| Previous changeset 2:3106dcd651f5 (2018-01-03) Next changeset 4:d5bf6e7d3800 (2018-04-27) |
|
Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 |
|
modified:
hicTransform.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 |
|
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 |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 hicTransform.xml --- a/hicTransform.xml Wed Jan 03 13:31:00 2018 -0500 +++ b/hicTransform.xml Wed Mar 07 03:41:00 2018 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description> <macros> <token name="@BINARY@">hicTransform</token> @@ -54,7 +54,7 @@ <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> <param name="outputFormat" value="cool" /> <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/> - <output name="pearson" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/> + <output name="pearson" file="pearson_small_50kb_transform.cool" ftype="cool" compare="sim_size"/> <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/> </test> </tests> |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 involucro |
| b |
| Binary file involucro has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 macros.xml --- a/macros.xml Wed Jan 03 13:31:00 2018 -0500 +++ b/macros.xml Wed Mar 07 03:41:00 2018 -0500 |
| b |
| @@ -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> |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml.orig Wed Mar 07 03:41:00 2018 -0500 |
| [ |
| 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' |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/Li_chrX30-35_cool.png |
| b |
| Binary file test-data/Li_chrX30-35_cool.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/compare_matrices_log2ratio.h5 |
| b |
| Binary file test-data/compare_matrices_log2ratio.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/compare_matrices_pearson_ratio.cool |
| b |
| Binary file test-data/compare_matrices_pearson_ratio.cool has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/covariance_small_50kb.cool |
| b |
| Binary file test-data/covariance_small_50kb.cool has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/covariance_small_50kb.h5 |
| b |
| Binary file test-data/covariance_small_50kb.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/diagnostic_plot.png |
| b |
| Binary file test-data/diagnostic_plot.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicAggregateContacts_results1.png |
| b |
| Binary file test-data/hicAggregateContacts_results1.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicCorrectMatrix_result1.npz.h5 |
| b |
| Binary file test-data/hicCorrectMatrix_result1.npz.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicCorrelate_heatmap_result1.png |
| b |
| Binary file test-data/hicCorrelate_heatmap_result1.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicCorrelate_scatter_result1.png |
| b |
| Binary file test-data/hicCorrelate_scatter_result1.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicMergeMatrixBins_result1.npz.h5 |
| b |
| Binary file test-data/hicMergeMatrixBins_result1.npz.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicPlotDistVsCounts_result2.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result2.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/hicSumMatrices_result1.npz.h5 |
| b |
| Binary file test-data/hicSumMatrices_result1.npz.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/li_viewpoint_32-33Mb.png |
| b |
| Binary file test-data/li_viewpoint_32-33Mb.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/li_viewpoint_32Mb.png |
| b |
| Binary file test-data/li_viewpoint_32Mb.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/master_TADs_plot.png |
| b |
| Binary file test-data/master_TADs_plot.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/master_matrix_plot.png |
| b |
