:0.8;"/>\n+" id="m007817c1d4" style="stroke:#000000;stroke-width:0.8;"/>\n </defs>\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m646aa5daad" y="36.3125"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m007817c1d4" y="36.3125"/>\n </g>\n </g>\n <g id="text_7">\n@@ -426,7 +426,7 @@\n <g id="ytick_2">\n <g id="line2d_7">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m646aa5daad" y="118.692242"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m007817c1d4" y="118.692242"/>\n </g>\n </g>\n <g id="text_8">\n@@ -443,7 +443,7 @@\n <g id="ytic'..b'.675676 \n L 254.776136 525.344717 \n L 254.776136 461.675676 \n L 254.776136 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 263.944318 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 263.944318 461.675676 \n L 263.944318 525.344717 \n L 268.528409 525.344717 \n L 273.1125 525.344717 \n@@ -844,7 +844,7 @@\n L 263.944318 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 305.201136 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 305.201136 461.675676 \n L 305.201136 525.344717 \n L 309.785227 525.344717 \n L 314.369318 525.344717 \n@@ -866,7 +866,7 @@\n L 305.201136 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 351.042045 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 351.042045 461.675676 \n L 351.042045 525.344717 \n L 355.626136 525.344717 \n L 360.210227 525.344717 \n@@ -880,7 +880,7 @@\n L 351.042045 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 396.882955 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 396.882955 461.675676 \n L 396.882955 525.344717 \n L 401.467045 525.344717 \n L 401.467045 461.675676 \n@@ -888,7 +888,7 @@\n L 396.882955 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 410.635227 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 410.635227 461.675676 \n L 410.635227 525.344717 \n L 415.219318 525.344717 \n L 419.803409 525.344717 \n@@ -904,7 +904,7 @@\n L 410.635227 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 442.723864 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 442.723864 461.675676 \n L 442.723864 525.344717 \n L 447.307955 525.344717 \n L 447.307955 461.675676 \n@@ -912,7 +912,7 @@\n L 442.723864 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 479.396591 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 479.396591 461.675676 \n L 479.396591 525.344717 \n L 483.980682 525.344717 \n L 488.564773 525.344717 \n@@ -922,13 +922,13 @@\n L 479.396591 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 497.732955 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 497.732955 461.675676 \n L 497.732955 525.344717 \n L 497.732955 461.675676 \n L 497.732955 461.675676 \n z\n " style="fill:#1f77b4;"/>\n- <path clip-path="url(#pde4865bb25)" d="M 525.2375 461.675676 \n+ <path clip-path="url(#pfb06fea9d9)" d="M 525.2375 461.675676 \n L 525.2375 525.344717 \n L 525.2375 461.675676 \n L 525.2375 461.675676 \n@@ -939,7 +939,7 @@\n <g id="ytick_15">\n <g id="line2d_20">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m646aa5daad" y="525.344717"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m007817c1d4" y="525.344717"/>\n </g>\n </g>\n <g id="text_22">\n@@ -952,7 +952,7 @@\n <g id="ytick_16">\n <g id="line2d_21">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m646aa5daad" y="493.510197"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m007817c1d4" y="493.510197"/>\n </g>\n </g>\n <g id="text_23">\n@@ -965,7 +965,7 @@\n <g id="ytick_17">\n <g id="line2d_22">\n <g>\n- <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m646aa5daad" y="461.675676"/>\n+ <use style="stroke:#000000;stroke-width:0.8;" x="71.4125" xlink:href="#m007817c1d4" y="461.675676"/>\n </g>\n </g>\n <g id="text_24">\n@@ -980,10 +980,10 @@\n </g>\n </g>\n <defs>\n- <clipPath id="p32fba8a540">\n+ <clipPath id="p1d24998020">\n <rect height="407.779724" width="35.6625" x="536.0375" y="36.3125"/>\n </clipPath>\n- <clipPath id="pde4865bb25">\n+ <clipPath id="pfb06fea9d9">\n <rect height="70.035945" width="453.825" x="71.4125" y="458.492224"/>\n </clipPath>\n </defs>\n' |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotSVL/p_values.txt --- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotSVL/plot.png |
| b |
| Binary file test-data/hicPlotSVL/plot.png has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicPlotSVL/ratios.txt --- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicQuickQC/QC.log --- a/test-data/hicQuickQC/QC.log Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicTADClassifier/unittest_classifier.BIN |
| b |
| Binary file test-data/hicTADClassifier/unittest_classifier.BIN has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e 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 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicTrainTADClassifier/small_test_matrix.cool |
| b |
| Binary file test-data/hicTrainTADClassifier/small_test_matrix.cool has changed |
| b |
| diff -r 41dbf4d162a2 -r 77919cc3618e test-data/hicValidateLocations/overlap_smc3_matched_locations --- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/hicValidateLocations/overlap_smc3_statistics --- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:39:52 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 41dbf4d162a2 -r 77919cc3618e test-data/raw_qc_report --- a/test-data/raw_qc_report Tue Jan 10 18:56:55 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 10:39:52 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) |
