| Previous changeset 5:d04398893232 (2018-01-03) Next changeset 7:c14ba4629233 (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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modified:
hicMergeMatrixBins.xml macros.xml test-data/Li_chrX30-35_cool.png test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/diagnostic_plot.png test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicSumMatrices_result1.npz.h5 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/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/raw_qc_report test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_matrix_2.h5 |
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added:
involucro macros.xml.orig test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/hicAggregateContacts_results1.png 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/pearson_small_50kb_transform.cool test-data/test_regions.bed |
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| diff -r d04398893232 -r 8926550196ce hicMergeMatrixBins.xml --- a/hicMergeMatrixBins.xml Wed Jan 03 13:29:09 2018 -0500 +++ b/hicMergeMatrixBins.xml Wed Mar 07 03:45:11 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>Merges bins from a Hi-C matrix</description> <macros> <token name="@BINARY@">hicMergeMatrixBins</token> |
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| diff -r d04398893232 -r 8926550196ce involucro |
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| Binary file involucro has changed |
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| diff -r d04398893232 -r 8926550196ce macros.xml --- a/macros.xml Wed Jan 03 13:29:09 2018 -0500 +++ b/macros.xml Wed Mar 07 03:45:11 2018 -0500 |
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| @@ -1,6 +1,13 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">2.0</token> + <token name="@WRAPPER_VERSION@">2.1</token> + + <token name="@USE_RANGE@"> + #if $use_range.select_use_range == "yes_use_range": + --range $range_min:$range_max + #end if + </token> + <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> @@ -19,6 +26,23 @@ <xml name="zMax"> <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 --> </xml> + <xml name="use_range"> + <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> + <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> + <option value="no_use_range">No restriction</option> + <option value="yes_use_range">Only consider counts within a range</option> + </param> + <when value="no_use_range"/> + <when value="yes_use_range"> + <expand macro='range' /> + </when> + </conditional> + </xml> + + <xml name="range"> + <param name="range_min" type="integer" value="" min="0"/> + <param name="range_max" type="integer" value="" min="0"/> + </xml> <xml name="colormap"> <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"> @@ -300,13 +324,12 @@ <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> </xml> <xml name='matrix_h5_cooler_macro'> - <param name='matrix_h5_cooler' type="data" format="h5,cool" - label="Matrix to compute on."/> - + <param name='matrix_h5_cooler' type="data" format="h5,cool" + label="Matrix to compute on"/> </xml> <xml name='matrix_h5_cooler_multiple_macro'> - <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" - label="Matrix to compute on." multiple="True"/> + <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" + label="Matricies to compute on" multiple="true"/> </xml> <token name="@REFERENCES@"> @@ -556,9 +579,9 @@ <xml name="spacer_macro"> <param name="spacer_width" type="float" value="" optional="True" - label="Include spacer at the end of the track." help="Width of the spacer." /> + label="Include spacer at the end of the track." help="Width of the spacer." /> </xml> <xml name="fontsize_macro"> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> </xml> </macros> |
