| Next changeset 1:08e157ceda6f (2018-04-27) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 |
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added:
hicCompareMatrices.xml involucro macros.xml macros.xml.orig static/images/SRR027956.svg static/images/SRR0279XX_perChr_eigenvector1.png static/images/diagnostic_plot.png static/images/hicCorrelate_pearson.png static/images/hicCorrelate_pearson_scatter.png static/images/hicCorrelate_spearman.png static/images/hicCorrelate_spearman_scatter.png static/images/hicPlotDistVsCounts_result1.png static/images/hicPlotDistVsCounts_result2.png static/images/hicQC.png static/images/master_TADs_plot.png static/images/z-score.svg test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool test-data/Li_et_al_2015.h5 test-data/bedgraph_chrx_2e6_5e6.bg test-data/bigwig_chrx_2e6_5e6.bw test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/diagnostic_plot.png test-data/dm3_genes.bed.gz test-data/dm3_genes.bed6.gz test-data/domains.bed test-data/find_TADs/multiBonferroni_boundaries.bed test-data/find_TADs/multiBonferroni_boundaries.gff test-data/find_TADs/multiBonferroni_domains.bed test-data/find_TADs/multiBonferroni_score.bedgraph test-data/find_TADs/multiBonferroni_tad_score.bm test-data/find_TADs/multiBonferroni_zscore_matrix.h5 test-data/find_TADs/multiFDR_boundaries.bed test-data/find_TADs/multiFDR_boundaries.gff test-data/find_TADs/multiFDR_domains.bed test-data/find_TADs/multiFDR_score.bedgraph test-data/find_TADs/multiFDR_tad_score.bm test-data/find_TADs/multiFDR_zscore_matrix.h5 test-data/find_TADs/multiNone_boundaries.bed test-data/find_TADs/multiNone_boundaries.gff test-data/find_TADs/multiNone_domains.bed test-data/find_TADs/multiNone_score.bedgraph test-data/find_TADs/multiNone_tad_score.bm test-data/find_TADs/multiNone_zscore_matrix.h5 test-data/hicAggregateContacts_results1.png test-data/hicBuildMatrix_result1.bam test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicFindTADs_TAD_score.tabular test-data/hicFindTADs_find_boundaries.bed test-data/hicFindTADs_find_boundaries.gff test-data/hicFindTADs_find_domains.bed test-data/hicFindTADs_find_score.bedgraph test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotTADs_result1.svg test-data/hicSumMatrices_result1.npz.h5 test-data/li_32-33mb_interactions.bedgraph test-data/li_32mb_interactions.bedgraph test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/master_TADs_plot.png test-data/master_matrix_plot.png test-data/merged_matrix.npz.h5 test-data/multiFDR_boundaries.bed test-data/multiFDR_boundaries.gff test-data/multiFDR_domains.bed test-data/multiFDR_score.bedgraph test-data/multiFDR_tad_score.bm test-data/multiFDR_zscore_matrix.h5 test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bedgraph test-data/pca1.bw test-data/pca2.bedgraph test-data/pca2.bw test-data/pearson_small_50kb.cool test-data/pearson_small_50kb.h5 test-data/pearson_small_50kb_transform.cool test-data/raw_qc_report test-data/small_matrix_50kb_pearson_pca1_plot.png test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_R1_unsorted.bam test-data/small_test_R1_unsorted.sam test-data/small_test_R2_unsorted.bam test-data/small_test_R2_unsorted.sam test-data/small_test_matrix.h5 test-data/small_test_matrix_2.h5 test-data/small_test_matrix_50kb_res.h5 test-data/small_test_matrix_result.bam test-data/small_test_matrix_result_sorted.bam test-data/tad_classification.bed test-data/tad_score.gz test-data/test_regions.bed |
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| diff -r 000000000000 -r a0ab04565c73 hicCompareMatrices.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicCompareMatrices.xml Wed Mar 07 03:37:57 2018 -0500 |
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| @@ -0,0 +1,75 @@ +<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>normalize and compare two HiC matricies</description> + <macros> + <token name="@BINARY@">hicCompareMatrices</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + @BINARY@ + --matrices '$matrix1' '$matrix2' + --operation $operation + --outFileName matrix.$outputFormat + + && mv matrix.$outputFormat matrix +]]> + </command> + <inputs> + <param name='matrix1' type="data" format="h5,cool" + label="First matrix"/> + <param name='matrix2' type="data" format="h5,cool" + label="Second matrix to compare against the first"/> + + <param name='operation' type='select' label="Operation to be used for the comparison"> + <option value='diff'>diff</option> + <option value="ratio">ratio</option> + <option value="log2ratio">log2ratio</option> + </param> + <param name='outputFormat' type='select' label="Output file format"> + <option value='h5'>HiCExplorer format</option> + <option value="cool">cool</option> + </param> + </inputs> + <outputs> + <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="matrix1" value="small_test_matrix.h5"/> + <param name="matrix2" value="small_test_matrix.h5"/> + <param name="operation" value='log2ratio' /> + <param name="outputFormat" value="h5" /> + <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/> + </test> + <test> + <param name="matrix1" value="pearson_small_50kb.cool"/> + <param name="matrix2" value="pearson_small_50kb.cool"/> + <param name="operation" value='ratio' /> + <param name="outputFormat" value="cool" /> + <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/> + </test> + + </tests> + <help><![CDATA[ +Comparison of HiC matrices +========================== +`hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To +normalize the matrices each element is divided by sum of the matrix. + +Input +----- +- the matricies to be compared + + + +| For more information about HiCExplorer please consider our documentation on readthedocs.io_ + +.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r a0ab04565c73 involucro |
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| Binary file involucro has changed |
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| diff -r 000000000000 -r a0ab04565c73 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 07 03:37:57 2018 -0500 |
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| b'@@ -0,0 +1,587 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+ <token name="@WRAPPER_VERSION@">2.1</token>\n+\n+ <token name="@USE_RANGE@">\n+ #if $use_range.select_use_range == "yes_use_range":\n+ --range $range_min:$range_max\n+ #end if\n+ </token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.1133705</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n+ </xml>\n+ <xml name="use_range">\n+ <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->\n+ <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">\n+ <option value="no_use_range">No restriction</option>\n+ <option value="yes_use_range">Only consider counts within a range</option>\n+ </param>\n+ <when value="no_use_range"/>\n+ <when value="yes_use_range">\n+ <expand macro=\'range\' />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="range">\n+ <param name="range_min" type="integer" value="" min="0"/>\n+ <param name="range_max" type="integer" value="" min="0"/>\n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option '..b'/>\n+ <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="track_input_h5_macro">\n+ <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n+ </xml>\n+ <xml name="track_input_bed_macro">\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_macro">\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n+ </xml>\n+ <xml name="track_input_bigwig_macro">\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_matrix_macro">\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_tabular_macro">\n+ <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n+ </xml>\n+ <xml name="plot_title">\n+ <param name="title" type="text" optional="true" label="Plot title"/>\n+ </xml>\n+\n+ <xml name="spacer_macro">\n+ <param name="spacer_width" type="float" value="" optional="True"\n+ label="Include spacer at the end of the track." help="Width of the spacer." />\n+ </xml>\n+ <xml name="fontsize_macro">\n+ <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r a0ab04565c73 macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml.orig Wed Mar 07 03:37:57 2018 -0500 |