| Binary file test-data/master_matrix_plot.png has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.bed Wed Mar 07 03:41:00 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B04585 -0.068256362891 . +chrX 87500 92500 B19358 -0.072020401017 . |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.gff Wed Mar 07 03:41:00 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_score.bedgraph Wed Mar 07 03:41:00 2018 -0500 |
| b |
| b'@@ -0,0 +1,23814 @@\n+chr2L\t2500\t7500\t-0.164488846397\n+chr2L\t7500\t12500\t0.004155516280\n+chr2L\t12500\t17500\t0.260509497302\n+chr2L\t17500\t22500\t0.126728724578\n+chr2L\t22500\t27500\t0.107536542495\n+chr2L\t27500\t32500\t0.067996441287\n+chr2L\t32500\t37500\t0.180067325085\n+chr2L\t37500\t42500\t0.188704045555\n+chr2L\t42500\t47500\t0.123071283383\n+chr2L\t47500\t52500\t0.090946822420\n+chr2L\t52500\t57500\t0.050290136708\n+chr2L\t57500\t62500\t0.043738171585\n+chr2L\t62500\t67500\t0.036458137676\n+chr2L\t67500\t72500\t-0.008311665224\n+chr2L\t72500\t77500\t-0.025506335364\n+chr2L\t77500\t82500\t-0.028782499450\n+chr2L\t82500\t87500\t-0.008859983289\n+chr2L\t87500\t92500\t0.012581289189\n+chr2L\t92500\t97500\t-0.026656341295\n+chr2L\t97500\t102500\t-0.064470557052\n+chr2L\t102500\t107500\t-0.022699733707\n+chr2L\t107500\t112500\t-0.026264267296\n+chr2L\t112500\t117500\t-0.009926677809\n+chr2L\t117500\t122500\t-0.006876513913\n+chr2L\t122500\t127500\t0.016147318959\n+chr2L\t127500\t132500\t0.022378914981\n+chr2L\t132500\t137500\t0.070952047599\n+chr2L\t137500\t142500\t0.071053469305\n+chr2L\t142500\t147500\t0.068034199638\n+chr2L\t147500\t152500\t0.067090397637\n+chr2L\t152500\t157500\t0.057311311696\n+chr2L\t157500\t162500\t0.067610279560\n+chr2L\t162500\t167500\t0.029002777185\n+chr2L\t167500\t172500\t0.029002777185\n+chr2L\t172500\t177500\t0.008980247068\n+chr2L\t177500\t182500\t0.016907224460\n+chr2L\t182500\t187500\t-0.000150569937\n+chr2L\t187500\t192500\t0.010495785312\n+chr2L\t192500\t197500\t-0.048163268016\n+chr2L\t197500\t202500\t-0.039867994837\n+chr2L\t202500\t207500\t-0.046910414090\n+chr2L\t207500\t212500\t-0.055696730183\n+chr2L\t212500\t217500\t-0.036501614110\n+chr2L\t217500\t222500\t-0.036501614110\n+chr2L\t222500\t227500\t-0.023335648652\n+chr2L\t227500\t232500\t-0.023335648652\n+chr2L\t232500\t237500\t-0.038011760274\n+chr2L\t237500\t242500\t-0.040574053585\n+chr2L\t242500\t247500\t-0.052320501930\n+chr2L\t247500\t252500\t-0.065486467388\n+chr2L\t252500\t257500\t-0.053000848584\n+chr2L\t257500\t262500\t-0.053000848584\n+chr2L\t262500\t267500\t-0.022469370040\n+chr2L\t267500\t272500\t-0.038170498789\n+chr2L\t272500\t277500\t-0.059012201761\n+chr2L\t277500\t282500\t-0.086006441495\n+chr2L\t282500\t287500\t-0.053031533287\n+chr2L\t287500\t292500\t-0.053031533287\n+chr2L\t292500\t297500\t-0.083051915395\n+chr2L\t297500\t302500\t-0.083051915395\n+chr2L\t302500\t307500\t-0.051758175573\n+chr2L\t307500\t312500\t-0.044639541179\n+chr2L\t312500\t317500\t-0.043712800180\n+chr2L\t317500\t322500\t-0.019156222003\n+chr2L\t322500\t327500\t-0.017442079268\n+chr2L\t327500\t332500\t0.041070352715\n+chr2L\t332500\t337500\t0.049256940562\n+chr2L\t337500\t342500\t0.053147123147\n+chr2L\t342500\t347500\t0.053147123147\n+chr2L\t347500\t352500\t0.078905602777\n+chr2L\t352500\t357500\t0.093459536727\n+chr2L\t357500\t362500\t0.079684892703\n+chr2L\t362500\t367500\t0.063143859889\n+chr2L\t367500\t372500\t0.092016050812\n+chr2L\t372500\t377500\t0.061075544744\n+chr2L\t377500\t382500\t0.013498603323\n+chr2L\t382500\t387500\t0.029781933737\n+chr2L\t387500\t392500\t-0.021388944213\n+chr2L\t392500\t397500\t-0.038792978876\n+chr2L\t397500\t402500\t-0.050263472402\n+chr2L\t402500\t407500\t-0.044321193230\n+chr2L\t407500\t412500\t-0.007732343879\n+chr2L\t412500\t417500\t-0.013295314500\n+chr2L\t417500\t422500\t-0.013295314500\n+chr2L\t422500\t427500\t-0.021132388853\n+chr2L\t427500\t432500\t-0.021015012893\n+chr2L\t432500\t437500\t-0.015982567418\n+chr2L\t437500\t442500\t-0.049145302596\n+chr2L\t442500\t447500\t-0.064964420946\n+chr2L\t447500\t452500\t-0.051664858126\n+chr2L\t452500\t457500\t-0.071914886809\n+chr2L\t457500\t462500\t-0.069724393991\n+chr2L\t462