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| diff -r d04398893232 -r 8926550196ce macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml.orig Wed Mar 07 03:45:11 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 d04398893232 -r 8926550196ce test-data/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.bed Wed Mar 07 03:45:11 2018 -0500 |
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| @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B04585 -0.068256362891 . +chrX 87500 92500 B19358 -0.072020401017 . |
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| diff -r d04398893232 -r 8926550196ce test-data/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.gff Wed Mar 07 03:45:11 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 d04398893232 -r 8926550196ce test-data/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_score.bedgraph Wed Mar 07 03:45:11 2018 -0500 |
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| b'@@ -0,0 +1,23814 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5\n+chrX\t21987500\t21992500\t0.014258261416\n+chrX\t21992500\t21997500\t0.007002028225\n+chrX\t21997500\t22002500\t0.007002028225\n+chrX\t22002500\t22007500\t0.007002028225\n+chrX\t22007500\t22012500\t0.007002028225\n+chrX\t22012500\t22017500\t0.008342793298\n+chrX\t22017500\t22022500\t-0.027906452100\n+chrX\t22022500\t22027500\t-0.011579927421\n+chrX\t22027500\t22032500\t0.018541128313\n+chrX\t22032500\t22037500\t0.060917271058\n+chrX\t22037500\t22042500\t0.096648799655\n+chrX\t22042500\t22047500\t0.101910874976\n+chrX\t22047500\t22052500\t0.171651092137\n+chrX\t22052500\t22057500\t0.155429497270\n+chrX\t22057500\t22062500\t0.164581916727\n+chrX\t22062500\t22067500\t0.173227480473\n+chrX\t22067500\t22072500\t0.106125179900\n+chrX\t22072500\t22077500\t0.080747570696\n+chrX\t22077500\t22082500\t0.106743160746\n+chrX\t22082500\t22087500\t0.132120769950\n+chrX\t22087500\t22092500\t0.132120769950\n+chrX\t22092500\t22097500\t0.096957859903\n+chrX\t22097500\t22102500\t0.052654600230\n+chrX\t22102500\t22107500\t0.048816592592\n+chrX\t22107500\t22112500\t0.024811309127\n+chrX\t22112500\t22117500\t-0.000883655236\n+chrX\t22117500\t22122500\t0.015442869443\n+chrX\t22122500\t22127500\t0.022485603024\n+chrX\t22127500\t22132500\t0.044543449145\n+chrX\t22132500\t22137500\t0.032640726462\n+chrX\t22137500\t22142500\t0.033129068940\n+chrX\t22142500\t22147500\t0.059285004895\n+chrX\t22147500\t22152500\t0.059285004895\n+chrX\t22152500\t22157500\t0.059285004895\n+chrX\t22157500\t22162500\t0.059285004895\n+chrX\t22162500\t22167500\t0.147596677095\n+chrX\t22167500\t22172500\t0.134240838041\n+chrX\t22172500\t22177500\t0.126984604850\n+chrX\t22177500\t22182500\t0.135348355500\n+chrX\t22182500\t22187500\t0.156774459894\n+chrX\t22187500\t22192500\t0.164412573558\n+chrX\t22192500\t22197500\t0.122190643761\n+chrX\t22197500\t22202500\t0.106308425117\n+chrX\t22202500\t22207500\t0.106308425117\n+chrX\t22207500\t22212500\t0.131868113654\n+chrX\t22212500\t22217500\t0.104929080207\n+chrX\t22217500\t22222500\t0.115109012439\n+