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| b'@@ -0,0 +1,585 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+<<<<<<< HEAD\n+ <token name="@WRAPPER_VERSION@">2.0</token>\n+\n+ <token name="@USE_RANGE@">\n+ #if $use_range.select_use_range == "yes_use_range":\n+ --range $range_min:$range_max\n+ #end if\n+ </token>\n+\n+=======\n+ <token name="@WRAPPER_VERSION@">2.1alpha1</token>\n+>>>>>>> joachimwolff-master\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.1133705</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n+ </xml>\n+ <xml name="use_range">\n+ <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->\n+ <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">\n+ <option value="no_use_range">No restriction</option>\n+ <option value="yes_use_range">Only consider counts within a range</option>\n+ </param>\n+ <when value="no_use_range"/>\n+ <when value="yes_use_range">\n+ <param name="range_min" type="integer" value="" min="0"/>\n+ <param name="range_max" type="integer" value="" min="0"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="'..b'/>\n+ <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="track_input_h5_macro">\n+ <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n+ </xml>\n+ <xml name="track_input_bed_macro">\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_macro">\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n+ </xml>\n+ <xml name="track_input_bigwig_macro">\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_matrix_macro">\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_tabular_macro">\n+ <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n+ </xml>\n+ <xml name="plot_title">\n+ <param name="title" type="text" optional="true" label="Plot title"/>\n+ </xml>\n+\n+ <xml name="spacer_macro">\n+ <param name="spacer_width" type="float" value="" optional="True"\n+ label="Include spacer at the end of the track." help="Width of the spacer." />\n+ </xml>\n+ <xml name="fontsize_macro">\n+ <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r a0ab04565c73 static/images/SRR027956.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/SRR027956.svg Wed Mar 07 03:37:57 2018 -0500 |
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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiBonferroni_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiBonferroni_boundaries.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B09504 -0.06825625 . +chrX 87500 92500 B09542 -0.0720205 . |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiBonferroni_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiBonferroni_boundaries.gff Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chr2L HiCExplorer boundary 22922500 22927500 -0.06825625 . . ID=B09504;delta=0.0219547105263;pvalue=0.0547512191318;tad_sep=-0.06825625 +chrX HiCExplorer boundary 87500 92500 -0.0720205 . . ID=B09542;delta=0.0197999736842;pvalue=0.0890201733631;tad_sep=-0.0720205 |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiBonferroni_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiBonferroni_score.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23814 @@\n+chr2RHet\t2500\t3286880\t0.0\n+chr3RHet\t2500\t2516253\t0.0\n+chr2LHet\t2500\t366936\t0.0\n+chr4\t2500\t1350928\t0.0\n+chrYHet\t2500\t346019\t0.0\n+chr3L\t2500\t7500\t-0.15973725\n+chr3L\t7500\t12500\t-0.1550825\n+chr3L\t12500\t17500\t-0.1511685\n+chr3L\t17500\t22500\t-0.14787325\n+chr3L\t22500\t27500\t-0.14477275\n+chr3L\t27500\t32500\t-0.141869\n+chr3L\t32500\t37500\t-0.13920825\n+chr3L\t37500\t42500\t-0.13669525\n+chr3L\t42500\t47500\t-0.13435775\n+chr3L\t47500\t52500\t-0.13219825\n+chr3L\t52500\t57500\t-0.13013875\n+chr3L\t57500\t62500\t-0.09402375\n+chr3L\t62500\t67500\t-0.076427\n+chr3L\t67500\t72500\t-0.04183125\n+chr3L\t72500\t77500\t0.0197075\n+chr3L\t77500\t82500\t0.07052875\n+chr3L\t82500\t87500\t0.07283975\n+chr3L\t87500\t92500\t0.07045525\n+chr3L\t92500\t97500\t0.0683615\n+chr3L\t97500\t102500\t0.06999375\n+chr3L\t102500\t107500\t0.0683285\n+chr3L\t107500\t112500\t0.066853\n+chr3L\t112500\t117500\t0.06554\n+chr3L\t117500\t122500\t0.06436125\n+chr3L\t122500\t127500\t0.00960325\n+chr3L\t127500\t132500\t0.012285\n+chr3L\t132500\t137500\t-0.00142775\n+chr3L\t137500\t142500\t-0.060362\n+chr3L\t142500\t147500\t-0.05156225\n+chr3L\t147500\t152500\t-0.0552185\n+chr3L\t152500\t157500\t-0.06660375\n+chr3L\t157500\t162500\t-0.070088\n+chr3L\t162500\t167500\t-0.10316675\n+chr3L\t167500\t172500\t-0.10316675\n+chr3L\t172500\t177500\t-0.10316675\n+chr3L\t177500\t182500\t-0.089227\n+chr3L\t182500\t187500\t-0.0778915\n+chr3L\t187500\t192500\t-0.0547475\n+chr3L\t192500\t197500\t-0.06240725\n+chr3L\t197500\t202500\t-0.040267\n+chr3L\t202500\t207500\t-0.018089\n+chr3L\t207500\t212500\t-0.018089\n+chr3L\t212500\t217500\t-0.018089\n+chr3L\t217500\t222500\t0.0190635\n+chr3L\t222500\t227500\t0.01122225\n+chr3L\t227500\t232500\t-0.00338425\n+chr3L\t232500\t237500\t0.018671\n+chr3L\t237500\t242500\t0.015759\n+chr3L\t242500\t247500\t0.015759\n+chr3L\t247500\t252500\t-0.00807575\n+chr3L\t252500\t257500\t-0.01047525\n+chr3L\t257500\t262500\t-0.026655\n+chr3L\t262500\t267500\t-0.01461\n+chr3L\t267500\t272500\t-0.01739225\n+chr3L\t272500\t277500\t0.006616\n+chr3L\t277500\t282500\t0.02626725\n+chr3L\t282500\t287500\t0.02671675\n+chr3L\t287500\t292500\t0.04431375\n+chr3L\t292500\t297500\t0.075128\n+chr3L\t297500\t302500\t0.0517535\n+chr3L\t302500\t307500\t0.03498275\n+chr3L\t307500\t312500\t0.04280875\n+chr3L\t312500\t317500\t-0.00566075\n+chr3L\t317500\t322500\t-0.00566075\n+chr3L\t322500\t327500\t-0.01699625\n+chr3L\t327500\t332500\t0.0001575\n+chr3L\t332500\t337500\t-0.030848\n+chr3L\t337500\t342500\t-0.02264125\n+chr3L\t342500\t347500\t-0.01607175\n+chr3L\t347500\t352500\t-0.03003825\n+chr3L\t352500\t357500\t-0.0029145\n+chr3L\t357500\t362500\t-0.0580815\n+chr3L\t362500\t367500\t-0.042338\n+chr3L\t367500\t372500\t-0.0243195\n+chr3L\t372500\t377500\t-0.0233235\n+chr3L\t377500\t382500\t0.01665375\n+chr3L\t382500\t387500\t0.01665375\n+chr3L\t387500\t392500\t0.030134\n+chr3L\t392500\t397500\t0.01966325\n+chr3L\t397500\t402500\t0.0270555\n+chr3L\t402500\t407500\t0.03715275\n+chr3L\t407500\t412500\t0.03215025\n+chr3L\t412500\t417500\t0.007102\n+chr3L\t417500\t422500\t0.01531925\n+chr3L\t422500\t427500\t0.04944275\n+chr3L\t427500\t432500\t0.017395\n+chr3L\t432500\t437500\t0.0233485\n+chr3L\t437500\t442500\t0.010935\n+chr3L\t442500\t447500\t0.015241\n+chr3L\t447500\t452500\t-0.00172725\n+chr3L\t452500\t457500\t-0.006215\n+chr3L\t457500\t462500\t-0.0121685\n+chr3L\t462500\t467500\t-0.0042425\n+chr3L\t467500\t472500\t0.00083775\n+chr3L\t472500\t477500\t-0.02013475\n+chr3L\t477500\t482500\t-0.058266\n+chr3L\t482500\t487500\t-0.07169775\n+chr3L\t487500\t492500\t-0.04601075\n+chr3L\t492500\t497500\t-0.02333825\n+chr3L\t497500\t502500\t-0.00838725\n+chr3L\t502500\t507500\t-0.0641845\n+chr3L\t507500\t512500\t-0.067458\n+chr3L\t512500\t517500\t-0.067458\n+chr3L\t517500\t522500\t-0.09926975\n+chr3L\t522500\t527500\t-0.1060405\n+chr3L\t527500\t532500\t-0.07751675\n+chr3L\t532500\t537500\t-0.07751675\n+chr3L\t537500\t542500\t-0.07751675\n+chr3L\t542500\t547500\t-0.06945475\n+chr3L\t547500\t552500\t-0.06322125\n+chr3L\t552500\t557500\t0.00947925\n+chr3L\t557500