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Changeset 0:2074627b0f83 (2018-06-23)

Next changeset 1:0ea86f6bf2a1 (2018-07-02)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363

added:
macros.xml
pyGenomeTracks.xml
static/images/pyGenomeTracks.png
test-data/Li_et_al_2015.h5
test-data/bedgraph_chrx_2e6_5e6.bg
test-data/bigwig_chrx_2e6_5e6.bw
test-data/bigwig_multiple.png
test-data/dm3_genes.bed.gz
test-data/dm3_genes.bed6.gz
test-data/domains.bed
test-data/master_TADs_plot.png
test-data/tad_classification.bed
test-data/tad_score.gz

diff -r 000000000000 -r 2074627b0f83 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Jun 23 02:28:35 2018 -0400

b'@@ -0,0 +1,210 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+ <token name="@WRAPPER_VERSION@">2.0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</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="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 value="GnBu">GnBu</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="YlGn">YlGn</option>\n+ <option value="PuBuGn">PuBuGn</option>\n+ <option value="RdYlGn">RdYlGn</option>\n+ <option value="YlGnBu">YlGnBu</option>\n+ <option value="YlOrBr">YlOrBr</option>\n+ <option value="YlOrRd">YlOrRd</option>\n+ <option value="gist_gray">gist_gray</option>\n+ <option value="gist_stern">gist_stern</option>\n+ <option value="gist_earth">gist_earth</option>\n+ <option value="gist_yarg">gist_yarg</option>\n+ <option value="gist_ncar">gist_ncar</option>\n+ <option value="gist_rainbow">gist_rainbow</option>\n+ <option value="gist_heat">gist_heat</option'..b'on>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="region">\n+ <param argument="--region" type="text" label="Region of the genome to limit the operation"\n+ help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />\n+ </xml>\n+\n+ <xml name=\'matrix_h5_cooler_multiple_macro\'>\n+ <param name=\'matrix_h5_cooler_multiple\' type="data" format="h5,cool"\n+ label="Matricies to compute on" multiple="true"/>\n+ </xml>\n+ <token name="@REFERENCES@">\n+\n+.. class:: infomark\n+\n+For more information on the tools, please visit our `help site`_.\n+\n+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com\n+\n+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for\n+Immunobiology and Epigenetics`_.\n+\n+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/\n+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de\n+.. _help site: https://github.com/deeptools/pyGenomeTracks\n+\n+ </token>\n+\n+ <xml name="track_input_bed_macro">\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple=\'True\'/>\n+ </xml>\n+ <xml name="track_input_bed_single_macro">\n+ <param name="track_input_bed_single" 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" multiple=\'True\'/>\n+ </xml>\n+ <xml name="track_input_bigwig_macro">\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple=\'True\'/>\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" multiple=\'True\'/>\n+ </xml>\n+ <xml name="plot_title">\n+ <param name="title" type="text" optional="true" label="Plot title" multiple=\'True\'/>\n+ </xml>\n+ <xml name="spacer_macro">\n+ <param name="spacer_height" type="float" value="" optional="True"\n+ label="Include spacer at the end of the track" help="Height of the spacer." />\n+ </xml>\n+</macros>\n'

diff -r 000000000000 -r 2074627b0f83 pyGenomeTracks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pyGenomeTracks.xml Sat Jun 23 02:28:35 2018 -0400