chrX\t22222500\t22227500\t0.076406798215\n+chrX\t22227500\t22232500\t0.097294803085\n+chrX\t22232500\t22237500\t0.090252069504\n+chrX\t22237500\t22242500\t0.090252069504\n+chrX\t22242500\t22247500\t0.056001520895\n+chrX\t22247500\t22252500\t0.056001520895\n+chrX\t22252500\t22257500\t0.031199069260\n+chrX\t22257500\t22262500\t0.031363850474\n+chrX\t22262500\t22267500\t-0.007556876367\n+chrX\t22267500\t22272500\t-0.006993474280\n+chrX\t22272500\t22277500\t-0.020337459503\n+chrX\t22277500\t22282500\t0.006546907334\n+chrX\t22282500\t22287500\t0.038722263967\n+chrX\t22287500\t22292500\t0.028601375545\n+chrX\t22292500\t22297500\t0.022101371933\n+chrX\t22297500\t22302500\t0.022499357552\n+chrX\t22302500\t22307500\t0.129379428086\n+chrX\t22307500\t22312500\t0.171671654101\n+chrX\t22312500\t22317500\t0.201364155908\n+chrX\t22317500\t22322500\t0.229564260376\n+chrX\t22322500\t22327500\t0.229859357747\n+chrX\t22327500\t22332500\t0.272616621770\n+chrX\t22332500\t22337500\t0.237284734617\n+chrX\t22337500\t22342500\t0.198850098100\n+chrX\t22342500\t22347500\t0.191681320909\n+chrX\t22347500\t22352500\t0.202835839679\n+chrX\t22352500\t22357500\t0.215783374482\n+chrX\t22357500\t22362500\t0.230956918733\n+chrX\t22362500\t22367500\t0.177785960304\n+chrX\t22367500\t22372500\t0.171517172517\n+chrX\t22372500\t22377500\t0.164090449782\n+chrX\t22377500\t22382500\t0.193182460259\n+chrX\t22382500\t22387500\t0.128770173959\n+chrX\t22387500\t22392500\t-0.008920627195\n+chrX\t22392500\t22397500\t0.004303375190\n+chrX\t22397500\t22402500\t-0.087847665198\n+chrX\t22402500\t22407500\t-0.090053401346\n+chrX\t22407500\t22412500\t-0.092797878579\n+chrX\t22412500\t22417500\t-0.096193150539\n+chrX\t22417500\t22421413\t0.000000000000\n+chrXHet\t2500\t202056\t0.000000000000\n+chrYHet\t2500\t346019\t0.000000000000\n' |
| b |
| diff -r d04398893232 -r 8926550196ce 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 03:45:11 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 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|
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| diff -r d04398893232 -r 8926550196ce test-data/multiFDR_zscore_matrix.h5 |
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| Binary file test-data/multiFDR_zscore_matrix.h5 has changed |
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| diff -r d04398893232 -r 8926550196ce test-data/obs_exp_small_50kb.cool |
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| Binary file test-data/obs_exp_small_50kb.cool has changed |
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| diff -r d04398893232 -r 8926550196ce test-data/obs_exp_small_50kb.h5 |
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| Binary file test-data/obs_exp_small_50kb.h5 has changed |
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| diff -r d04398893232 -r 8926550196ce test-data/pca1.bedgraph --- a/test-data/pca1.bedgraph Wed Jan 03 13:29:09 2018 -0500 +++ b/test-data/pca1.bedgraph Wed Mar 07 03:45:11 2018 -0500 |
| b |