\t562500\t-0.02586475\n+chr3L\t562500\t567500\t0.030247\n+chr3L\t567500\t572500\t0.04485875\n+chr3L\t572500\t577500\t0.0579985\n+chr3L\t577500\t582500\t0.085449\n+chr3L\t582500\t587500\t0.10347075\n+chr3L\t587500\t592500\t0.1197795\n+chr3L\t592500\t597500\t0.115187\n+chr3L\t597500\t602500\t0.099483\n+chr3L\t602500\t607500\t0.100333\n+chr3L\t607500\t612500\t0.1935635\n+chr3L\t612500\t6'..b'52500\t27357500\t0.02843225\n+chr3R\t27357500\t27362500\t0.003006\n+chr3R\t27362500\t27367500\t0.02624575\n+chr3R\t27367500\t27372500\t0.01185675\n+chr3R\t27372500\t27377500\t0.0101145\n+chr3R\t27377500\t27382500\t-0.005061\n+chr3R\t27382500\t27387500\t-0.041305\n+chr3R\t27387500\t27392500\t-0.00143125\n+chr3R\t27392500\t27397500\t0.04561275\n+chr3R\t27397500\t27402500\t0.02985575\n+chr3R\t27402500\t27407500\t0.0173185\n+chr3R\t27407500\t27412500\t0.0272775\n+chr3R\t27412500\t27417500\t0.01093175\n+chr3R\t27417500\t27422500\t-0.0499295\n+chr3R\t27422500\t27427500\t-0.04139125\n+chr3R\t27427500\t27432500\t-0.0366555\n+chr3R\t27432500\t27437500\t-0.0366555\n+chr3R\t27437500\t27442500\t-0.04748775\n+chr3R\t27442500\t27447500\t-0.05511025\n+chr3R\t27447500\t27452500\t-0.05736225\n+chr3R\t27452500\t27457500\t-0.0233205\n+chr3R\t27457500\t27462500\t-0.0020265\n+chr3R\t27462500\t27467500\t0.02501975\n+chr3R\t27467500\t27472500\t0.036331\n+chr3R\t27472500\t27477500\t0.036331\n+chr3R\t27477500\t27482500\t0.036331\n+chr3R\t27482500\t27487500\t0.06726625\n+chr3R\t27487500\t27492500\t0.06726625\n+chr3R\t27492500\t27497500\t0.0926245\n+chr3R\t27497500\t27502500\t0.098145\n+chr3R\t27502500\t27507500\t0.088452\n+chr3R\t27507500\t27512500\t0.0991195\n+chr3R\t27512500\t27517500\t0.07477075\n+chr3R\t27517500\t27522500\t0.07477075\n+chr3R\t27522500\t27527500\t0.07477075\n+chr3R\t27527500\t27532500\t0.07477075\n+chr3R\t27532500\t27537500\t0.07667425\n+chr3R\t27537500\t27542500\t0.08198875\n+chr3R\t27542500\t27547500\t0.068792\n+chr3R\t27547500\t27552500\t0.00660575\n+chr3R\t27552500\t27557500\t-0.06866275\n+chr3R\t27557500\t27562500\t-0.063076\n+chr3R\t27562500\t27567500\t-0.063076\n+chr3R\t27567500\t27572500\t-0.08094325\n+chr3R\t27572500\t27577500\t-0.07177225\n+chr3R\t27577500\t27582500\t0.00014175\n+chr3R\t27582500\t27587500\t-0.004425\n+chr3R\t27587500\t27592500\t-0.0055905\n+chr3R\t27592500\t27597500\t0.0107725\n+chr3R\t27597500\t27602500\t0.012076\n+chr3R\t27602500\t27607500\t0.00204375\n+chr3R\t27607500\t27612500\t0.01391525\n+chr3R\t27612500\t27617500\t0.02616875\n+chr3R\t27617500\t27622500\t0.02862975\n+chr3R\t27622500\t27627500\t0.02862975\n+chr3R\t27627500\t27632500\t0.03521625\n+chr3R\t27632500\t27637500\t0.00040125\n+chr3R\t27637500\t27642500\t0.0303095\n+chr3R\t27642500\t27647500\t0.090842\n+chr3R\t27647500\t27652500\t0.10491025\n+chr3R\t27652500\t27657500\t0.11880175\n+chr3R\t27657500\t27662500\t0.09649925\n+chr3R\t27662500\t27667500\t0.07636225\n+chr3R\t27667500\t27672500\t0.06380525\n+chr3R\t27672500\t27677500\t0.04760175\n+chr3R\t27677500\t27682500\t0.02274975\n+chr3R\t27682500\t27687500\t0.015637\n+chr3R\t27687500\t27692500\t0.015637\n+chr3R\t27692500\t27697500\t0.025063\n+chr3R\t27697500\t27702500\t-0.01535\n+chr3R\t27702500\t27707500\t-0.01535\n+chr3R\t27707500\t27712500\t0.00155075\n+chr3R\t27712500\t27717500\t0.006288\n+chr3R\t27717500\t27722500\t0.006288\n+chr3R\t27722500\t27727500\t-0.00858325\n+chr3R\t27727500\t27732500\t0.02622075\n+chr3R\t27732500\t27737500\t0.097312\n+chr3R\t27737500\t27742500\t0.067952\n+chr3R\t27742500\t27747500\t0.0387865\n+chr3R\t27747500\t27752500\t0.01357725\n+chr3R\t27752500\t27757500\t0.02531675\n+chr3R\t27757500\t27762500\t0.033303\n+chr3R\t27762500\t27767500\t0.050386\n+chr3R\t27767500\t27772500\t0.0229625\n+chr3R\t27772500\t27777500\t0.04058825\n+chr3R\t27777500\t27782500\t0.03747975\n+chr3R\t27782500\t27787500\t0.0294565\n+chr3R\t27787500\t27792500\t0.07453225\n+chr3R\t27792500\t27797500\t0.08362425\n+chr3R\t27797500\t27802500\t0.06882\n+chr3R\t27802500\t27807500\t0.075945\n+chr3R\t27807500\t27812500\t0.11806575\n+chr3R\t27812500\t27817500\t0.152855\n+chr3R\t27817500\t27822500\t0.1721425\n+chr3R\t27822500\t27827500\t0.17090925\n+chr3R\t27827500\t27832500\t0.15466375\n+chr3R\t27832500\t27837500\t0.1765955\n+chr3R\t27837500\t27842500\t0.16170225\n+chr3R\t27842500\t27847500\t0.16431675\n+chr3R\t27847500\t27852500\t0.20353925\n+chr3R\t27852500\t27857500\t0.19259975\n+chr3R\t27857500\t27862500\t0.13903775\n+chr3R\t27862500\t27867500\t0.1658075\n+chr3R\t27867500\t27872500\t0.033584\n+chr3R\t27872500\t27877500\t-0.044813\n+chr3R\t27877500\t27882500\t-0.1079445\n+chr3R\t27882500\t27887500\t-0.1024605\n+chr3R\t27887500\t27892500\t-0.09179375\n+chr3R\t27892500\t27897500\t-0.1533095\n+chr3R\t27897500\t27902500\t-0.15876925\n+chr3R\t27902500\t27905026\t0.0\n+chrUextra\t2500\t29002328\t0.0\n+chrM\t2500\t17258\t0.0\n+chr3LHet\t2500\t2555245\t0.0\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiBonferroni_tad_score.bm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiBonferroni_tad_score.bm Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiBonferroni_zscore_matrix.h5 |
| b |
| Binary file test-data/find_TADs/multiBonferroni_zscore_matrix.h5 has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_boundaries.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B09504 -0.0682563628914 . +chrX 87500 92500 B09542 -0.0720204010166 . |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_boundaries.gff Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chr2L HiCExplorer boundary 22922500 22927500 -0.0682563628914 . . ID=B09504;delta=0.0219548467205;pvalue=3.39647761363e-05;tad_sep=-0.0682563628914 +chrX HiCExplorer boundary 87500 92500 -0.0720204010166 . . ID=B09542;delta=0.0197999801036;pvalue=5.52234326074e-05;tad_sep=-0.0720204010166 |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_score.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23814 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r3R\t27492500\t27497500\t0.0926243695908\n+chr3R\t27497500\t27502500\t0.0981449030292\n+chr3R\t27502500\t27507500\t0.0884518556514\n+chr3R\t27507500\t27512500\t0.0991195811149\n+chr3R\t27512500\t27517500\t0.0747706741268\n+chr3R\t27517500\t27522500\t0.0747706741268\n+chr3R\t27522500\t27527500\t0.0747706741268\n+chr3R\t27527500\t27532500\t0.0747706741268\n+chr3R\t27532500\t27537500\t0.0766743472887\n+chr3R\t27537500\t27542500\t0.0819888617495\n+chr3R\t27542500\t27547500\t0.0687920794808\n+chr3R\t27547500\t27552500\t0.00660554313528\n+chr3R\t27552500\t27557500\t-0.068663015437\n+chr3R\t27557500\t27562500\t-0.0630758560148\n+chr3R\t27562500\t27567500\t-0.0630758560148\n+chr3R\t27567500\t27572500\t-0.0809430698515\n+chr3R\t27572500\t27577500\t-0.0717723999989\n+chr3R\t27577500\t27582500\t0.000141647672875\n+chr3R\t27582500\t27587500\t-0.00442507235603\n+chr3R\t27587500\t27592500\t-0.00559045677864\n+chr3R\t27592500\t27597500\t0.0107725606946\n+chr3R\t27597500\t27602500\t0.0120760744751\n+chr3R\t27602500\t27607500\t0.00204356889653\n+chr3R\t27607500\t27612500\t0.0139153913065\n+chr3R\t27612500\t27617500\t0.0261687926169\n+chr3R\t27617500\t27622500\t0.0286298507012\n+chr3R\t27622500\t27627500\t0.0286298507012\n+chr3R\t27627500\t27632500\t0.0352164944657\n+chr3R\t27632500\t27637500\t0.000401173118025\n+chr3R\t27637500\t27642500\t0.0303094054812\n+chr3R\t27642500\t27647500\t0.0908420094422\n+chr3R\t27647500\t27652500\t0.104910058763\n+chr3R\t27652500\t27657500\t0.118801510524\n+chr3R\t27657500\t27662500\t0.0964990987183\n+chr3R\t27662500\t27667500\t0.0763621831154\n+chr3R\t27667500\t27672500\t0.0638054902132\n+chr3R\t27672500\t27677500\t0.0476018389011\n+chr3R\t27677500\t27682500\t0.0227499384692\n+chr3R\t27682500\t27687500\t0.0156368494306\n+chr3R\t27687500\t27692500