[

b'@@ -0,0 +1,768 @@\n+<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+ <description>plot genomic data tracks</description>\n+ <macros>\n+ <token name="@BINARY@">pyGenomeTracks</token>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+\n+ sed \'/^$/d\' \'$tracks_config\' &&\n+ @BINARY@\n+ --tracks \'$tracks_config\'\n+ #if $region and $region is not None:\n+ --region \'$region\'\n+ #end if\n+ --outFileName plot.$image_file_format\n+ && mv plot.$image_file_format plot\n+]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="tracks_config">\n+#if $x_axis.x_axis_select == "yes":\n+[x-axis]\n+#if $x_axis.fontsize:\n+fontsize = $x_axis.fontsize\n+#end if\n+#if $x_axis.where:\n+where = $x_axis.where\n+#end if\n+#end if\n+#for $counter, $track in enumerate($tracks):\n+#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n+\n+#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):\n+[hic_section_$counter]\n+file = $data_matrix\n+file_type = hic_matrix\n+#if $track.track_file_style_conditional.title:\n+title = $track.track_file_style_conditional.title\n+#else:\n+title = $data_matrix.name\n+#end if\n+#if $track.track_file_style_conditional.depth:\n+depth = $track.track_file_style_conditional.depth\n+#end if\n+#if $track.track_file_style_conditional.colormap:\n+colormap = $track.track_file_style_conditional.colormap\n+#end if\n+#if $track.track_file_style_conditional.min_value:\n+min_value = $track.track_file_style_conditional.min_value\n+#end if\n+#if $track.track_file_style_conditional.max_value:\n+max_value = $track.track_file_style_conditional.max_value\n+#end if\n+transform = $track.track_file_style_conditional.transform\n+height = $track.track_file_style_conditional.height_matrix\n+\n+#if $track.track_file_style_conditional.boundaries_file is not None:\n+#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]\n+boundaries_file = $boundary_file\n+#end if\n+\n+#if $track.track_file_style_conditional.x_labels:\n+x labels = $track.track_file_style_conditional.x_labels\n+#end if\n+#if $track.track_file_style_conditional.type:\n+type = $track.track_file_style_conditional.type\n+#end if\n+#if $track.track_file_style_conditional.show_masked_bins:\n+show_masked_bins = $track.track_file_style_conditional.show_masked_bins\n+#end if\n+#if $track.track_file_style_conditional.scale_factor:\n+scale factor = $track.track_file_style_conditional.scale_factor\n+#end if\n+\n+[spacer]\n+#if $track.track_file_style_conditional.spacer_height:\n+height = $track.track_file_style_conditional.spacer_height\n+#end if\n+#end for\n+\n+#end if\n+\n+\n+\n+#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":\n+\n+#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:\n+[tad_score_$counter]\n+file = $data_bedgraph \n+#if $track.track_file_style_conditional.title:\n+title = $track.track_file_style_conditional.title\n+#else:\n+title = $data_bedgraph.name\n+#end if\n+#if $track.track_file_style_conditional.color:\n+color = $track.track_file_style_conditional.color\n+#end if\n+#if $track.track_file_style_conditional.height_tad:\n+height = $track.track_file_style_conditional.height_tad\n+#end if\n+#if $track.track_file_style_conditional.type_lines:\n+type = $track.track_file_style_conditional.type_lines\n+#end if\n+#if $track.track_file_style_conditional.show_data:\n+show data range = $track.track_file_style_conditional.show_data\n+#end if\n+\n+#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split(\'\\t\'))\n+#if $columns > 5:\n+file_type = bedgraph_matrix\n+#else:\n+file_type = bedgraph\n+#end if\n+type = lines\n+[spacer]\n+#if $track.track_file_style_conditional.spacer_height:\n+height = $track.track_file_style_conditional.space'..b'ue="chrX:3000000-3500000"/>\n+ <conditional name="x_axis">\n+ <param name="x_axis_select" value="yes" />\n+ </conditional>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="bigwig_track_option" />\n+ <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />\n+ <param name="title" value="rep 1 test line" />\n+ <param name="height_bigwig" value="4" />\n+ <param name="color" value="red" />\n+ <conditional name="type_conditional">\n+ <param name="type_selector" value="line_option" />\n+ <param name="width_line" value="1" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+pyGenomeTracks\n+==============\n+\n+**pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. \n+ Currently, it is possible to plot: \n+\n+ - bigwig\n+ - bed (many options)\n+ - bedgraph\n+ - links (represented as arcs)\n+ - Hi-C matrices\n+\n+_________________\n+\n+Usage\n+-----\n+\n+This tool takes various types of tracks as input:\n+\n+ - **Chromatin states:** display blocks of different colors following a bed file.\n+ - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.\n+ - **Bigwig track:** generic bigwig track plotting.\n+ - **Bedgraph track:** generic bedgraph track plotting.\n+ - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer\'s ``hicFindTADs`` (TAD seperation scores).\n+ - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer\'s ``hicFindTADs``.\n+ - **Spacer:** Add some space between two tracks.\n+ - **Hi-C tracks:**\n+ - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer\'s ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer\'s ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.\n+ - **TAD score:** display TAD seperation score computed by HiCExplorer\'s ``hicFindTADs``.\n+\n+\n+For each track, parameters for the color, the width or the font size can be defined.\n+\n+_________________\n+\n+Output\n+------\n+\n+**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) \n+also contains Hi-C data. The plot is composed of tracks that need to be specified.\n+Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.\n+TADs were computed by HiCExplorer\'s ``hicFindTADs``. The additional tracks added correspond to: \n+TAD-separation score (as reported by HiCExplorer\'s ``hicFindTADs``), chromatin states, \n+principal component 1 (A/B compartment) computed using HiCExplorer\'s ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. \n+Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.\n+\n+.. image:: $PATH_TO_IMAGES/pyGenomeTracks.png\n+ :width: 70 %\n+\n+_________________\n+\n+| For more information about pyGenomeTracks please consider our documentation on github_\n+\n+.. _github: https://github.com/deeptools/pyGenomeTracks\n+.. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9\n+]]></help>\n+ <expand macro="citations" />\n+</tool>\n'