| b'@@ -1,1145 +1,1145 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chr2RHet\t2000000\t2050000\t0.000000000000\n-chr2RHet\t2050000\t2100000\t-0.149103236664\n-chr2RHet\t2100000\t2150000\t-0.068106793337\n-chr2RHet\t2150000\t2200000\t-0.074447119055\n-chr2RHet\t2200000\t2250000\t-0.106426882635\n-chr2RHet\t2250000\t2300000\t-0.128602801613\n-chr2RHet\t2300000\t2350000\t-0.180547894737\n-chr2RHet\t2350000\t2400000\t-0.170497365083\n-chr2RHet\t2400000\t2450000\t-0.032159018102\n-chr2RHet\t2550000\t2600000\t-0.120071184197\n-chr2RHet\t2600000\t2650000\t-0.004828668875\n+chr2RHet\t2050000\t2100000\t0.226048172597\n+chr2RHet\t2100000\t2150000\t-0.009032181245\n+chr2RHet\t2150000\t2200000\t-0.156931793125\n+chr2RHet\t2200000\t2250000\t-0.076913071464\n+chr2RHet\t2250000\t2300000\t0.013015414891\n+chr2RHet\t2300000\t2350000\t0.260358373936\n+chr2RHet\t2350000\t2400000\t0.170971324927\n+chr2RHet\t2400000\t2450000\t-0.112722101985\n+chr2RHet\t2550000\t2600000\t0.012191890450\n+chr2RHet\t2600000\t2650000\t-0.022853015897\n chr2RHet\t2750000\t2800000\t0.000000000000\n-chr2RHet\t2800000\t2850000\t-0.005101482828\n-chr2RHet\t2850000\t2900000\t-0.000992135835\n-chr2RHet\t2900000\t2950000\t-0.000992135835\n+chr2RHet\t2800000\t2850000\t-0.025282155888\n+chr2RHet\t2850000\t2900000\t-0.007270539302\n+chr2RHet\t2900000\t2950000\t-0.007270539302\n chr2RHet\t3000000\t3050000\t0.000'..b'\t400000\t-0.500000000000\n chrUextra\t400000\t450000\t0.000000000000\n chrUextra\t450000\t500000\t0.000000000000\n chrUextra\t500000\t550000\t0.000000000000\n@@ -2669,49 +2669,49 @@\n chrUextra\t28150000\t28200000\t0.000000000000\n chrUextra\t28650000\t28700000\t0.000000000000\n chr3LHet\t0\t50000\t0.000000000000\n-chr3LHet\t200000\t250000\t0.144509113902\n-chr3LHet\t250000\t300000\t0.145646037045\n-chr3LHet\t300000\t350000\t0.118985357619\n-chr3LHet\t350000\t400000\t0.043423176974\n-chr3LHet\t400000\t450000\t0.028483551995\n-chr3LHet\t450000\t500000\t0.155229023170\n-chr3LHet\t500000\t550000\t0.167032856035\n-chr3LHet\t550000\t600000\t-0.029445295268\n-chr3LHet\t600000\t650000\t0.175757900533\n-chr3LHet\t650000\t700000\t0.044986523886\n-chr3LHet\t700000\t750000\t0.089036809909\n-chr3LHet\t750000\t800000\t0.189426816665\n-chr3LHet\t800000\t850000\t-0.265646838742\n-chr3LHet\t850000\t900000\t0.221831756303\n-chr3LHet\t900000\t950000\t0.178725974166\n-chr3LHet\t950000\t1000000\t0.009104035833\n-chr3LHet\t1000000\t1050000\t-0.250828406646\n-chr3LHet\t1050000\t1100000\t0.005927138353\n-chr3LHet\t1100000\t1150000\t0.015496712512\n-chr3LHet\t1150000\t1200000\t0.247273827380\n-chr3LHet\t1200000\t1250000\t0.174397654007\n-chr3LHet\t1250000\t1300000\t-0.205398010788\n-chr3LHet\t1300000\t1350000\t-0.103032791480\n-chr3LHet\t1350000\t1400000\t0.080660632206\n-chr3LHet\t1400000\t1450000\t0.053520493661\n+chr3LHet\t200000\t250000\t-0.210056157210\n+chr3LHet\t250000\t300000\t-0.278330320933\n+chr3LHet\t300000\t350000\t-0.055100055965\n+chr3LHet\t350000\t400000\t-0.069642912829\n+chr3LHet\t400000\t450000\t-0.083316978782\n+chr3LHet\t450000\t500000\t-0.140301691658\n+chr3LHet\t500000\t550000\t0.269481838116\n+chr3LHet\t550000\t600000\t-0.005358082584\n+chr3LHet\t600000\t650000\t-0.319092470373\n+chr3LHet\t650000\t700000\t0.229084689369\n+chr3LHet\t700000\t750000\t0.152302615974\n+chr3LHet\t750000\t800000\t0.256485434822\n+chr3LHet\t800000\t850000\t0.068577471044\n+chr3LHet\t850000\t900000\t0.348905816697\n+chr3LHet\t900000\t950000\t-0.045867421719\n+chr3LHet\t950000\t1000000\t0.015178610180\n+chr3LHet\t1000000\t1050000\t0.005353441294\n+chr3LHet\t1050000\t1100000\t-0.077444381781\n+chr3LHet\t1100000\t1150000\t-0.037035229858\n+chr3LHet\t1150000\t1200000\t0.355887225929\n+chr3LHet\t1200000\t1250000\t-0.276957717661\n+chr3LHet\t1250000\t1300000\t-0.057145437346\n+chr3LHet\t1300000\t1350000\t0.029163723803\n+chr3LHet\t1350000\t1400000\t-0.069551840640\n+chr3LHet\t1400000\t1450000\t-0.029448632444\n