500\t467500\t-0.069724393991\n+chr2L\t467500\t472500\t-0.059605045512\n+chr2L\t472500\t477500\t-0.051309772332\n+chr2L\t477500\t482500\t-0.048373705573\n+chr2L\t482500\t487500\t-0.048373705573\n+chr2L\t487500\t492500\t-0.014227247533\n+chr2L\t492500\t497500\t-0.064541001831\n+chr2L\t497500\t502500\t-0.064541001831\n+chr2L\t502500\t507500\t-0.056245728652\n+chr2L\t507500\t512500\t-0.064541001831\n+chr2L\t512500\t517500\t-0.071946857401\n+chr2L\t517500\t522500\t-0.071946857401\n+chr2L\t522500\t527500\t-0.071946857401\n+chr2L\t527500\t532500\t-0.076979302876\n+chr2L\t532500\t537500\t-0.076979302876\n+chr2L\t537500\t542500\t-0.076979302876\n+chr2L\t542500\t547500\t-0.120135452320\n+chr2L\t547500\t552500\t-0.10'..b'873550\n+chrX\t21922500\t21927500\t-0.021312400735\n+chrX\t21927500\t21932500\t-0.057645152033\n+chrX\t21932500\t21937500\t-0.057645152033\n+chrX\t21937500\t21942500\t-0.036897150779\n+chrX\t21942500\t21947500\t-0.036897150779\n+chrX\t21947500\t21952500\t-0.036897150779\n+chrX\t21952500\t21957500\t-0.053223675458\n+chrX\t21957500\t21962500\t-0.012125141728\n+chrX\t21962500\t21967500\t0.014172905654\n+chrX\t21967500\t21972500\t0.014172905654\n+chrX\t21972500\t21977500\t0.014172905654\n+chrX\t21977500\t21982500\t-0.008400059504\n+chrX\t21982500\t21987500\t0.007215527835\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 3106dcd651f5 -r 303558d3bc11 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 03:41:00 2018 -0500 |
| b |
| b'@@ -0,0 +1,23830 @@\n+#{"step":20000,"minDepth":60000,"maxDepth":180000,"binsize":5000}\n+chr2L\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr2L\t5000\t10000\t-0.190625\t-0.174707\t-0.154720\t-0.137904\n+chr2L\t10000\t15000\t0.066682\t0.018642\t-0.025257\t-0.043446\n+chr2L\t15000\t20000\t0.322345\t0.375915\t0.213391\t0.130387\n+chr2L\t20000\t25000\t0.151060\t0.206256\t0.100913\t0.048686\n+chr2L\t25000\t30000\t0.223202\t0.136530\t0.054937\t0.015478\n+chr2L\t30000\t35000\t0.162034\t0.091008\t0.025000\t-0.006056\n+chr2L\t35000\t40000\t0.278414\t0.244807\t0.127984\t0.069064\n+chr2L\t40000\t45000\t0.345475\t0.229249\t0.118039\t0.062053\n+chr2L\t45000\t50000\t0.244443\t0.153776\t0.068088\t0.025978\n+chr2L\t50000\t55000\t0.194732\t0.116754\t0.043771\t0.008530\n+chr2L\t55000\t60000\t0.131922\t0.069954\t0.012953\t-0.013669\n+chr2L\t60000\t65000\t0.110947\t0.054570\t0.003034\t0.006401\n+chr2L\t65000\t70000\t0.110947\t0.041677\t-0.005275\t-0.001516\n+chr2L\t70000\t75000\t0.046047\t-0.010891\t-0.040001\t-0.028401\n+chr2L\t75000\t80000\t-0.017064\t-0.022169\t-0.047198\t-0.015595\n+chr2L\t80000\t85000\t-0.017064\t-0.027382\t-0.050361\t-0.020323\n+chr2L\t85000\t90000\t0.016118\t-0.039716\t-0.016677\t0.004835\n+chr2L\t90000\t95000\t0.041799\t-0.025271\t-0.012418\t0.046215\n+chr2L\t95000\t100000\t-0.054440\t-0.050431\t-0.030731\t0.028976\n+chr2L\t100000\t105000\t-0.096240\t-0.102918\t-0.061669\t0.002945\n+chr2L\t105000\t110000\t-0.054522\t-0.046705\t-0.010830\t0.021258\n+chr2L\t110000\t115000\t-0.057517\t-0.048390\t-0.015117\t0.015967\n+chr2L\t115000\t120000\t-0.021451\t-0.028103\t-0.008769\t0.018616\n+chr2L\t120000\t125000\t-0.021451\t-0.028103\t0.007490\t0.014557\n+chr2L\t125000\t130000\t0.036764\t0.009461\t0.007490\t0.010874\n+chr2L\t130000\t135000\t0.032259\t0.044144\t0.006364\t0.006749\n+chr2L\t135000\t140000\t0.132222\t0.100373\t0.031355\t0.019858\n+chr2L\t140000\t145000\t0.134148\t0.101456\t0.031836\t0.016774\n+chr2L\t145000\t150000\t0.073990\t0.131362\t0.045128\t0.021656\n+chr2L\t150000\t155000\t0.106030\t0.112168\t0.036597\t0.013567\n+chr2L\t155000\t160000\t0.133532\t0.059076\t0.029695\t0.006942\n+chr2L\t160000\t165000\t0.133532\t0.102675\t0.029695\t0.004539\n+chr2L\t165000\t170000\t0.071956\t0.028910\t0.012210\t0.002935\n+chr2L\t170000\t175000\t0.071956\t0.028910\t0.012210\t0.002935\n+chr2L\t175000\t180000\t0.030773\t0.005744\t0.001914\t-0.002510\n+chr2L\t180000\t185000\t0.058380\t0.021273\t0.008816\t-0.020839\n+chr2L\t185000\t190000\t0.053874\t-0.018479\t-0.006865\t-0.029133\n