| Previous changeset 1:608538d083a2 (2023-01-12) Next changeset 3:5dfba24d7bdd (2024-07-01) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 |
|
modified:
hicDifferentialTAD.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 608538d083a2 -r 77d8e0fd162a hicDifferentialTAD.xml --- a/hicDifferentialTAD.xml Thu Jan 12 17:40:56 2023 +0000 +++ b/hicDifferentialTAD.xml Wed Oct 18 11:06:49 2023 +0000 |
| b |
| @@ -30,11 +30,11 @@ ]]> </command> <inputs> - <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" /> - <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" /> + <param name="matrix_h5_cooler_target" type="data" format="h5,cool" label="Target matrix to compute on" /> + <param name="matrix_h5_cooler_control" type="data" format="h5,cool" label="Control matrix to compute on" /> - <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> - <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' /> + <param argument="--tadDomains" type="data" format="bed" optional="false" label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> + <param argument="--pValue" type="float" label="P-value" min="0.0" max="1.0" help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value="0.05" /> <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression"> <option value="intra-TAD">intra-TAD</option> <option value="left-inter-TAD">left-inter-TAD</option> @@ -48,15 +48,15 @@ </param> </inputs> <outputs> - <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' /> - <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' /> + <data name="acceptedTADs" from_work_dir="galaxy_differential_tad_accepted.diff_tad" format="txt" label="Accepted TADs" /> + <data name="rejectedTADs" from_work_dir="galaxy_differential_tad_rejected.diff_tad" format="txt" label="Rejected TADs" /> </outputs> <tests> <test> <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" /> <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" /> - <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" /> + <param name="tadDomains" ftype="bed" value="hicDifferentialTAD/multiNone_domains.bed" /> <param name="pValue" value="1.0" /> <param name="mode_selector" value="all" /> <param name="modeReject" value="one" /> |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a macros.xml --- a/macros.xml Thu Jan 12 17:40:56 2023 +0000 +++ b/macros.xml Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/aggregate.tar.gz |
| b |
| Binary file test-data/cHi-C/aggregate.tar.gz has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 |
| b |
| Binary file test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicDifferentialTest/differential.hdf5 |
| b |
| Binary file test-data/cHi-C/chicDifferentialTest/differential.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicExportData/aggregate.tar.gz |
| b |
| Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 608538d083a2 -r 77d8e0fd162a 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicQualityControl/histogram.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicQualityControl/sparsity.png |
| b |
| Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 |
| b |
| Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/chicViewpoint/two_matrices.hdf5 |
| b |
| Binary file test-data/cHi-C/chicViewpoint/two_matrices.hdf5 has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/plots.tar.gz |
| b |
| Binary file test-data/cHi-C/plots.tar.gz has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/cHi-C/referencePoints_chicViewpoint.bed --- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/distVsCounts.txt --- a/test-data/distVsCounts.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/distVsCounts.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicCompartmentsPolarization/output_matrix.npz |
| b |
| Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicConvertFormat/small_test_matrix_chr4.homer |
| b |
| Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicDifferentialTAD/accepted.txt --- a/test-data/hicDifferentialTAD/accepted.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicDifferentialTAD/rejected.txt --- a/test-data/hicDifferentialTAD/rejected.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicInfo/hicInfo_output.txt --- a/test-data/hicInfo/hicInfo_output.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicInterIntraTAD/matrix.cool |
| b |
| Binary file test-data/hicInterIntraTAD/matrix.cool has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicInterIntraTAD/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicInterIntraTAD/plot.png |
| b |
| Binary file test-data/hicInterIntraTAD/plot.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicMergeLoops/gm12878_all.bedgraph --- a/test-data/hicMergeLoops/gm12878_all.bedgraph Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca1_test1.bw |
| b |
| Binary file test-data/hicPCA/pca1_test1.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca1_test2.bw |
| b |
| Binary file test-data/hicPCA/pca1_test2.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca1_test3.bw |
| b |
| Binary file test-data/hicPCA/pca1_test3.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca2_test1.bw |
| b |
| Binary file test-data/hicPCA/pca2_test1.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca2_test2.bw |
| b |
| Binary file test-data/hicPCA/pca2_test2.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPCA/pca2_test3.bw |
| b |
| Binary file test-data/hicPCA/pca2_test3.bw has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPlotDistVsCounts_result2.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result2.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPlotMatrix/plot2.pdf |
| b |
| Binary file test-data/hicPlotMatrix/plot2.pdf has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPlotMatrix/plot3_pca.svg --- a/test-data/hicPlotMatrix/plot3_pca.svg Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicPlotMatrix/plot3_pca.svg Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicPlotSVL/p_values.txt --- a/test-data/hicPlotSVL/p_values.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicPlotSVL/plot.png |
| b |
| Binary file test-data/hicPlotSVL/plot.png has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicPlotSVL/ratios.txt --- a/test-data/hicPlotSVL/ratios.txt Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicQuickQC/QC.log --- a/test-data/hicQuickQC/QC.log Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicTADClassifier/unittest_classifier.BIN |
| b |
| Binary file test-data/hicTADClassifier/unittest_classifier.BIN has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a 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 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicTrainTADClassifier/small_test_matrix.cool |
| b |
| Binary file test-data/hicTrainTADClassifier/small_test_matrix.cool has changed |
| b |
| diff -r 608538d083a2 -r 77d8e0fd162a test-data/hicValidateLocations/overlap_smc3_matched_locations --- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/hicValidateLocations/overlap_smc3_statistics --- a/test-data/hicValidateLocations/overlap_smc3_statistics Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 11:06:49 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 608538d083a2 -r 77d8e0fd162a test-data/raw_qc_report --- a/test-data/raw_qc_report Thu Jan 12 17:40:56 2023 +0000 +++ b/test-data/raw_qc_report Wed Oct 18 11:06:49 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) |