chr3LHet\t1450000\t1500000\t0.000000000000\n-chr3LHet\t1500000\t1550000\t0.111775730828\n-chr3LHet\t1550000\t1600000\t0.082008066935\n-chr3LHet\t1600000\t1650000\t-0.020338141452\n-chr3LHet\t1650000\t1700000\t-0.220317246321\n-chr3LHet\t1700000\t1750000\t0.128077572584\n-chr3LHet\t1750000\t1800000\t-0.047849168769\n-chr3LHet\t1800000\t1850000\t-0.009032304931\n-chr3LHet\t1850000\t1900000\t0.264650385615\n-chr3LHet\t1900000\t1950000\t-0.009306004735\n-chr3LHet\t1950000\t2000000\t-0.045777533627\n-chr3LHet\t2000000\t2050000\t0.012202721174\n-chr3LHet\t2050000\t2100000\t-0.173614339488\n-chr3LHet\t2100000\t2150000\t0.096991371407\n-chr3LHet\t2150000\t2200000\t-0.216598240748\n-chr3LHet\t2200000\t2250000\t0.088166994456\n-chr3LHet\t2250000\t2300000\t-0.018145354633\n-chr3LHet\t2350000\t2400000\t-0.206664945110\n-chr3LHet\t2400000\t2450000\t-0.147187884513\n-chr3LHet\t2450000\t2500000\t-0.191085296488\n-chr3LHet\t2500000\t2550000\t-0.296583312679\n+chr3LHet\t1500000\t1550000\t-0.048835301188\n+chr3LHet\t1550000\t1600000\t0.134916091147\n+chr3LHet\t1600000\t1650000\t0.002820924111\n+chr3LHet\t1650000\t1700000\t0.050068885530\n+chr3LHet\t1700000\t1750000\t-0.289127295687\n+chr3LHet\t1750000\t1800000\t0.015375380499\n+chr3LHet\t1800000\t1850000\t-0.025843566926\n+chr3LHet\t1850000\t1900000\t0.218661985809\n+chr3LHet\t1900000\t1950000\t-0.003333591616\n+chr3LHet\t1950000\t2000000\t0.007516537831\n+chr3LHet\t2000000\t2050000\t-0.081389328152\n+chr3LHet\t2050000\t2100000\t0.023356421879\n+chr3LHet\t2100000\t2150000\t-0.056498312798\n+chr3LHet\t2150000\t2200000\t0.075990113878\n+chr3LHet\t2200000\t2250000\t-0.033435151720\n+chr3LHet\t2250000\t2300000\t-0.003463835990\n+chr3LHet\t2350000\t2400000\t0.045158473409\n+chr3LHet\t2400000\t2450000\t0.012934382803\n+chr3LHet\t2450000\t2500000\t0.046643643739\n+chr3LHet\t2500000\t2550000\t0.038522077967\n' |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pca2.bedgraph --- a/test-data/pca2.bedgraph Wed Jan 03 13:29:09 2018 -0500 +++ b/test-data/pca2.bedgraph Wed Mar 07 03:45:11 2018 -0500 |
| b |
| b'@@ -1,60 +1,60 @@\n-chr2RHet\t0\t50000\t0.177193350469\n-chr2RHet\t50000\t100000\t0.032204538347\n-chr2RHet\t100000\t150000\t-0.282387463612\n-chr2RHet\t150000\t200000\t0.011825630271\n-chr2RHet\t200000\t250000\t0.041231230909\n-chr2RHet\t300000\t350000\t0.002926389428\n-chr2RHet\t350000\t400000\t-0.254508542308\n-chr2RHet\t400000\t450000\t0.026450269267\n-chr2RHet\t450000\t500000\t-0.240952240415\n-chr2RHet\t500000\t550000\t0.293599828712\n-chr2RHet\t550000\t600000\t0.289808428461\n-chr2RHet\t600000\t650000\t-0.303424484938\n-chr2RHet\t650000\t700000\t-0.021093016199\n-chr2RHet\t700000\t750000\t-0.010960418117\n-chr2RHet\t750000\t800000\t-0.289273219599\n-chr2RHet\t800000\t850000\t0.091930713152\n-chr2RHet\t850000\t900000\t-0.128622195308\n-chr2RHet\t900000\t950000\t0.002472300051\n-chr2RHet\t950000\t1000000\t-0.114441574570\n-chr2RHet\t1000000\t1050000\t-0.017909752708\n-chr2RHet\t1050000\t1100000\t0.016855223244\n+chr2RHet\t0\t50000\t-0.177193350469\n+chr2RHet\t50000\t100000\t-0.032204538347\n+chr2RHet\t100000\t150000\t0.282387463612\n+chr2RHet\t150000\t200000\t-0.011825630271\n+chr2RHet\t200000\t250000\t-0.041231230909\n+chr2RHet\t300000\t350000\t-0.002926389428\n+chr2RHet\t350000\t400000\t0.254508542308\n+chr2RHet\t400000\t450000\t-0.026450269267\n+chr2RHet\t450000\t500000\t0.240952240415\n+chr2RHet\t500000\t550000\t-0.293599828712\n+chr2RHet\t550000\t600000\t-0.289808428461\n+chr2RHet\t600000\t650000\t0.303424484938\n+chr2RHet\t650000\t700000\t0.021093016199\n+chr2RHet\t700000\t750000\t0.010960418117\n+chr2RHet\t750000\t800000\t0.289273219599\n+chr2RHet\t800000\t850000\t-0.091930713152\n+chr2RHet\t850000\t900000\t0.128622195308\n+chr2RHet\t900000\t950000\t-0.002472300051\n+chr2RHet\t950000\t1000000\t0.114441574570\n+chr2RHet\t1000000\t1050000\t0.017909752708\n+chr2RHet\t1050000\t1100000\t-0.016855223244\n