\t0.0156368494306\n+chr3R\t27692500\t27697500\t0.0250628717201\n+chr3R\t27697500\t27702500\t-0.0153501339631\n+chr3R\t27702500\t27707500\t-0.0153501339631\n+chr3R\t27707500\t27712500\t0.00155093677552\n+chr3R\t27712500\t27717500\t0.00628832953637\n+chr3R\t27717500\t27722500\t0.00628832953637\n+chr3R\t27722500\t27727500\t-0.00858313357697\n+chr3R\t27727500\t27732500\t0.0262206216996\n+chr3R\t27732500\t27737500\t0.0973120916552\n+chr3R\t27737500\t27742500\t0.0679519287234\n+chr3R\t27742500\t27747500\t0.0387863613672\n+chr3R\t27747500\t27752500\t0.0135773284877\n+chr3R\t27752500\t27757500\t0.0253166135267\n+chr3R\t27757500\t27762500\t0.0333030070633\n+chr3R\t27762500\t27767500\t0.0503863505993\n+chr3R\t27767500\t27772500\t0.0229622694476\n+chr3R\t27772500\t27777500\t0.0405881951039\n+chr3R\t27777500\t27782500\t0.037479587368\n+chr3R\t27782500\t27787500\t0.029456572128\n+chr3R\t27787500\t27792500\t0.0745322715233\n+chr3R\t27792500\t27797500\t0.0836243348379\n+chr3R\t27797500\t27802500\t0.0688200327796\n+chr3R\t27802500\t27807500\t0.0759450550149\n+chr3R\t27807500\t27812500\t0.118065986623\n+chr3R\t27812500\t27817500\t0.152855110565\n+chr3R\t27817500\t27822500\t0.172142533307\n+chr3R\t27822500\t27827500\t0.170909037821\n+chr3R\t27827500\t27832500\t0.154663891259\n+chr3R\t27832500\t27837500\t0.176595521439\n+chr3R\t27837500\t27842500\t0.161702307533\n+chr3R\t27842500\t27847500\t0.164316603264\n+chr3R\t27847500\t27852500\t0.203539265274\n+chr3R\t27852500\t27857500\t0.192599593633\n+chr3R\t27857500\t27862500\t0.139037714041\n+chr3R\t27862500\t27867500\t0.165807374217\n+chr3R\t27867500\t27872500\t0.0335840423644\n+chr3R\t27872500\t27877500\t-0.0448126165606\n+chr3R\t27877500\t27882500\t-0.107944679472\n+chr3R\t27882500\t27887500\t-0.102460435442\n+chr3R\t27887500\t27892500\t-0.0917938917283\n+chr3R\t27892500\t27897500\t-0.153309285822\n+chr3R\t27897500\t27902500\t-0.158769428921\n+chr3R\t27902500\t27905026\t0.0\n+chrUextra\t2500\t29002328\t0.0\n+chrM\t2500\t17258\t0.0\n+chr3LHet\t2500\t2555245\t0.0\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiFDR_tad_score.bm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiFDR_tad_score.bm Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiFDR_zscore_matrix.h5 |
| b |
| Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiNone_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiNone_boundaries.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,1408 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52500\t20457500\tB22332\t-0.10752325\t.\n+chr3R\t20612500\t20617500\tB22364\t-0.099168\t.\n+chr3R\t20707500\t20712500\tB22383\t-0.07351875\t.\n+chr3R\t20717500\t20722500\tB22385\t-0.0705095\t.\n+chr3R\t20762500\t20767500\tB22394\t-0.0862985\t.\n+chr3R\t20857500\t20862500\tB22413\t-0.01276525\t.\n+chr3R\t20897500\t20902500\tB22421\t-0.02185325\t.\n+chr3R\t20932500\t20937500\tB22428\t-0.05891975\t.\n+chr3R\t20962500\t20967500\tB22434\t-0.0613935\t.\n+chr3R\t21082500\t21087500\tB22458\t-0.094928\t.\n+chr3R\t21172500\t21177500\tB22476\t-0.0413955\t.\n+chr3R\t21217500\t21222500\tB22485\t-0.05028725\t.\n+chr3R\t21317500\t21322500\tB22505\t-0.086029\t.\n+chr3R\t21332500\t21337500\tB22508\t-0.06100175\t.\n+chr3R\t21387500\t21392500\tB22519\t-0.0656765\t.\n+chr3R\t21472500\t21477500\tB22536\t-0.0932985\t.\n+chr3R\t21612500\t21617500\tB22564\t-0.081974\t.\n+chr3R\t21727500\t21732500\tB22587\t0.07025075\t.\n+chr3R\t21817500\t21822500\tB22605\t-0.00145975\t.\n+chr3R\t21842500\t21847500\tB22610\t0.0360515\t.\n+chr3R\t21947500\t21952500\tB22631\t0.002742\t.\n+chr3R\t21987500\t21992500\tB22639\t0.00713375\t.\n+chr3R\t22072500\t22077500\tB22656\t-0.087915\t.\n+chr3R\t22217500\t22222500\tB22685\t0.0614505\t.\n+chr3R\t22267500\t22272500\tB22695\t-0.02575325\t.\n+chr3R\t22307500\t22312500\tB22703\t-0.04946475\t.\n+chr3R\t22377500\t22382500\tB22717\t-0.055847\t.\n+chr3R\t22497500\t22502500\tB22741\t-0.0631105\t.\n+chr3R\t22517500\t22522500\tB22745\t-0.062648\t.\n+chr3R\t22602500\t22607500\tB22762\t-0.011252\t.\n+chr3R\t22692500\t22697500\tB22780\t-0.089033\t.\n+chr3R\t22777500\t22782500\tB22797\t-0.04050025\t.\n+chr3R\t22882500\t22887500\tB22818\t-0.05683475\t.\n+chr3R\t22982500\t22987500\tB22838\t-0.0237815\t.\n+chr3R\t23107500\t23112500\tB22863\t-0.100625\t.\n+chr3R\t23182500\t23187500\tB22878\t-0.00294725\t.\n+chr3R\t23192500\t23197500\tB22880\t-0.00275775\t.\n+chr3R\t23412500\t23417500\tB22924\t-0.090027\t.\n+chr3R\t23557500\t23562500\tB22953\t-0.104602\t.\n+chr3R\t23767500\t23772500\tB22995\t-0.1119105\t.\n+chr3R\t23812500\t23817500\tB23004\t-0.0660765\t.\n+chr3R\t23917500\t23922500\tB23025\t-0.04218475\t.\n+chr3R\t24027500\t24032500\tB23047\t-0.05579575\t.\n+chr3R\t24157500\t24162500\tB23073\t-0.01546725\t.\n+chr3R\t24202500\t24207500\tB23082\t-0.0326015\t.\n+chr3R\t24342500\t24347500\tB23110\t-0.0623065\t.\n+chr3R\t24372500\t24377500\tB23116\t-0.0749395\t.\n+chr3R\t24447500\t24452500\tB23131\t-0.09836075\t.\n+chr3R\t24622500\t24627500\tB23166\t-0.03171375\t.\n+chr3R\t24742500\t24747500\tB23190\t-0.08589625\t.\n+chr3R\t24882500\t24887500\tB23218\t-0.09323725\t.\n+chr3R\t24992500\t24997500\tB23240\t-0.0589785\t.\n+chr3R\t25087500\t25092500\tB23259\t0.03674225\t.\n+chr3R\t25162500\t25167500\tB23274\t-0.0462465\t.\n+chr3R\t25327500\t25332500\tB23307\t-0.08303325\t.\n+chr3R\t25402500\t25407500\tB23322\t-0.00546225\t.\n+chr3R\t25567500\t25572500\tB23355\t-0.04654075\t.\n+chr3R\t25577500\t25582500\tB23357\t-0.01871575\t.\n+chr3R\t25727500\t25732500\tB23387\t-0.00858875\t.\n+chr3R\t25877500\t25882500\tB23417\t-0.10581625\t.\n+chr3R\t25987500\t25992500\tB23439\t-0.090403\t.\n+chr3R\t26047500\t26052500\tB23451\t-0.0935315\t.\n+chr3R\t26177500\t26182500\tB23477\t-0.11469275\t.\n+chr3R\t26272500\t26277500\tB23496\t-0.1002735\t.\n+chr3R\t26327500\t26332500\tB23507\t-0.092304\t.\n+chr3R\t26487500\t26492500\tB23539\t0.0627965\t.\n+chr3R\t26562500\t26567500\tB23554\t-0.01974475\t.\n+chr3R\t26637500\t26642500\tB23569\t-0.07430725\t.\n+chr3R\t26712500\t26717500\tB23584\t-0.049789\t.\n+chr3R\t26867500\t26872500\tB23615\t-0.0249905\t.\n+chr3R\t27042500\t27047500\tB23650\t-0.074189\t.\n+chr3R\t27152500\t27157500\tB23672\t-0.00609925\t.\n+chr3R\t27182500\t27187500\tB23678\t-0.01281025\t.\n+chr3R\t27247500\t27252500\tB23691\t-0.04990275\t.\n+chr3R\t27382500\t27387500\tB23718\t-0.041305\t.\n+chr3R\t27417500\t27422500\tB23725\t-0.0499295\t.\n+chr3R\t27567500\t27572500\tB23755\t-0.08094325\t.\n+chr3R\t27697500\t27702500\tB23781\t-0.01535\t.\n+chr3R\t27747500\t27752500\tB23791\t0.01357725\t.\n+chr3R\t27767500\t27772500\tB23795\t0.0229625\t.\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiNone_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiNone_boundaries.gff Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,1408 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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiNone_domains.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiNone_domains.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,1403 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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiNone_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiNone_score.