+chr2L\t190000\t195000\t0.065421\t-0.011983\t0.009188\t-0.020642\n+chr2L\t195000\t200000\t-0.046647\t-0.075021\t-0.035524\t-0.035461\n+chr2L\t200000\t205000\t-0.029585\t-0.065424\t-0.031258\t-0.033205\n+chr2L\t205000\t210000\t-0.071569\t-0.028418\t-0.047355\t-0.040300\n+chr2L\t210000\t215000\t-0.071569\t-0.028418\t-0.063896\t-0.058904\n+chr2L\t215000\t220000\t-0.005316\t-0.022150\t-0.061110\t-0.057431\n+chr2L\t220000\t225000\t-0.005316\t-0.022150\t-0.061110\t-0.057431\n+chr2L\t225000\t230000\t0.047347\t-0.022150\t-0.061110\t-0.057431\n+chr2L\t230000\t235000\t0.047347\t-0.022150\t-0.061110\t-0.057431\n+chr2L\t235000\t240000\t0.017161\t-0.039130\t-0.068656\t-0.061422\n+chr2L\t240000\t245000\t0.017161\t-0.039130\t-0.068656\t-0.071671\n+chr2L\t245000\t250000\t-0.020460\t-0.060292\t-0.078062\t-0.050469\n+chr2L\t250000\t255000\t-0.073124\t-0.060292\t-0.078062\t-0.050469\n+chr2L\t255000\t260000\t-0.047443\t-0.045846\t-0.071641\t-0.047073\n+chr2L\t260000\t265000\t-0.047443\t-0.045846\t-0.071641\t-0.047073\n+chr2L\t265000\t270000\t0.007611\t-0.014878\t-0.057878\t-0.024732\n+chr2L\t270000\t275000\t-0.009451\t-0.054099\t-0.062143\t-0.026988\n+chr2L\t275000\t280000\t-0.045518\t-0.074386\t-0.071160\t-0.044985\n+chr2L\t280000\t285000\t-0.110418\t-0.110893\t-0.087385\t-0.035330\n+chr2L\t285000\t290000\t-0.047443\t-0.075470\t-0.067013\t-0.022201\n+chr2L\t290000\t295000\t-0.047443\t-0.075470\t-0.067013\t-0.022201\n+chr2L\t295000\t300000\t-0.109190\t-0.110202\t-0.082450\t-0.030366\n+chr2L\t300000\t305000\t-0.109190\t-0.110202\t-0.082450\t-0.030366\n+chr2L\t305000\t310000\t-0.057829\t-0.081311\t-0.053068\t-0.014825\n+chr2L\t310000\t315000\t-0.057829\t-0.081311\t-0.024594\t-0.014825\n+chr2L\t315000\t320000\t-0.058947\t-0.081940\t-0.022407\t-0.011557\n+chr2L\t320000\t325000\t-0.070559\t-0.026475\t0.018928\t0.001481\n+chr2L\t325000\t330000\t-0.087621\t0.003965\t0.014663\t-0.000775\n+chr2L\t330000\t335000\t0.055695\t0.059801\t0.045183'..b'776\t0.034708\n+chrX\t22115000\t22120000\t-0.085916\t-0.018370\t0.055167\t0.045584\n+chrX\t22120000\t22125000\t-0.085916\t0.046936\t0.055167\t0.045584\n+chrX\t22125000\t22130000\t-0.085916\t0.046936\t0.083338\t0.045584\n+chrX\t22130000\t22135000\t-0.011185\t0.031873\t0.102021\t0.055466\n+chrX\t22135000\t22140000\t-0.011185\t-0.033434\t0.102021\t0.073161\n+chrX\t22140000\t22145000\t-0.011185\t-0.033434\t0.103974\t0.073161\n+chrX\t22145000\t22150000\t0.062565\t0.008051\t0.097034\t0.069490\n+chrX\t22150000\t22155000\t0.062565\t0.008051\t0.097034\t0.069490\n+chrX\t22155000\t22160000\t0.062565\t0.008051\t0.097034\t0.069490\n+chrX\t22160000\t22165000\t0.062565\t0.008051\t0.097034\t0.069490\n+chrX\t22165000\t22170000\t0.169640\t0.190155\t0.123803\t0.106789\n+chrX\t22170000\t22175000\t0.142169\t0.174703\t0.116935\t0.103156\n+chrX\t22175000\t22180000\t0.142169\t0.174703\t0.087910\t0.103156\n+chrX\t22180000\t22185000\t0.142169\t0.174703\t0.121365\t0.103156\n+chrX\t22185000\t22190000\t0.246152\t0.174703\t0.108735\t0.097509\n+chrX\t22190000\t22195000\t0.246152\t0.174703\t0.108735\t0.128061\n+chrX\t22195000\t22200000\t0.172402\t0.069834\t0.115099\t0.131428\n+chrX\t22200000\t22205000\t0.068419\t0.125639\t0.115099\t0.116076\n+chrX\t22205000\t22210000\t0.068419\t0.125639\t0.115099\t0.116076\n+chrX\t22210000\t22215000\t0.068419\t0.184129\t0.158848\t0.116076\n+chrX\t22215000\t22220000\t0.068419\t0.184129\t0.081644\t0.085523\n+chrX\t22220000\t22225000\t0.167629\t0.125639\t0.081644\t0.085523\n+chrX\t22225000\t22230000\t0.088025\t0.080862\t0.061743\t0.074997\n+chrX\t22230000\t22235000\t0.192007\t0.080862\t0.061743\t0.054567\n+chrX\t22235000\t22240000\t0.192007\t0.080862\t0.033572\t0.054567\n+chrX\t22240000\t22245000\t0.192007\t0.080862\t0.033572\t0.054567\n+chrX\t22245000\t22250000\t0.088025\t0.080862\t0.007577\t0.047542\n+chrX\t22250000\t22255000\t0.088025\t0.080862\t0.007577\t0.047542\n+chrX\t22255000\t22260000\t-0.011185\t0.080862\t0.007577\t0.047542\n+chrX\t22260000\t22265000\t-0.011185\t0.080862\t0.033572\t0.022206\n+