chr2RHet\t1100000\t1150000\t0.000000000000\n-chr2RHet\t1250000\t1300000\t-0.102697089188\n-chr2RHet\t1300000\t1350000\t-0.075340309339\n-chr2RHet\t1350000\t1400000\t0.035326054956\n-chr2RHet\t1400000\t1450000\t0.141721952912\n-chr2RHet\t1450000\t1500000\t-0.051213364907\n+chr2RHet\t1250000\t1300000\t0.102697089188\n+chr2RHet\t1300000\t1350000\t0.075340309339\n+chr2RHet\t1350000\t1400000\t-0.035326054956\n+chr2RHet\t1400000\t1450000\t-0.141721952912\n+chr2RHet\t1450000\t1500000\t0.051213364907\n chr2RHet\t1500000\t1550000\t0.000000000000\n-chr2RHet\t1550000\t1600000\t0.288446354623\n-chr2RHet\t1600000\t1650000\t-0.027506039012\n-chr2RHet\t1650000\t1700000\t-0.050134411794\n-chr2RHet\t1700000\t1750000\t-0.013977802418\n+chr2RHet\t1550000\t1600000\t-0.288446354623\n+chr2RHet\t1600000\t1650000\t0.027506039012\n+chr2RHet\t1650000\t1700000\t0.050134411794\n+chr2RHet\t1700000\t1750000\t0.013977802418\n chr2RHet\t1750000\t1800000\t0.000000000000\n-chr2RHet\t1850000\t1900000\t0.062535524405\n-chr2RHet\t1900000\t1950000\t0.102423419951\n-chr2RHet\t1950000\t2000000\t0.000255452186\n+chr2RHet\t1850000\t1900000\t-0.062535524405\n+chr2RHet\t1900000\t1950000\t-0.102423419951\n+chr2RHet\t1950000\t2000000\t-0.000255452186\n 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chrUextra\t0\t50000\t0.000000000000\n chrUextra\t50000\t100000\t-0.500000000000\n chrUextra\t100000\t150000\t0.000000000000\n' |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pca2.bw |
| b |
| Binary file test-data/pca2.bw has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pearson_small_50kb.cool |
| b |
| Binary file test-data/pearson_small_50kb.cool has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pearson_small_50kb.h5 |
| b |
| Binary file test-data/pearson_small_50kb.h5 has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/pearson_small_50kb_transform.cool |
| b |
| Binary file test-data/pearson_small_50kb_transform.cool has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/raw_qc_report --- a/test-data/raw_qc_report Wed Jan 03 13:29:09 2018 -0500 +++ b/test-data/raw_qc_report Wed Mar 07 03:45:11 2018 -0500 |
| b |
| @@ -1,5 +1,5 @@ -File text_matrix.h5 +File matrix.h5 Pairs considered 983 Min rest. site distance 300 Max library insert size 1000 |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/small_matrix_50kb_pearson_pca1_plot.svg --- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Jan 03 13:29:09 2018 -0500 +++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:45:11 2018 -0500 |
| b |
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| diff -r d04398893232 -r 8926550196ce test-data/small_test_matrix_2.h5 |
| b |
| Binary file test-data/small_test_matrix_2.h5 has changed |
| b |
| diff -r d04398893232 -r 8926550196ce test-data/test_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_regions.bed Wed Mar 07 03:45:11 2018 -0500 |
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