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23814 @@\n+chr2RHet\t2500\t3286880\t0.0\n+chr3RHet\t2500\t2516253\t0.0\n+chr2LHet\t2500\t366936\t0.0\n+chr4\t2500\t1350928\t0.0\n+chrYHet\t2500\t346019\t0.0\n+chr3L\t2500\t7500\t-0.15973725\n+chr3L\t7500\t12500\t-0.1550825\n+chr3L\t12500\t17500\t-0.1511685\n+chr3L\t17500\t22500\t-0.14787325\n+chr3L\t22500\t27500\t-0.14477275\n+chr3L\t27500\t32500\t-0.141869\n+chr3L\t32500\t37500\t-0.13920825\n+chr3L\t37500\t42500\t-0.13669525\n+chr3L\t42500\t47500\t-0.13435775\n+chr3L\t47500\t52500\t-0.13219825\n+chr3L\t52500\t57500\t-0.13013875\n+chr3L\t57500\t62500\t-0.09402375\n+chr3L\t62500\t67500\t-0.076427\n+chr3L\t67500\t72500\t-0.04183125\n+chr3L\t72500\t77500\t0.0197075\n+chr3L\t77500\t82500\t0.07052875\n+chr3L\t82500\t87500\t0.07283975\n+chr3L\t87500\t92500\t0.07045525\n+chr3L\t92500\t97500\t0.0683615\n+chr3L\t97500\t102500\t0.06999375\n+chr3L\t102500\t107500\t0.0683285\n+chr3L\t107500\t112500\t0.066853\n+chr3L\t112500\t117500\t0.06554\n+chr3L\t117500\t122500\t0.06436125\n+chr3L\t122500\t127500\t0.00960325\n+chr3L\t127500\t132500\t0.012285\n+chr3L\t132500\t137500\t-0.00142775\n+chr3L\t137500\t142500\t-0.060362\n+chr3L\t142500\t147500\t-0.05156225\n+chr3L\t147500\t152500\t-0.0552185\n+chr3L\t152500\t157500\t-0.06660375\n+chr3L\t157500\t162500\t-0.070088\n+chr3L\t162500\t167500\t-0.10316675\n+chr3L\t167500\t172500\t-0.10316675\n+chr3L\t172500\t177500\t-0.10316675\n+chr3L\t177500\t182500\t-0.089227\n+chr3L\t182500\t187500\t-0.0778915\n+chr3L\t187500\t192500\t-0.0547475\n+chr3L\t192500\t197500\t-0.06240725\n+chr3L\t197500\t202500\t-0.040267\n+chr3L\t202500\t207500\t-0.018089\n+chr3L\t207500\t212500\t-0.018089\n+chr3L\t212500\t217500\t-0.018089\n+chr3L\t217500\t222500\t0.0190635\n+chr3L\t222500\t227500\t0.01122225\n+chr3L\t227500\t232500\t-0.00338425\n+chr3L\t232500\t237500\t0.018671\n+chr3L\t237500\t242500\t0.015759\n+chr3L\t242500\t247500\t0.015759\n+chr3L\t247500\t252500\t-0.00807575\n+chr3L\t252500\t257500\t-0.01047525\n+chr3L\t257500\t262500\t-0.026655\n+chr3L\t262500\t267500\t-0.01461\n+chr3L\t267500\t272500\t-0.01739225\n+chr3L\t272500\t277500\t0.006616\n+chr3L\t277500\t282500\t0.02626725\n+chr3L\t282500\t287500\t0.02671675\n+chr3L\t287500\t292500\t0.04431375\n+chr3L\t292500\t297500\t0.075128\n+chr3L\t297500\t302500\t0.0517535\n+chr3L\t302500\t307500\t0.03498275\n+chr3L\t307500\t312500\t0.04280875\n+chr3L\t312500\t317500\t-0.00566075\n+chr3L\t317500\t322500\t-0.00566075\n+chr3L\t322500\t327500\t-0.01699625\n+chr3L\t327500\t332500\t0.0001575\n+chr3L\t332500\t337500\t-0.030848\n+chr3L\t337500\t342500\t-0.02264125\n+chr3L\t342500\t347500\t-0.01607175\n+chr3L\t347500\t352500\t-0.03003825\n+chr3L\t352500\t357500\t-0.0029145\n+chr3L\t357500\t362500\t-0.0580815\n+chr3L\t362500\t367500\t-0.042338\n+chr3L\t367500\t372500\t-0.0243195\n+chr3L\t372500\t377500\t-0.0233235\n+chr3L\t377500\t382500\t0.01665375\n+chr3L\t382500\t387500\t0.01665375\n+chr3L\t387500\t392500\t0.030134\n+chr3L\t392500\t397500\t0.01966325\n+chr3L\t397500\t402500\t0.0270555\n+chr3L\t402500\t407500\t0.03715275\n+chr3L\t407500\t412500\t0.03215025\n+chr3L\t412500\t417500\t0.007102\n+chr3L\t417500\t422500\t0.01531925\n+chr3L\t422500\t427500\t0.04944275\n+chr3L\t427500\t432500\t0.017395\n+chr3L\t432500\t437500\t0.0233485\n+chr3L\t437500\t442500\t0.010935\n+chr3L\t442500\t447500\t0.015241\n+chr3L\t447500\t452500\t-0.00172725\n+chr3L\t452500\t457500\t-0.006215\n+chr3L\t457500\t462500\t-0.0121685\n+chr3L\t462500\t467500\t-0.0042425\n+chr3L\t467500\t472500\t0.00083775\n+chr3L\t472500\t477500\t-0.02013475\n+chr3L\t477500\t482500\t-0.058266\n+chr3L\t482500\t487500\t-0.07169775\n+chr3L\t487500\t492500\t-0.04601075\n+chr3L\t492500\t497500\t-0.02333825\n+chr3L\t497500\t502500\t-0.00838725\n+chr3L\t502500\t507500\t-0.0641845\n+chr3L\t507500\t512500\t-0.067458\n+chr3L\t512500\t517500\t-0.067458\n+chr3L\t517500\t522500\t-0.09926975\n+chr3L\t522500\t527500\t-0.1060405\n+chr3L\t527500\t532500\t-0.07751675\n+chr3L\t532500\t537500\t-0.07751675\n+chr3L\t537500\t542500\t-0.07751675\n+chr3L\t542500\t547500\t-0.06945475\n+chr3L\t547500\t552500\t-0.06322125\n+chr3L\t552500\t557500\t0.00947925\n+chr3L\t557500\t562500\t-0.02586475\n+chr3L\t562500\t567500\t0.030247\n+chr3L\t567500\t572500\t0.04485875\n+chr3L\t572500\t577500\t0.0579985\n+chr3L\t577500\t582500\t0.085449\n+chr3L\t582500\t587500\t0.10347075\n+chr3L\t587500\t592500\t0.1197795\n+chr3L\t592500\t597500\t0.115187\n+chr3L\t597500\t602500\t0.099483\n+chr3L\t602500\t607500\t0.100333\n+chr3L\t607500\t612500\t0.1935635\n+chr3L\t612500\t6'..b'52500\t27357500\t0.02843225\n+chr3R\t27357500\t27362500\t0.003006\n+chr3R\t27362500\t27367500\t0.02624575\n+chr3R\t27367500\t27372500\t0.01185675\n+chr3R\t27372500\t27377500\t0.0101145\n+chr3R\t27377500\t27382500\t-0.005061\n+chr3R\t27382500\t27387500\t-0.041305\n+chr3R\t27387500\t27392500\t-0.00143125\n+chr3R\t27392500\t27397500\t0.04561275\n+chr3R\t27397500\t27402500\t0.02985575\n+chr3R\t27402500\t27407500\t0.0173185\n+chr3R\t27407500\t27412500\t0.0272775\n+chr3R\t27412500\t27417500\t0.01093175\n+chr3R\t27417500\t27422500\t-0.0499295\n+chr3R\t27422500\t27427500\t-0.04139125\n+chr3R\t27427500\t27432500\t-0.0366555\n+chr3R\t27432500\t27437500\t-0.0366555\n+chr3R\t27437500\t27442500\t-0.04748775\n+chr3R\t27442500\t27447500\t-0.05511025\n+chr3R\t27447500\t27452500\t-0.05736225\n+chr3R\t27452500\t27457500\t-0.0233205\n+chr3R\t27457500\t27462500\t-0.0020265\n+chr3R\t27462500\t27467500\t0.02501975\n+chr3R\t27467500\t27472500\t0.036331\n+chr3R\t27472500\t27477500\t0.036331\n+chr3R\t27477500\t27482500\t0.036331\n+chr3R\t27482500\t27487500\t0.06726625\n+chr3R\t27487500\t27492500\t0.06726625\n+chr3R\t27492500\t27497500\t0.0926245\n+chr3R\t27497500\t27502500\t0.098145\n+chr3R\t27502500\t27507500\t0.088452\n+chr3R\t27507500\t27512500\t0.0991195\n+chr3R\t27512500\t27517500\t0.07477075\n+chr3R\t27517500\t27522500\t0.07477075\n+chr3R\t27522500\t27527500\t0.07477075\n+chr3R\t27527500\t27532500\t0.07477075\n+chr3R\t27532500\t27537500\t0.07667425\n+chr3R\t27537500\t27542500\t0.08198875\n+chr3R\t27542500\t27547500\t0.068792\n+chr3R\t27547500\t27552500\t0.00660575\n+chr3R\t27552500\t27557500\t-0.06866275\n+chr3R\t27557500\t27562500\t-0.063076\n+chr3R\t27562500\t27567500\t-0.063076\n+chr3R\t27567500\t27572500\t-0.08094325\n+chr3R\t27572500\t27577500\t-0.07177225\n+chr3R\t27577500\t27582500\t0.00014175\n+chr3R\t27582500\t27587500\t-0.004425\n+chr3R\t27587500\t27592500\t-0.0055905\n+chr3R\t27592500\t27597500\t0.0107725\n+chr3R\t27597500\t27602500\t0.012076\n+chr3R\t27602500\t27607500\t0.00204375\n+chr3R\t27607500\t27612500\t0.01391525\n+chr3R\t27612500\t27617500\t0.02616875\n+chr3R\t27617500\t27622500\t0.02862975\n+chr3R\t27622500\t27627500\t0.02862975\n+chr3R\t27627500\t27632500\t0.03521625\n+chr3R\t27632500\t27637500\t0.00040125\n+chr3R\t27637500\t27642500\t0.0303095\n+chr3R\t27642500\t27647500\t0.090842\n+chr3R\t27647500\t27652500\t0.10491025\n+chr3R\t27652500\t27657500\t0.11880175\n+chr3R\t27657500\t27662500\t0.09649925\n+chr3R\t27662500\t27667500\t0.07636225\n+chr3R\t27667500\t27672500\t0.06380525\n+chr3R\t27672500\t27677500\t0.04760175\n+chr3R\t27677500\t27682500\t0.02274975\n+chr3R\t27682500\t27687500\t0.015637\n+chr3R\t27687500\t27692500\t0.015637\n+chr3R\t27692500\t27697500\t0.025063\n+chr3R\t27697500\t27702500\t-0.01535\n+chr3R\t27702500\t27707500\t-0.01535\n+chr3R\t27707500\t27712500\t0.00155075\n+chr3R\t27712500\t27717500\t0.006288\n+chr3R\t27717500\t27722500\t0.006288\n+chr3R\t27722500\t27727500\t-0.00858325\n+chr3R\t27727500\t27732500\t0.02622075\n+chr3R\t27732500\t27737500\t0.097312\n+chr3R\t27737500\t27742500\t0.067952\n+chr3R\t27742500\t27747500\t0.0387865\n+chr3R\t27747500\t27752500\t0.01357725\n+chr3R\t27752500\t27757500\t0.02531675\n+chr3R\t27757500\t27762500\t0.033303\n+chr3R\t27762500\t27767500\t0.050386\n+chr3R\t27767500\t27772500\t0.0229625\n+chr3R\t27772500\t27777500\t0.04058825\n+chr3R\t27777500\t27782500\t0.03747975\n+chr3R\t27782500\t27787500\t0.0294565\n+chr3R\t27787500\t27792500\t0.07453225\n+chr3R\t27792500\t27797500\t0.08362425\n+chr3R\t27797500\t27802500\t0.06882\n+chr3R\t27802500\t27807500\t0.075945\n+chr3R\t27807500\t27812500\t0.11806575\n+chr3R\t27812500\t27817500\t0.152855\n+chr3R\t27817500\t27822500\t0.1721425\n+chr3R\t27822500\t27827500\t0.17090925\n+chr3R\t27827500\t27832500\t0.15466375\n+chr3R\t27832500\t27837500\t0.1765955\n+chr3R\t27837500\t27842500\t0.16170225\n+chr3R\t27842500\t27847500\t0.16431675\n+chr3R\t27847500\t27852500\t0.20353925\n+chr3R\t27852500\t27857500\t0.19259975\n+chr3R\t27857500\t27862500\t0.13903775\n+chr3R\t27862500\t27867500\t0.1658075\n+chr3R\t27867500\t27872500\t0.033584\n+chr3R\t27872500\t27877500\t-0.044813\n+chr3R\t27877500\t27882500\t-0.1079445\n+chr3R\t27882500\t27887500\t-0.1024605\n+chr3R\t27887500\t27892500\t-0.09179375\n+chr3R\t27892500\t27897500\t-0.1533095\n+chr3R\t27897500\t27902500\t-0.15876925\n+chr3R\t27902500\t27905026\t0.0\n+chrUextra\t2500\t29002328\t0.0\n+chrM\t2500\t17258\t0.0\n+chr3LHet\t2500\t2555245\t0.0\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/find_TADs/multiNone_tad_score.bm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_TADs/multiNone_tad_score.bm Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 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| diff -r 000000000000 -r a0ab04565c73 test-data/hicFindTADs_TAD_score.