chrX\t22265000\t22270000\t-0.085916\t-0.019664\t0.044893\t0.030459\n+chrX\t22270000\t22275000\t-0.085916\t-0.019664\t0.044893\t0.032712\n+chrX\t22275000\t22280000\t-0.085916\t-0.075470\t0.044893\t0.035142\n+chrX\t22280000\t22285000\t-0.012165\t-0.033985\t0.038528\t0.033810\n+chrX\t22285000\t22290000\t-0.012165\t0.092013\t0.038528\t0.036513\n+chrX\t22290000\t22295000\t-0.012165\t0.092013\t0.012533\t0.022025\n+chrX\t22295000\t22300000\t-0.012165\t0.092013\t0.012533\t-0.003975\n+chrX\t22300000\t22305000\t-0.012165\t0.092013\t0.012533\t-0.002383\n+chrX\t22305000\t22310000\t0.288555\t0.135170\t0.061021\t0.032772\n+chrX\t22310000\t22315000\t0.288555\t0.248101\t0.093651\t0.056380\n+chrX\t22315000\t22320000\t0.288555\t0.305226\t0.129413\t0.082263\n+chrX\t22320000\t22325000\t0.281418\t0.359702\t0.167374\t0.109763\n+chrX\t22325000\t22330000\t0.262960\t0.359702\t0.178810\t0.117966\n+chrX\t22330000\t22335000\t0.389975\t0.370602\t0.198066\t0.131823\n+chrX\t22335000\t22340000\t0.313251\t0.327445\t0.185726\t0.122716\n+chrX\t22340000\t22345000\t0.309535\t0.214480\t0.164346\t0.107040\n+chrX\t22345000\t22350000\t0.309535\t0.160722\t0.178928\t0.117541\n+chrX\t22350000\t22355000\t0.309535\t0.176511\t0.195663\t0.129634\n+chrX\t22355000\t22360000\t0.309535\t0.194851\t0.215077\t0.143670\n+chrX\t22360000\t22365000\t0.309535\t0.216340\t0.237810\t0.160142\n+chrX\t22365000\t22370000\t0.235638\t0.241958\t0.142695\t0.090852\n+chrX\t22370000\t22375000\t0.144441\t0.272856\t0.163157\t0.105614\n+chrX\t22375000\t22380000\t0.033332\t0.310817\t0.188354\t0.123859\n+chrX\t22380000\t22385000\t0.047108\t0.358633\t0.220115\t0.146874\n+chrX\t22385000\t22390000\t0.065244\t0.162319\t0.174180\t0.113338\n+chrX\t22390000\t22395000\t-0.096387\t0.049914\t0.014061\t-0.003271\n+chrX\t22395000\t22400000\t-0.098757\t0.075839\t0.031161\t0.008970\n+chrX\t22400000\t22405000\t-0.101349\t-0.094042\t-0.082297\t-0.073703\n+chrX\t22405000\t22410000\t-0.104371\t-0.096430\t-0.084079\t-0.075333\n+chrX\t22410000\t22415000\t-0.108137\t-0.099498\t-0.086325\t-0.077231\n+chrX\t22415000\t22420000\t-0.112872\t-0.103287\t-0.089234\t-0.079379\n+chrX\t22420000\t22422827\t0.000000\t0.000000\t0.000000\t0.000000\n+chrXHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chrXHet\t200000\t204112\t0.000000\t0.000000\t0.000000\t0.000000\n+chrYHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chrYHet\t345000\t347038\t0.000000\t0.000000\t0.000000\t0.000000\n' |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/multiFDR_zscore_matrix.h5 |
| b |
| Binary file test-data/multiFDR_zscore_matrix.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/obs_exp_small_50kb.cool |
| b |
| Binary file test-data/obs_exp_small_50kb.cool has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/obs_exp_small_50kb.h5 |
| b |
| Binary file test-data/obs_exp_small_50kb.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pca1.bedgraph --- a/test-data/pca1.bedgraph Wed Jan 03 13:31:00 2018 -0500 +++ b/test-data/pca1.bedgraph Wed Mar 07 03:41:00 2018 -0500 |
| b |
| b'@@ -1,1145 +1,1145 @@\n-chr2RHet\t0\t50000\t-0.017944626132\n-chr2RHet\t50000\t100000\t0.432419437313\n-chr2RHet\t100000\t150000\t0.201996316592\n-chr2RHet\t150000\t200000\t0.106388016465\n-chr2RHet\t200000\t250000\t0.376170623545\n-chr2RHet\t300000\t350000\t0.188470174777\n-chr2RHet\t350000\t400000\t-0.131288575898\n-chr2RHet\t400000\t450000\t0.104207776277\n-chr2RHet\t450000\t500000\t0.123004242005\n-chr2RHet\t500000\t550000\t0.008984911212\n-chr2RHet\t550000\t600000\t-0.031398613786\n-chr2RHet\t600000\t650000\t0.062864646867\n-chr2RHet\t650000\t700000\t-0.068120893974\n-chr2RHet\t700000\t750000\t0.022713862733\n-chr2RHet\t750000\t800000\t0.117863782190\n-chr2RHet\t800000\t850000\t-0.041490013039\n-chr2RHet\t850000\t900000\t-0.003117752390\n-chr2RHet\t900000\t950000\t0.403981736093\n-chr2RHet\t950000\t1000000\t-0.082639723384\n-chr2RHet\t1000000\t1050000\t-0.020353697788\n-chr2RHet\t1050000\t1100000\t0.055439327684\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