diff -r 000000000000 -r 2074627b0f83 static/images/pyGenomeTracks.png

Binary file static/images/pyGenomeTracks.png has changed

diff -r 000000000000 -r 2074627b0f83 test-data/Li_et_al_2015.h5

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diff -r 000000000000 -r 2074627b0f83 test-data/bedgraph_chrx_2e6_5e6.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedgraph_chrx_2e6_5e6.bg Sat Jun 23 02:28:35 2018 -0400

b'@@ -0,0 +1,11308 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/domains.bed Sat Jun 23 02:28:35 2018 -0400

b'@@ -0,0 +1,498 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diff -r 000000000000 -r 2074627b0f83 test-data/master_TADs_plot.png

Binary file test-data/master_TADs_plot.png has changed

diff -r 000000000000 -r 2074627b0f83 test-data/tad_classification.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tad_classification.bed Sat Jun 23 02:28:35 2018 -0400

b'@@ -0,0 +1,2685 @@\n+chr2L\t73103\t94543\tactive\t2\t.\t73103\t94543\t255,255,153\n+chr2L\t94543\t108120\tactive\t4\t.\t94543\t108120\t255,255,153\n+chr2L\t108120\t132269\tactive\t2\t.\t108120\t132269\t255,255,153\n+chr2L\t132269\t143461\tactive\t2\t.\t132269\t143461\t255,255,153\n+chr2L\t143461\t159101\tactive\t2\t.\t143461\t159101\t255,255,153\n+chr2L\t159101\t181297\tinactive\t1\t.\t159101\t181297\t0,0,0\n+chr2L\t181297\t207416\tactive\t4\t.\t181297\t207416\t255,255,153\n+chr2L\t207416\t248687\tactive\t4\t.\t207416\t248687\t255,255,153\n+chr2L\t248687\t271451\tinactive\t1\t.\t248687\t271451\t0,0,0\n+chr2L\t271451\t283072\tactive\t4\t.\t271451\t283072\t255,255,153\n+chr2L\t283072\t294919\tactive\t2\t.\t283072\t294919\t255,255,153\n+chr2L\t294919\t306028\tactive\t4\t.\t294919\t306028\t255,255,153\n+chr2L\t306028\t357775\tinactive\t1\t.\t306028\t357775\t0,0,0\n+chr2L\t357775\t403068\tinactive\t1\t.\t357775\t403068\t0,0,0\n+chr2L\t403068\t421370\tactive\t4\t.\t403068\t421370\t255,255,153\n+chr2L\t421370\t472506\tactive\t2\t.\t421370\t472506\t255,255,153\n+chr2L\t472506\t490303\tactive\t2\t.\t472506\t490303\t255,255,153\n+chr2L\t490303\t541886\tactive\t2\t.\t490303\t541886\t255,255,153\n+chr2L\t541886\t553339\tactive\t2\t.\t541886\t553339\t255,255,153\n+chr2L\t553339\t559789\tactive\t4\t.\t553339\t559789\t255,255,153\n+chr2L\t559789\t574511\tactive\t4\t.\t559789\t574511\t255,255,153\n+chr2L\t574511\t602435\tPcG\t0\t.\t574511\t602435\t56,108,176\n+chr2L\t602435\t810330\tinactive\t1\t.\t602435\t810330\t0,0,0\n+chr2L\t810330\t825970\tactive\t4\t.\t810330\t825970\t255,255,153\n+chr2L\t825970\t853278\tactive\t2\t.\t825970\t853278\t255,255,153\n+chr2L\t853278\t871106\tactive\t2\t.\t853278\t871106\t255,255,153\n+chr2L\t871106\t887664\tactive\t2\t.\t871106\t887664\t255,255,153\n+chr2L\t887664\t1006986\tinactive\t1\t.\t887664\t1006986\t0,0,0\n+chr2L\t1006986\t1077753\tinactive\t1\t.\t1006986\t1077753\t0,0,0\n+chr2L\t1077753\t1102940\tinactive\t1\t.\t1077753\t1102940\t0,0,0\n+chr2L\t1102940\t1108427\tactive\t4\t.\t1102940\t1108427\t255,255,153\n+chr2L\t1108427\t1142854\tactive\t2\t.