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindTADs_TAD_score.tabular Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,25261 @@\n+#{"numberOfProcessors":1,"minDepth":20000,"matrix":"matrix.npz.h5","outFileName":"./tadScoreFile.tabular","binsize":5000,"step":100000,"command":"TAD_score","maxDepth":60000,"zscore_matrix":"./tadScoreFile.tabular_zscore_matrix.h5"}\n+chr2RHet\t0\t5000\t0.000000\n+chr2RHet\t5000\t10000\t-0.095120\n+chr2RHet\t10000\t15000\t-0.086382\n+chr2RHet\t15000\t20000\t-0.080500\n+chr2RHet\t20000\t25000\t-0.075802\n+chr2RHet\t25000\t30000\t0.847009\n+chr2RHet\t30000\t35000\t-0.075802\n+chr2RHet\t35000\t40000\t-0.075802\n+chr2RHet\t40000\t45000\t-0.075802\n+chr2RHet\t45000\t50000\t-0.075802\n+chr2RHet\t50000\t55000\t-0.075802\n+chr2RHet\t55000\t60000\t-0.075802\n+chr2RHet\t60000\t65000\t-0.075802\n+chr2RHet\t65000\t70000\t-0.075802\n+chr2RHet\t70000\t75000\t-0.075802\n+chr2RHet\t75000\t80000\t-0.075802\n+chr2RHet\t80000\t85000\t0.580227\n+chr2RHet\t85000\t90000\t0.580227\n+chr2RHet\t90000\t95000\t0.580227\n+chr2RHet\t95000\t100000\t0.339230\n+chr2RHet\t100000\t105000\t0.339230\n+chr2RHet\t105000\t110000\t-0.075802\n+chr2RHet\t110000\t115000\t-0.075802\n+chr2RHet\t115000\t120000\t-0.075802\n+chr2RHet\t120000\t125000\t1.054400\n+chr2RHet\t125000\t130000\t1.054400\n+chr2RHet\t130000\t135000\t-0.075802\n+chr2RHet\t135000\t140000\t-0.075802\n+chr2RHet\t140000\t145000\t0.339230\n+chr2RHet\t145000\t150000\t0.339230\n+chr2RHet\t150000\t155000\t-0.075802\n+chr2RHet\t155000\t160000\t-0.075802\n+chr2RHet\t160000\t165000\t-0.075802\n+chr2RHet\t165000\t170000\t-0.075802\n+chr2RHet\t170000\t175000\t-0.075802\n+chr2RHet\t175000\t180000\t-0.075802\n+chr2RHet\t180000\t185000\t-0.075802\n+chr2RHet\t185000\t190000\t-0.075802\n+chr2RHet\t190000\t195000\t-0.075802\n+chr2RHet\t195000\t200000\t0.328485\n+chr2RHet\t200000\t205000\t1.712156\n+chr2RHet\t205000\t210000\t1.712156\n+chr2RHet\t210000\t215000\t1.712156\n+chr2RHet\t215000\t220000\t1.056126\n+chr2RHet\t220000\t225000\t-0.075802\n+chr2RHet\t225000\t230000\t-0.075802\n+chr2RHet\t230000\t235000\t-0.075802\n+chr2RHet\t235000\t240000\t-0.075802\n+chr2RHet\t240000\t245000\t-0.075802\n+chr2RHet\t245000\t250000\t-0.075802\n+chr2RHet\t250000\t255000\t-0.075802\n+chr2RHet\t255000\t260000\t-0.075802\n+chr2RHet\t260000\t265000\t-0.075802\n+chr2RHet\t265000\t270000\t-0.075802\n+chr2RHet\t270000\t275000\t-0.075802\n+chr2RHet\t275000\t280000\t-0.075802\n+chr2RHet\t280000\t285000\t-0.075802\n+chr2RHet\t285000\t290000\t-0.075802\n+chr2RHet\t290000\t295000\t-0.075802\n+chr2RHet\t295000\t300000\t-0.075802\n+chr2RHet\t300000\t305000\t-0.075802\n+chr2RHet\t305000\t310000\t-0.075802\n+chr2RHet\t310000\t315000\t-0.075802\n+chr2RHet\t315000\t320000\t-0.075802\n+chr2RHet\t320000\t325000\t-0.075802\n+chr2RHet\t325000\t330000\t-0.075802\n+chr2RHet\t330000\t335000\t-0.075802\n+chr2RHet\t335000\t340000\t-0.075802\n+chr2RHet\t340000\t345000\t-0.075802\n+chr2RHet\t345000\t350000\t-0.075802\n+chr2RHet\t350000\t355000\t-0.075802\n+chr2RHet\t355000\t360000\t-0.075802\n+chr2RHet\t360000\t365000\t-0.075802\n+chr2RHet\t365000\t370000\t-0.075802\n+chr2RHet\t370000\t375000\t-0.075802\n+chr2RHet\t375000\t380000\t1.056126\n+chr2RHet\t380000\t385000\t1.056126\n+chr2RHet\t385000\t390000\t1.056126\n+chr2RHet\t390000\t395000\t1.056126\n+chr2RHet\t395000\t400000\t-0.075802\n+chr2RHet\t400000\t405000\t-0.075802\n+chr2RHet\t405000\t410000\t-0.075802\n+chr2RHet\t410000\t415000\t-0.075802\n+chr2RHet\t415000\t420000\t-0.075802\n+chr2RHet\t420000\t425000\t-0.075802\n+chr2RHet\t425000\t430000\t-0.075802\n+chr2RHet\t430000\t435000\t-0.075802\n+chr2RHet\t435000\t440000\t-0.075802\n+chr2RHet\t440000\t445000\t-0.075802\n+chr2RHet\t445000\t450000\t-0.075802\n+chr2RHet\t450000\t455000\t-0.075802\n+chr2RHet\t455000\t460000\t-0.075802\n+chr2RHet\t460000\t465000\t-0.075802\n+chr2RHet\t465000\t470000\t-0.075802\n+chr2RHet\t470000\t475000\t-0.075802\n+chr2RHet\t475000\t480000\t-0.075802\n+chr2RHet\t480000\t485000\t-0.075802\n+chr2RHet\t485000\t490000\t-0.075802\n+chr2RHet\t490000\t495000\t-0.075802\n+chr2RHet\t495000\t500000\t-0.075802\n+chr2RHet\t500000\t505000\t-0.075802\n+chr2RHet\t505000\t510000\t-0.075802\n+chr2RHet\t510000\t515000\t-0.075802\n+chr2RHet\t515000\t520000\t-0.075802\n+chr2RHet\t520000\t525000\t-0.075802\n+chr2RHet\t525000\t530000\t-0.075802\n+chr2RHet\t530000\t535000\t-0.075802\n+chr2RHet\t535000\t540000\t-0.075802\n+chr2RHet\t540000\t545000\t-0.075802\n+chr2RHet\t545000\t550000\t-0.075802\n+chr2RHet\t550000\t555000\t0.848419\n+chr2RHet\t555000\t560000\t1.504449\n+chr'..b'\n+chr3R\t27375000\t27380000\t-0.202334\n+chr3R\t27380000\t27385000\t-0.202334\n+chr3R\t27385000\t27390000\t-0.202334\n+chr3R\t27390000\t27395000\t-0.202334\n+chr3R\t27395000\t27400000\t0.199516\n+chr3R\t27400000\t27405000\t0.726185\n+chr3R\t27405000\t27410000\t1.190531\n+chr3R\t27410000\t27415000\t0.833625\n+chr3R\t27415000\t27420000\t-0.202334\n+chr3R\t27420000\t27425000\t-0.202334\n+chr3R\t27425000\t27430000\t0.368686\n+chr3R\t27430000\t27435000\t0.691346\n+chr3R\t27435000\t27440000\t0.691346\n+chr3R\t27440000\t27445000\t0.430560\n+chr3R\t27445000\t27450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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/hicFindTADs_find_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindTADs_find_score.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
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| diff -r 000000000000 -r a0ab04565c73 test-data/li_viewpoint_32-33Mb.png |
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| diff -r 000000000000 -r a0ab04565c73 test-data/li_viewpoint_32Mb.png |
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| Binary file test-data/li_viewpoint_32Mb.png has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/master_TADs_plot.png |
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| Binary file test-data/master_TADs_plot.png has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/master_matrix_plot.png |
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| Binary file test-data/master_matrix_plot.png has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/merged_matrix.npz.h5 |
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| Binary file test-data/merged_matrix.npz.h5 has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.bed Wed Mar 07 03:37:57 2018 -0500 |
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| @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B04585 -0.068256362891 . +chrX 87500 92500 B19358 -0.072020401017 . |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.gff Wed Mar 07 03:37:57 2018 -0500 |