-0.017953445783\n-chr2RHet\t1300000\t1350000\t-0.092690961385\n-chr2RHet\t1350000\t1400000\t0.366065212983\n-chr2RHet\t1400000\t1450000\t-0.043093389177\n-chr2RHet\t1450000\t1500000\t-0.063880277445\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\t-0.058255230768\n-chr2RHet\t1600000\t1650000\t-0.042164910199\n-chr2RHet\t1650000\t1700000\t-0.122493740682\n-chr2RHet\t1700000\t1750000\t-0.098496951080\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\t-0.046696857069\n-chr2RHet\t1900000\t1950000\t-0.126748537805\n-chr2RHet\t1950000\t2000000\t-0.050512240388\n+chr2RHet\t1850000\t1900000\t-0.062535524405\n+chr2RHet\t1900000\t1950000\t-0.102423419951\n+chr2RHet\t1950000\t2000000\t-0.000255452186\n 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 3106dcd651f5 -r 303558d3bc11 test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pca2.bedgraph --- a/test-data/pca2.bedgraph Wed Jan 03 13:31:00 2018 -0500 +++ b/test-data/pca2.bedgraph Wed Mar 07 03:41:00 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 chr2RHet\t2000000\t2050000\t0.000000000000\n-chr2RHet\t2050000\t2100000\t-0.226048172597\n-chr2RHet\t2100000\t2150000\t0.009032181245\n-chr2RHet\t2150000\t2200000\t0.156931793125\n-chr2RHet\t2200000\t2250000\t0.076913071464\n-chr2RHet\t2250000\t2300000\t-0.013015414891\n-chr2RHet\t2300000\t2350000\t-0.260358373936\n-chr2RHet\t2350000\t2400000\t-0.170971324927\n-chr2RHet\t2400000\t2450000\t0.112722101985\n-chr2RHet\t2550000\t2600000\t-0.012191890450\n-chr2RHet\t2600000\t2650000\t0.022853015897\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\t0.025282155888\n-chr2RHet\t2850000\t2900000\t0.007270539302\n-chr2RHet\t2900000\t2950000\t0.007270539302\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\t0.000000000000\n-chr2'..b'7531\n+chr3R\t23150000\t23200000\t-0.021139900425\n+chr3R\t23200000\t23250000\t-0.019229121816\n+chr3R\t23250000\t23300000\t-0.009690567129\n+chr3R\t23300000\t23350000\t0.054754024235\n+chr3R\t23350000\t23400000\t-0.019183929399\n+chr3R\t23400000\t23450000\t-0.009001010535\n+chr3R\t23450000\t23500000\t-0.014080121036\n+chr3R\t23500000\t23550000\t-0.014148152871\n+chr3R\t23550000\t23600000\t0.000823607962\n+chr3R\t23600000\t23650000\t-0.001342597761\n+chr3R\t23650000\t23700000\t-0.016420950052\n+chr3R\t23700000\t23750000\t0.001853957729\n+chr3R\t23750000\t23800000\t-0.001299023555\n+chr3R\t23800000\t23850000\t0.013463430574\n+chr3R\t23850000\t23900000\t0.009506792191\n+chr3R\t23900000\t23950000\t-0.025453892320\n+chr3R\t23950000\t24000000\t-0.004084370281\n+chr3R\t24000000\t24050000\t-0.011214748717\n+chr3R\t24050000\t24100000\t-0.000884263486\n+chr3R\t24100000\t24150000\t-0.010009891693\n+chr3R\t24150000\t24200000\t-0.017486383439\n+chr3R\t24200000\t24250000\t-0.017625216534\n+chr3R\t24250000\t24300000\t-0.003149454746\n+chr3R\t24300000\t24350000\t-0.006722580710\n+chr3R\t24350000\t24400000\t-0.014904417790\n+chr3R\t24400000\t24450000\t-0.018419583813\n+chr3R\t24450000\t24500000\t-0.003341196950\n+chr3R\t24500000\t24550000\t-0.025261148540\n+chr3R\t24550000\t24600000\t-0.019264667191\n+chr3R\t24600000\t24650000\t0.008777164463\n+chr3R\t24650000\t24700000\t-0.058820013736\n+chr3R\t24700000\t24750000\t0.133965949564\n+chr3R\t24750000\t24800000\t-0.025635328935\n+chr3R\t24800000\t24850000\t-0.015432657902\n+chr3R\t24850000\t24900000\t-0.019947306994\n+chr3R\t24900000\t24950000\t-0.007310175809\n+chr3R\t24950000\t25000000\t-0.007969634132\n+chr3R\t25000000\t25050000\t-0.022938987231\n+chr3R\t25050000\t25100000\t-0.024696997428\n+chr3R\t25100000\t25150000\t-0.022842885214\n+chr3R\t25150000\t25200000\t-0.006497320312\n+chr3R\t25200000\t25250000\t-0.019900948067\n+chr3R\t25250000\t25300000\t0.000501891895\n+chr3R\t25300000\t25350000\t-0.017603651243\n+chr3R\t25350000\t25400000\t-0.006229941026\n+chr3R\t25400000\t25450000\t-0.006007854292\n+chr3R\t25450000\t25500000\t-0.019454905301\n+chr3R\t25500000\t25550000\t-0.037170029699\n+chr3R\t25550000\t25600000\t-0.014728682