\t1108427\t1142854\t255,255,153\n+chr2L\t1142854\t1157702\tactive\t4\t.\t1142854\t1157702\t255,255,153\n+chr2L\t1157702\t1185674\tactive\t4\t.\t1157702\t1185674\t255,255,153\n+chr2L\t1185674\t1246112\tinactive\t1\t.\t1185674\t1246112\t0,0,0\n+chr2L\t1246112\t1348267\tinactive\t1\t.\t1246112\t1348267\t0,0,0\n+chr2L\t1348267\t1492300\tinactive\t1\t.\t1348267\t1492300\t0,0,0\n+chr2L\t1492300\t1504156\tinactive\t1\t.\t1492300\t1504156\t0,0,0\n+chr2L\t1504156\t1614536\tinactive\t1\t.\t1504156\t1614536\t0,0,0\n+chr2L\t1614536\t1705229\tPcG\t0\t.\t1614536\t1705229\t56,108,176\n+chr2L\t1705229\t1728747\tactive\t2\t.\t1705229\t1728747\t255,255,153\n+chr2L\t1728747\t1818391\tinactive\t1\t.\t1728747\t1818391\t0,0,0\n+chr2L\t1818391\t1884683\tinactive\t1\t.\t1818391\t1884683\t0,0,0\n+chr2L\t1884683\t1909751\tinactive\t1\t.\t1884683\t1909751\t0,0,0\n+chr2L\t1909751\t1937585\tactive\t2\t.\t1909751\t1937585\t255,255,153\n+chr2L\t1937585\t1974067\tPcG\t0\t.\t1937585\t1974067\t56,108,176\n+chr2L\t1974067\t1987851\tactive\t4\t.\t1974067\t1987851\t255,255,153\n+chr2L\t1987851\t2037530\tinactive\t1\t.\t1987851\t2037530\t0,0,0\n+chr2L\t2037530\t2130843\tinactive\t1\t.\t2037530\t2130843\t0,0,0\n+chr2L\t2130843\t2151583\tactive\t4\t.\t2130843\t2151583\t255,255,153\n+chr2L\t2151583\t2193334\tactive\t2\t.\t2151583\t2193334\t255,255,153\n+chr2L\t2193334\t2216423\tactive\t2\t.\t2193334\t2216423\t255,255,153\n+chr2L\t2216423\t2221910\tactive\t4\t.\t2216423\t2221910\t255,255,153\n+chr2L\t2221910\t2237044\tactive\t4\t.\t2221910\t2237044\t255,255,153\n+chr2L\t2237044\t2362172\tinactive\t1\t.\t2237044\t2362172\t0,0,0\n+chr2L\t2362172\t2383056\tactive\t4\t.\t2362172\t2383056\t255,255,153\n+chr2L\t2383056\t2492696\tinactive\t1\t.\t2383056\t2492696\t0,0,0\n+chr2L\t2492696\t2561589\tinactive\t1\t.\t2492696\t2561589\t0,0,0\n+chr2L\t2561589\t2591551\tactive\t2\t.\t2561589\t2591551\t255,255,153\n+chr2L\t2591551\t2724465\tinactive\t1\t.\t2591551\t2724465\t0,0,0\n+chr2L\t2724465\t2740126\tactive\t2\t.\t2724465\t2740126\t255,255,153\n+chr2L\t2740126\t2750826\tactive\t4\t.\t2740126\t2750826\t255,255,153\n+chr2L\t2750826\t2770137\tactive\t4\t.\t2750826\t2770137\t255,255,153\n+chr2L\t2770137\t2809031\tactive\t2\t.\t2770137\t2809031\t255,255,153\n+chr2L\t2809031\t2855746\tinactive\t1\t.\t2809031\t2855746\t0,0,0\n+chr2L\t2855746\t2874843\tactive\t2\t.\t2855746\t2874843\t255,255,153\n+chr2L\t2874843\t2885455\tactive\t4\t.\t2874843\t2885455\t255,255,153\n+chr2L\t2885455\t2969305\tactive\t2\t.\t2885455\t2969'..b'9171063\t19201498\t255,255,153\n+chrX\t19201498\t19220554\tactive\t2\t.\t19201498\t19220554\t255,255,153\n+chrX\t19220554\t19242911\tinactive\t1\t.\t19220554\t19242911\t0,0,0\n+chrX\t19242911\t19366620\tinactive\t1\t.\t19242911\t19366620\t0,0,0\n+chrX\t19366620\t19374360\tactive\t4\t.\t19366620\t19374360\t255,255,153\n+chrX\t19374360\t19389270\tactive\t4\t.\t19374360\t19389270\t255,255,153\n+chrX\t19389270\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'

diff -r 000000000000 -r 2074627b0f83 test-data/tad_score.gz

Binary file test-data/tad_score.gz has changed