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| @@ -0,0 +1,2 @@ +chr2L HiCExplorer boundary 22922500 22927500 -0.068256362891 . . ID=B04585;delta=0.021954846720;pvalue=0.000033964776;tad_sep=-0.068256362891 +chrX HiCExplorer boundary 87500 92500 -0.072020401017 . . ID=B19358;delta=0.019799980104;pvalue=0.000055223433;tad_sep=-0.072020401017 |
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| diff -r 000000000000 -r a0ab04565c73 test-data/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_score.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/multiFDR_tad_score.bm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_tad_score.bm Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 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| diff -r 000000000000 -r a0ab04565c73 test-data/pca1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca1.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
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|
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/pca2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca2.bedgraph Wed Mar 07 03:37:57 2018 -0500 |
| b |
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|
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| diff -r 000000000000 -r a0ab04565c73 test-data/pca2.bw |
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| Binary file test-data/pca2.bw has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/pearson_small_50kb.cool |
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| Binary file test-data/pearson_small_50kb.cool has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/pearson_small_50kb.h5 |
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| Binary file test-data/pearson_small_50kb.h5 has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/pearson_small_50kb_transform.cool |
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| Binary file test-data/pearson_small_50kb_transform.cool has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/raw_qc_report --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_qc_report Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,29 @@ + +File matrix.h5 +Pairs considered 983 +Min rest. site distance 300 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Pairs used 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +One mate low quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 0 (0.00) +self ligation (removed) 0 (0.00) +One mate not close to rest site 0 (0.00) +same fragment 85 (28.33) +self circle 0 (0.00) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +short range < 20kb 61 (28.37) +long range 130 (60.47) +inward pairs 42 (19.53) +outward pairs 66 (30.70) +left pairs 48 (22.33) +right pairs 35 (16.28) |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_matrix_50kb_pearson_pca1_plot.png |
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| Binary file test-data/small_matrix_50kb_pearson_pca1_plot.png has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_matrix_50kb_pearson_pca1_plot.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:37:57 2018 -0500 |
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:Z:22\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6008:2166\t0\tchr3R\t7743490\t41\t50M\t*\t0\t0\tGACGGTCAGTCCGAGAAGCATCTGGAGCCGATGGCCAGTTTCNNNNNGCG\t@@@FFDDDHAHFFFHIJIGIJEIGGGGGHGHIHIFGHJEHDI########\tAS:i:77\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:16G25G0G0G0G0C3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6164:2167\t0\tchrU\t1886379\t2\t14S36M\t*\t0\t0\tCGCATTTGAAAGCTAGCTTTCTAGTTTCACTTGTTTGTTTTTNNNNGTTT\tB@CFFFFFHHHHGJHIIIJJJJIJIIJJJJIJIIIJIGIJJJ########\tAS:i:60\tXS:i:56\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:28T0T0T0T4\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6028:2168\t16\tchr3L\t23880171\t0\t27S23M\t*\t0\t0\tAGGAANNNGGACACTATCGAAAAAGCTAGCTTGCAAAGTTCAAATGACCG\t?B800###IIHC<GGFCIHIJJJJJJIJJJJJIJJIIHHGHGFFFDB@@B\tAS:i:46\tXS:i:46\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:23\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2172\t0\tchr3L\t20041224\t44\t50M\t*\t0\t0\tCGAGGAAGCTGCAAATGGTACGGAGCTGCTGGCTGAGGACGTGTTTGTTG\t@@@BDDDDDFDDF9ABGH<CFFHHHGIIIIGIDEG@F)?FG6B8BB;B@@\tAS:i:96\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T12\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6218:2174\t16\tchr2R\t19978961\t44\t50M\t*\t0\t0\tAGGAGCGTTCGTACAAGCGAAGCTCGCCGGAGGACGACAAGCTGAGGCGC\t3>9;AEEE?G@=@@@/A:=<BDDGIFC:AGIGFCGHBDDFHDDDDDD@@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6240:2175\t16\tchr2L\t8736543\t42\t50M\t*\t0\t0\tTTAAGTGGACTTCGTTAATGTTTTAAATTTGAAGAATATTTTACGAGTTA\tHIGIHEHFBGIIFJJJIGGJJIJJIJJJJJIIIJIJJHHHHHDFFFFB@@\tAS:i:85\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A25C19\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2181\t0\tchr2L\t22737721\t44\t1S49M\t*\t0\t0\tACTCAGTATATATTAAAAGTTTGTTTATACAATATCCTTTTAATAGGTAT\t<@@FFFDDHAHHHJJIEGICHHGFHHEIJJJIIJJJJJIJJGIJIII?FI\tAS:i:98\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:49\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6184:2183\t16\tchr2L\t1627623\t44\t50M\t*\t0\t0\tTTTAGTTATTGGGCTTTAAAAAAATCTAAATTCTGTCATGATTGATTCTG\tJJJJJJIGIIIIIIJIJJJJJJJJJJJJJJIIJIJIJHHHHHFFFFFBCC\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6206:2186\t16\tchr3R\t5530104\t44\t50M\t*\t0\t0\tCACGACGGGACGCCCTAACGGTATCGTGTGTAATTGCAGTTGCACAAGCA\t<@GHCBJIHBJIJJJJJHIJJJIJJJJIGJIIIIGIGHHHGGFDFFFC@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6022:2190\t0\tchr3R\t17305312\t36\t40M10S\t*\t0\t0\tACTATAGAAATCTATTAAAAGTATTCCATGTAAGCTAGCTTCTCCACTGT\t?@@BDDDFG?HHHEHIIIIIIHHIIIIFIGIIIIIIIIIGDDHGFFHDGD\tAS:i:72\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:36T3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2190\t0\tchr2R\t13131924\t36\t36M14S\t*\t0\t0\tATATTGAATTCGAGTCAGAAAAAATAAAACGAAGCTAGCTTATCTGTCAT\tCCCFFDFFGGGHDHHGEIHIIJEIJJJJIJJGIJJJJJJJJJJJJIIIJJ\tAS:i:72\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:36\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6163:2192\t16\tchr2L\t7371337\t2\t26M24S\t*\t0\t0\tGGGTTCTCCACCAGCCGGCAAAAGCTAGCTTAAATTAACTTTTAGTTTTA\tFB)B;B=HD9JJJJIJJJJJJJJJJJJJJJJJJJJJHFHHGHFFFFFCCC\tAS:i:52\tXS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:26\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6060:2193\t16\tchr3R\t9331177\t44\t50M\t*\t0\t0\tGCTTACTCCTTTGCAGCACTAGTACTAATTTTTTATTTTTTCGAATTTTC\tGGHFCHFGGIJJIGIIHGIIEFGDIJJJIJJJJJIJIHHHHHFFFFFCC@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6038:2194\t0\tchrYHet\t283249\t2\t17S33M\t*\t0\t0\tAGGCAGTAAGGCAGTAAGCTAGCTTGCTATGGTATTTTTCCTTAAGTTCC\t@@@DDDDDHHHHHIIGIDC<<EEHICG@?<C>11?ECG<CCDHAAAFFGE\tAS:i:66\tXS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:33\tYT:Z:UU\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_R2_unsorted.bam |
| b |
| Binary file test-data/small_test_R2_unsorted.bam has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_R2_unsorted.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_test_R2_unsorted.sam Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,1000 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| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_matrix.h5 |
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| Binary file test-data/small_test_matrix.h5 has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_matrix_2.h5 |
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| Binary file test-data/small_test_matrix_2.h5 has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_matrix_50kb_res.h5 |
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| Binary file test-data/small_test_matrix_50kb_res.h5 has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_matrix_result.bam |