126\n+chr3R\t25600000\t25650000\t-0.012392554433\n+chr3R\t25650000\t25700000\t-0.021669657931\n+chr3R\t25700000\t25750000\t-0.014814010181\n+chr3R\t25750000\t25800000\t0.001174221599\n+chr3R\t25800000\t25850000\t-0.015736076633\n+chr3R\t25850000\t25900000\t-0.014074776412\n+chr3R\t25900000\t25950000\t-0.023745014295\n+chr3R\t25950000\t26000000\t-0.014255084052\n+chr3R\t26000000\t26050000\t-0.042045651228\n+chr3R\t26050000\t26100000\t-0.002973822275\n+chr3R\t26100000\t26150000\t-0.011601011577\n+chr3R\t26150000\t26200000\t-0.003080115129\n+chr3R\t26200000\t26250000\t-0.000773390947\n+chr3R\t26250000\t26300000\t-0.006678588217\n+chr3R\t26300000\t26350000\t-0.022464183256\n+chr3R\t26350000\t26400000\t0.336277506961\n+chr3R\t26400000\t26450000\t-0.020529276334\n+chr3R\t26450000\t26500000\t-0.020476777284\n+chr3R\t26500000\t26550000\t-0.001186172146\n+chr3R\t26550000\t26600000\t-0.009825101636\n+chr3R\t26600000\t26650000\t-0.023312598767\n+chr3R\t26650000\t26700000\t-0.002950327838\n+chr3R\t26700000\t26750000\t-0.009440453475\n+chr3R\t26750000\t26800000\t-0.028720067774\n+chr3R\t26800000\t26850000\t-0.017654001455\n+chr3R\t26850000\t26900000\t-0.046571966675\n+chr3R\t26900000\t26950000\t-0.003652753512\n+chr3R\t26950000\t27000000\t-0.010239417783\n+chr3R\t27000000\t27050000\t-0.019533568627\n+chr3R\t27050000\t27100000\t-0.021952963940\n+chr3R\t27100000\t27150000\t0.003976448176\n+chr3R\t27150000\t27200000\t0.006475587749\n+chr3R\t27200000\t27250000\t0.013295160930\n+chr3R\t27250000\t27300000\t-0.002230665737\n+chr3R\t27300000\t27350000\t-0.015110366905\n+chr3R\t27350000\t27400000\t-0.010895888969\n+chr3R\t27400000\t27450000\t0.006708590043\n+chr3R\t27450000\t27500000\t-0.001539284189\n+chr3R\t27500000\t27550000\t-0.039593819794\n+chr3R\t27550000\t27600000\t-0.004930687122\n+chr3R\t27600000\t27650000\t-0.016285294706\n+chr3R\t27650000\t27700000\t-0.014471094581\n+chr3R\t27700000\t27750000\t-0.005251523359\n+chr3R\t27750000\t27800000\t0.017646363936\n+chr3R\t27800000\t27850000\t-0.004653315545\n+chr3R\t27850000\t27900000\t-0.011586685796\n chrUextra\t0\t50000\t0.000000000000\n chrUextra\t50000\t100000\t-0.500000000000\n chrUextra\t100000\t150000\t0.000000000000\n' |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pca2.bw |
| b |
| Binary file test-data/pca2.bw has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pearson_small_50kb.cool |
| b |
| Binary file test-data/pearson_small_50kb.cool has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pearson_small_50kb.h5 |
| b |
| Binary file test-data/pearson_small_50kb.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/pearson_small_50kb_transform.cool |
| b |
| Binary file test-data/pearson_small_50kb_transform.cool has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/raw_qc_report --- a/test-data/raw_qc_report Wed Jan 03 13:31:00 2018 -0500 +++ b/test-data/raw_qc_report Wed Mar 07 03:41:00 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 3106dcd651f5 -r 303558d3bc11 test-data/small_matrix_50kb_pearson_pca1_plot.svg --- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Jan 03 13:31:00 2018 -0500 +++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:41:00 2018 -0500 |
| b |
| b'@@ -19,25 +19,25 @@\n </g>\n <g id="axes_1">\n <g id="patch_2">\n- <path d="M 78.425 348.170436 \n-L 380.762475 348.170436 \n+ <path d="M 78.425 350.781389 \n+L 380.762475 350.781389 \n L 380.762475 65.420504 \n L 78.425 65.420504 \n z\n " style="fill:#ffffff;"/>\n </g>\n- <image height="283" id="image80d8ffe0f0" transform="scale(1 -1)translate(0 -283)" width="303" x="78" xlink:href="data:image/png;base64,\n-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'..b'idth="302.337475" x="519.569059" y="791.552869"/>\n+ <clipPath id="p6d16193564">\n+ <rect height="285.360885" width="22.756584" x="380.762475" y="490.557941"/>\n </clipPath>\n- <clipPath id="p199368b4ee">\n- <rect height="282.749932" width="22.756584" x="821.906535" y="492.170588"/>\n+ <clipPath id="pb716d09da1">\n+ <rect height="50.357803" width="302.337475" x="519.569059" y="792.70476"/>\n </clipPath>\n- <clipPath id="p8ff63f7282">\n- <rect height="49.897047" width="302.337475" x="960.713119" y="791.552869"/>\n+ <clipPath id="p1e15a2165e">\n+ <rect height="285.360885" width="22.756584" x="821.906535" y="490.557941"/>\n </clipPath>\n- <clipPath id="p51ccb1ed2d">\n- <rect height="282.749932" width="22.756584" x="1263.050594" y="492.170588"/>\n+ <clipPath id="pe12add889c">\n+ <rect height="50.357803" width="302.337475" x="960.713119" y="792.70476"/>\n </clipPath>\n- <clipPath id="pd2ea881de2">\n- <rect height="49.897047" width="302.337475" x="1401.857178" y="791.552869"/>\n+ <clipPath id="p0ff7293b63">\n+ <rect height="285.360885" width="22.756584" x="1263.050594" y="490.557941"/>\n </clipPath>\n- <clipPath id="p42c46ec016">\n- <rect height="282.749932" width="22.756584" x="1704.194653" y="492.170588"/>\n+ <clipPath id="p7c7dcb07c1">\n+ <rect height="50.357803" width="302.337475" x="1401.857178" y="792.70476"/>\n </clipPath>\n- <clipPath id="p9880cc90cb">\n- <rect height="49.897047" width="302.337475" x="1843.001238" y="791.552869"/>\n+ <clipPath id="pb3c3abb07e">\n+ <rect height="285.360885" width="22.756584" x="1704.194653" y="490.557941"/>\n </clipPath>\n- <clipPath id="p9c4026a661">\n- <rect height="282.749932" width="22.756584" x="2145.338713" y="492.170588"/>\n+ <clipPath id="p0a9c2d9b03">\n+ <rect height="50.357803" width="302.337475" x="1843.001238" y="792.70476"/>\n </clipPath>\n- <clipPath id="p3a9c31b5ad">\n- <rect height="49.897047" width="302.337475" x="78.425" y="1218.302953"/>\n+ <clipPath id="p28ff501d1c">\n+ <rect height="285.360885" width="22.756584" x="2145.338713" y="490.557941"/>\n </clipPath>\n- <clipPath id="p1a210732df">\n- <rect height="282.749932" width="22.756584" x="380.762475" y="918.920672"/>\n+ <clipPath id="pc4bad087e8">\n+ <rect height="50.357803" width="302.337475" x="78.425" y="1217.842197"/>\n </clipPath>\n- <clipPath id="p0bd21f574f">\n- <rect height="49.897047" width="302.337475" x="519.569059" y="1218.302953"/>\n+ <clipPath id="p55edf7d7cd">\n+ <rect height="285.360885" width="22.756584" x="380.762475" y="915.695378"/>\n </clipPath>\n- <clipPath id="p1257c93f5b">\n- <rect height="282.749932" width="22.756584" x="821.906535" y="918.920672"/>\n+ <clipPath id="p21774952d4">\n+ <rect height="50.357803" width="302.337475" x="519.569059" y="1217.842197"/>\n </clipPath>\n- <clipPath id="p27198c8206">\n- <rect height="49.897047" width="302.337475" x="960.713119" y="1218.302953"/>\n+ <clipPath id="pa5f3b38b09">\n+ <rect height="285.360885" width="22.756584" x="821.906535" y="915.695378"/>\n </clipPath>\n- <clipPath id="pb1b36a59a2">\n- <rect height="282.749932" width="22.756584" x="1263.050594" y="918.920672"/>\n+ <clipPath id="pe27500d3a6">\n+ <rect height="50.357803" width="302.337475" x="960.713119" y="1217.842197"/>\n </clipPath>\n- <clipPath id="pead5268bef">\n- <rect height="282.749932" width="22.756584" x="1704.194653" y="918.920672"/>\n+ <clipPath id="p2894034f0b">\n+ <rect height="285.360885" width="22.756584" x="1263.050594" y="915.695378"/>\n </clipPath>\n- <clipPath id="p72064159ac">\n- <rect height="49.897047" width="302.337475" x="1843.001238" y="1218.302953"/>\n+ <clipPath id="p7882d2f5e8">\n+ <rect height="50.357803" width="302.337475" x="1843.001238" y="1217.842197"/>\n </clipPath>\n- <clipPath id="pd355eb2eaa">\n- <rect height="282.749932" width="22.756584" x="2145.338713" y="918.920672"/>\n+ <clipPath id="pf64684458c">\n+ <rect height="285.360885" width="22.756584" x="2145.338713" y="915.695378"/>\n </clipPath>\n </defs>\n </svg>\n' |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/small_test_matrix_2.h5 |
| b |
| Binary file test-data/small_test_matrix_2.h5 has changed |
| b |
| diff -r 3106dcd651f5 -r 303558d3bc11 test-data/test_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_regions.bed Wed Mar 07 03:41:00 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 |