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| Binary file test-data/small_test_matrix_result.bam has changed |
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| diff -r 000000000000 -r a0ab04565c73 test-data/small_test_matrix_result_sorted.bam |
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| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/tad_classification.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tad_classification.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| b'@@ -0,0 +1,2685 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19389270\t19399952\tactive\t2\t.\t19389270\t19399952\t255,255,153\n+chrX\t19399952\t19416481\tactive\t4\t.\t19399952\t19416481\t255,255,153\n+chrX\t19416481\t19456185\tinactive\t1\t.\t19416481\t19456185\t0,0,0\n+chrX\t19456185\t19473065\tactive\t4\t.\t19456185\t19473065\t255,255,153\n+chrX\t19473065\t19491987\tinactive\t1\t.\t19473065\t19491987\t0,0,0\n+chrX\t19491987\t19507538\tactive\t2\t.\t19491987\t19507538\t255,255,153\n+chrX\t19507538\t19531934\tactive\t4\t.\t19507538\t19531934\t255,255,153\n+chrX\t19531934\t19557899\tactive\t4\t.\t19531934\t19557899\t255,255,153\n+chrX\t19557899\t19577569\tactive\t4\t.\t19557899\t19577569\t255,255,153\n+chrX\t19577569\t19607671\tactive\t4\t.\t19577569\t19607671\t255,255,153\n+chrX\t19607671\t19625150\tinactive\t1\t.\t19607671\t19625150\t0,0,0\n+chrX\t19625150\t19639107\tactive\t2\t.\t19625150\t19639107\t255,255,153\n+chrX\t19639107\t19644907\tactive\t4\t.\t19639107\t19644907\t255,255,153\n+chrX\t19644907\t19657054\tactive\t2\t.\t19644907\t19657054\t255,255,153\n+chrX\t19657054\t19686912\tinactive\t1\t.\t19657054\t19686912\t0,0,0\n+chrX\t19686912\t19745861\tinactive\t1\t.\t19686912\t19745861\t0,0,0\n+chrX\t19745861\t19760530\tactive\t4\t.\t19745861\t19760530\t255,255,153\n+chrX\t19760530\t19815382\tactive\t2\t.\t19760530\t19815382\t255,255,153\n+chrX\t19815382\t19987457\tinactive\t1\t.\t19815382\t19987457\t0,0,0\n+chrX\t19987457\t20054086\tinactive\t1\t.\t19987457\t20054086\t0,0,0\n+chrX\t20054086\t20068910\tactive\t2\t.\t20054086\t20068910\t255,255,153\n+chrX\t20068910\t20125761\tinactive\t1\t.\t20068910\t20125761\t0,0,0\n+chrX\t20125761\t20262048\tinactive\t1\t.\t20125761\t20262048\t0,0,0\n+chrX\t20262048\t20294608\tactive\t4\t.\t20262048\t20294608\t255,255,153\n+chrX\t20294608\t20305771\tactive\t4\t.\t20294608\t20305771\t255,255,153\n+chrX\t20305771\t20339275\tinactive\t1\t.\t20305771\t20339275\t0,0,0\n+chrX\t20339275\t20382809\tactive\t2\t.\t20339275\t20382809\t255,255,153\n+chrX\t20382809\t20395830\tactive\t4\t.\t20382809\t20395830\t255,255,153\n+chrX\t20395830\t20508892\tinactive\t1\t.\t20395830\t20508892\t0,0,0\n+chrX\t20508892\t20526971\tinactive\t1\t.\t20508892\t20526971\t0,0,0\n+chrX\t20526971\t20631727\tinactive\t1\t.\t20526971\t20631727\t0,0,0\n+chrX\t20631727\t20894364\tinactive\t1\t.\t20631727\t20894364\t0,0,0\n+chrX\t20894364\t20907117\tactive\t4\t.\t20894364\t20907117\t255,255,153\n+chrX\t20907117\t20916940\tactive\t4\t.\t20907117\t20916940\t255,255,153\n+chrX\t20916940\t20931445\tactive\t2\t.\t20916940\t20931445\t255,255,153\n+chrX\t20931445\t20944384\tactive\t2\t.\t20931445\t20944384\t255,255,153\n+chrX\t20944384\t20996348\tinactive\t1\t.\t20944384\t20996348\t0,0,0\n+chrX\t20996348\t21012072\tinactive\t1\t.\t20996348\t21012072\t0,0,0\n+chrX\t21012072\t21178100\tinactive\t1\t.\t21012072\t21178100\t0,0,0\n+chrX\t21178100\t21186628\tinactive\t1\t.\t21178100\t21186628\t0,0,0\n+chrX\t21186628\t21194946\tactive\t4\t.\t21186628\t21194946\t255,255,153\n+chrX\t21194946\t21220857\tactive\t4\t.\t21194946\t21220857\t255,255,153\n+chrX\t21220857\t21240098\tactive\t4\t.\t21220857\t21240098\t255,255,153\n+chrX\t21240098\t21271964\tinactive\t1\t.\t21240098\t21271964\t0,0,0\n+chrX\t21271964\t21343699\tinactive\t1\t.\t21271964\t21343699\t0,0,0\n+chrX\t21343699\t21656357\tinactive\t1\t.\t21343699\t21656357\t0,0,0\n+chrX\t21656357\t21857607\tHP1\t3\t.\t21656357\t21857607\t51,160,44\n+chrX\t21857607\t21873688\tactive\t4\t.\t21857607\t21873688\t255,255,153\n+chrX\t21873688\t21889804\tactive\t2\t.\t21873688\t21889804\t255,255,153\n+chrX\t21889804\t21907001\tactive\t4\t.\t21889804\t21907001\t255,255,153\n+chrX\t21907001\t21931844\tinactive\t1\t.\t21907001\t21931844\t0,0,0\n+chrX\t21931844\t21954371\tactive\t2\t.\t21931844\t21954371\t255,255,153\n+chrX\t21954371\t22120033\tinactive\t1\t.\t21954371\t22120033\t0,0,0\n+chrX\t22120033\t22274227\tinactive\t1\t.\t22120033\t22274227\t0,0,0\n+chrX\t22274227\t22287785\tinactive\t1\t.\t22274227\t22287785\t0,0,0\n+chrX\t22287785\t22349277\tinactive\t1\t.\t22287785\t22349277\t0,0,0\n+chrX\t22349277\t22380885\tinactive\t1\t.\t22349277\t22380885\t0,0,0\n+chrX\t22380885\t22421267\tinactive\t1\t.\t22380885\t22421267\t0,0,0\n' |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/tad_score.gz |
| b |
| Binary file test-data/tad_score.gz has changed |
| b |
| diff -r 000000000000 -r a0ab04565c73 test-data/test_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_regions.bed Wed Mar 07 03:37:57 2018 -0500 |
| b |
| @@ -0,0 +1,60 @@ +2L 7998826 7998827 msl2_peak_350 17.17982 +2L 9895070 9895071 msl2_peak_415 6.67520 +2L 14024214 14024215 msl2_peak_602 4.46806 +2L 19791941 19791942 msl2_peak_823 3.40020 +2L 21573354 21573355 msl2_peak_1023 10.76434 +2R 5441451 5441452 msl2_peak_1532 9.54697 +2R 8291271 8291272 msl2_peak_1644 7.36770 +2R 14575573 14575574 msl2_peak_1947 4.41313 +3L 628463 628464 msl2_peak_2780 11.60203 +3L 3903421 3903422 msl2_peak_2958 4.32242 +3L 8759529 8759530 msl2_peak_3195 4.10429 +3R 2901523 2901524 msl2_peak_4559 2.22040 +3R 3932152 3932153 msl2_peak_4603 9.59945 +3R 11851634 11851635 msl2_peak_4969 8.43238 +3R 20545331 20545332 msl2_peak_5267 4.72876 +X 147841 147842 msl2_peak_22671 16.59036 +X 366894 366895 msl2_peak_22686 25.37647 +X 517100 517101 msl2_peak_22694 8.54298 +X 548547 548548 msl2_peak_22696 27.53758 +X 656427 656428 msl2_peak_22697 14.11897 +X 692287 692288 msl2_peak_22698 15.96065 +X 818016 818017 msl2_peak_22713 10.66184 +X 937135 937136 msl2_peak_22717 67.84654 +X 1112721 1112722 msl2_peak_22727 26.81313 +X 1268823 1268824 msl2_peak_22735 29.73846 +X 1356647 1356648 msl2_peak_22736 9.58288 +X 1375009 1375010 msl2_peak_22738 4.49598 +X 1375616 1375617 msl2_peak_22739 128.36397 +X 1409093 1409094 msl2_peak_22742 14.72497 +X 1588015 1588016 msl2_peak_22757 102.61334 +X 1679121 1679122 msl2_peak_22767 16.12354 +X 1754043 1754044 msl2_peak_22769 20.51431 +X 1775025 1775026 msl2_peak_22773 43.05813 +X 1787755 1787756 msl2_peak_22774 142.73460 +X 1798236 1798237 msl2_peak_22775 80.66115 +X 1819545 1819546 msl2_peak_22777 11.21560 +X 1918989 1918990 msl2_peak_22793 74.48118 +X 1956476 1956477 msl2_peak_22794 32.73601 +X 1972291 1972292 msl2_peak_22795 37.39349 +X 2007235 2007236 msl2_peak_22798 11.21560 +X 2015927 2015928 msl2_peak_22799 68.80555 +X 2044335 2044336 msl2_peak_22804 36.60362 +X 2050114 2050115 msl2_peak_22805 47.23102 +X 2072937 2072938 msl2_peak_22807 52.37415 +X 2126007 2126008 msl2_peak_22808 42.23372 +X 2162302 2162303 msl2_peak_22810 78.64520 +X 2237610 2237611 msl2_peak_22817 43.05813 +X 2340287 2340288 msl2_peak_22825 14.72497 +X 2493295 2493296 msl2_peak_22827 23.47760 +X 2503119 2503120 msl2_peak_22828 80.83590 +X 2520611 2520612 msl2_peak_22839 17.87077 +X 2521079 2521080 msl2_peak_22840 60.08352 +X 2613112 2613113 msl2_peak_22844 43.87985 +X 2628624 2628625 msl2_peak_22847 115.37079 +X 3382405 3382406 msl2_peak_22879 6.13203 +X 3593688 3593689 msl2_peak_22908 10.66184 +X 3596515 3596516 msl2_peak_22909 6.59200 +X 3755342 3755343 msl2_peak_22919 164.76546 +X 3848197 3848198 msl2_peak_22920 74.65739 +X 4021813 4021814 msl2_peak_22929 32.73601 |
