├── Basic_Tutorials ├── example01_Density_heatmap │ ├── OUT1.png │ ├── OUT2.png │ ├── SNP.dis.gz │ ├── in1.conf │ ├── in2.conf │ ├── mat.fst │ ├── run.sh │ ├── test.conf │ └── yy.sh ├── example02_Density_hist │ ├── OUT1.png │ ├── OUT2.png │ ├── OUT3.png │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ └── run.sh ├── example03_GWAS_point │ ├── Gwas.data.pvalue.gz │ ├── OUT1.png │ ├── OUT2.png │ ├── in1.conf │ ├── in2.conf │ └── run.sh ├── example04_Pi_lines │ ├── OUT1.png │ ├── OUT2.png │ ├── OUT3.png │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ ├── line_colors.conf │ ├── poly.info.gz │ └── run1.sh ├── example05_Region_highlights │ ├── OUT1.png │ ├── OUT2.png │ ├── col.file │ ├── in1.conf │ ├── in2.conf │ └── run.sh ├── example06_sca2chr_text │ ├── OUT1.png │ ├── OUT2.png │ ├── in1.conf │ ├── in2.conf │ ├── maker.info.gz │ ├── run.sh │ └── scaf2chr.format2.gz ├── example07_QTL_shape │ ├── OUT1.png │ ├── OUT2.png │ ├── QTL.region │ ├── ee.pl │ ├── in1.conf │ ├── in2.conf │ ├── rod.data.gz │ ├── run.sh │ └── shape.type.data ├── example08_QTL_ridgeline │ ├── OUT1.png │ ├── in1.conf │ └── run.sh ├── example09_LDMap_PairWiseLink │ ├── OUT1.png │ ├── OUT2.png │ ├── OUT3.png │ ├── OUT4.png │ ├── RR.Value.gz │ ├── Value.data.gz │ ├── in.data │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ ├── in4.conf │ └── run.sh ├── example10_SV_LinkS │ ├── OUT1.png │ ├── SV.info │ ├── in1.conf │ └── run.sh ├── example11_Time_heatmapAnimated │ ├── OUT1.png │ ├── S01.bin.gz │ ├── in1.conf │ └── run.sh └── example12_Time_histAnimated │ ├── OUT1.png │ ├── S02.data.gz │ ├── in1.conf │ └── run.sh ├── ColorsBrewer ├── aaas ├── atlassian ├── bmj ├── bs5 ├── cosmic ├── d3 ├── flatui ├── frontiers ├── futurama ├── gsea ├── igv ├── jama ├── jco ├── lancet ├── locuszoom ├── material ├── nejm ├── npg ├── observable ├── primer ├── rickandmorty ├── simpsons ├── startrek ├── tmp │ └── get_colors.pl ├── tron ├── tw3 ├── uchicago └── ucscgb ├── LICENSE ├── NewParaList.xlsx ├── README.md ├── RectChr_manual_Chinese_251006.pdf ├── RectChr_manual_English_251006.pdf ├── Scene_Usage ├── example01_Density_heatmap │ ├── 01.SNP_density.gz │ ├── 02.gene_density.gz │ ├── 03.GC_density.gz │ ├── OUT1.png │ ├── OUT2.png │ ├── in1.conf │ ├── in2.conf │ └── run.sh ├── example02_T2T_telo │ ├── OUT1.png │ ├── OUT3.png │ ├── center.txt │ ├── chrlist.txt │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ ├── region.info │ ├── region2.txt │ ├── region3.txt │ ├── region4.txt │ ├── run.sh │ ├── telo.txt │ └── tmp.conf ├── example03_ParentalMaker │ ├── OUT1.png │ ├── diff.spe.maker.gz │ ├── in1.conf │ ├── run.sh │ └── sample.bin2.gz ├── example04_RILBinMap │ ├── Noname_1.pl │ ├── OUT1.png │ ├── README.md │ ├── cor.info │ ├── data │ │ ├── S01.bin.gz │ │ ├── S02.bin.gz │ │ ├── S03.bin.gz │ │ ├── S04.bin.gz │ │ ├── S05.bin.gz │ │ ├── S06.bin.gz │ │ ├── S07.bin.gz │ │ ├── S08.bin.gz │ │ ├── S09.bin.gz │ │ ├── S10.bin.gz │ │ ├── S11.bin.gz │ │ ├── S12.bin.gz │ │ ├── S13.bin.gz │ │ ├── S14.bin.gz │ │ ├── S15.bin.gz │ │ ├── S16.bin.gz │ │ ├── S17.bin.gz │ │ ├── S18.bin.gz │ │ ├── S19.bin.gz │ │ ├── S20.bin.gz │ │ ├── S21.bin.gz │ │ ├── S22.bin.gz │ │ ├── S23.bin.gz │ │ ├── S24.bin.gz │ │ ├── S25.bin.gz │ │ ├── S26.bin.gz │ │ ├── S27.bin.gz │ │ ├── S28.bin.gz │ │ ├── S29.bin.gz │ │ ├── S30.bin.gz │ │ ├── S31.bin.gz │ │ ├── S32.bin.gz │ │ ├── S33.bin.gz │ │ ├── S34.bin.gz │ │ ├── S35.bin.gz │ │ ├── S36.bin.gz │ │ ├── S37.bin.gz │ │ ├── S38.bin.gz │ │ ├── S39.bin.gz │ │ ├── S40.bin.gz │ │ ├── S41.bin.gz │ │ ├── S42.bin.gz │ │ ├── S43.bin.gz │ │ ├── S44.bin.gz │ │ ├── S45.bin.gz │ │ ├── S46.bin.gz │ │ ├── S47.bin.gz │ │ ├── S48.bin.gz │ │ ├── S49.bin.gz │ │ ├── S50.bin.gz │ │ ├── S51.bin.gz │ │ ├── S52.bin.gz │ │ ├── S53.bin.gz │ │ ├── S54.bin.gz │ │ ├── S55.bin.gz │ │ ├── S56.bin.gz │ │ ├── S57.bin.gz │ │ ├── S58.bin.gz │ │ ├── S59.bin.gz │ │ ├── S60.bin.gz │ │ ├── S61.bin.gz │ │ ├── S62.bin.gz │ │ ├── S63.bin.gz │ │ ├── S64.bin.gz │ │ ├── S65.bin.gz │ │ ├── S66.bin.gz │ │ ├── S67.bin.gz │ │ ├── S68.bin.gz │ │ ├── S69.bin.gz │ │ ├── S70.bin.gz │ │ ├── S71.bin.gz │ │ ├── S72.bin.gz │ │ ├── S73.bin.gz │ │ ├── S74.bin.gz │ │ ├── S75.bin.gz │ │ ├── S76.bin.gz │ │ ├── S77.bin.gz │ │ ├── S78.bin.gz │ │ └── S79.bin.gz │ ├── in1.conf │ └── run.sh ├── example05_RegionHaplotype │ ├── OutRegion.cofi │ ├── OutRegion.col │ ├── OutRegion.conf │ ├── OutRegion.genotype │ ├── OutRegion.png │ ├── in.vcf.gz │ ├── pop.info │ ├── run.sh │ └── sample.order.list ├── example06_DepthCov │ ├── 03.HIC.bed.gz │ ├── 03.HIFI.bed.gz │ ├── 03.NGS.bed.gz │ ├── 03.ONT.bed.gz │ ├── OUT1.png │ ├── in1.conf │ └── run.sh ├── example07_Genetics │ ├── OUT1.png │ ├── OUT2.png │ ├── in.data │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ ├── run.sh │ ├── sele.region │ ├── sys.data │ └── sys3.data ├── example08_GWASShape │ ├── OUT2.png │ ├── OUT3.png │ ├── OUT4.png │ ├── OUT5.png │ ├── in1.conf │ ├── in2.conf │ ├── in3.conf │ ├── in5.conf │ ├── run1.sh │ ├── run2.sh │ ├── run3.sh │ └── site.text.info └── example09_ZoomRegion │ ├── 01.repeat.bed.gz │ ├── 02.SSR.bed.gz │ ├── 02.Satellite.bed.gz │ ├── 03.RNA-seq.bed.gz │ ├── 04.MQ.A.bed.gz │ ├── 04.MQ.B.bed.gz │ ├── OUT1.png │ ├── in1.conf │ └── run.sh ├── bin ├── In-CN.conf ├── In-EN.conf ├── RectChr ├── in.conf ├── lib │ ├── ColorPaletteManager.pm │ ├── ConfigDataLoader.pm │ ├── GenomicLinkPlot.pm │ ├── LocalUtils.pm │ └── RectChrPlot.pm ├── script │ ├── ColorBrewer.pl │ ├── CountBinNumPlot.pl │ ├── GenotypeShow.pl │ ├── ParaOld2New.pl │ └── temp │ │ ├── paratemp.pl │ │ └── ttttttt │ │ ├── In-CN.conf │ │ ├── Run.pl │ │ ├── V1Ano │ │ └── bbbb.pl └── svg_kit │ ├── FontSize.pm │ ├── SVG.pm │ ├── SVG │ ├── DOM.pm │ ├── Element.pm │ ├── Extension.pm │ └── XML.pm │ ├── Switch.pm │ ├── batik-1.7 │ ├── LICENSE │ ├── NOTICE │ ├── README │ ├── batik-rasterizer.jar │ ├── batik-slideshow.jar │ ├── batik-squiggle.jar │ ├── batik-svgpp.jar │ ├── batik-ttf2svg.jar │ ├── batik.jar │ ├── buildInFont │ ├── docs │ │ ├── .htaccess │ │ ├── broken-links.xml │ │ ├── contributors.html │ │ ├── demo.html │ │ ├── demo │ │ │ ├── AppletDemo$1.class │ │ │ ├── AppletDemo$2.class │ │ │ ├── AppletDemo.class │ │ │ ├── AppletDemo.java │ │ │ ├── Makefile │ │ │ ├── barChart.svg │ │ │ ├── batik-awt-util.jar │ │ │ ├── batik-bridge.jar │ │ │ ├── batik-css.jar │ │ │ ├── batik-dom.jar │ │ │ ├── batik-ext.jar │ │ │ ├── batik-gvt.jar │ │ │ ├── batik-parser.jar │ │ │ ├── batik-script.jar │ │ │ ├── batik-svg-dom.jar │ │ │ ├── batik-swing.jar │ │ │ ├── batik-util.jar │ │ │ ├── batik-xml.jar │ │ │ ├── demo.html │ │ │ └── xml-apis-dom3.jar │ │ ├── dev │ │ │ ├── branches.html │ │ │ ├── index.html │ │ │ ├── svg12.html │ │ │ └── test.html │ │ ├── download.html │ │ ├── faq.html │ │ ├── images │ │ │ ├── batik.png │ │ │ ├── batikUses.jpg │ │ │ ├── built-with-forrest-button.png │ │ │ ├── group-logo.png │ │ │ └── instruction_arrow.png │ │ ├── index.html │ │ ├── install.html │ │ ├── jarDependImg.png │ │ ├── license.html │ │ ├── linkmap.html │ │ ├── mailing-lists.html │ │ ├── skin │ │ │ ├── CommonMessages_de.xml │ │ │ ├── CommonMessages_en_US.xml │ │ │ ├── CommonMessages_es.xml │ │ │ ├── CommonMessages_fr.xml │ │ │ ├── basic.css │ │ │ ├── breadcrumbs-optimized.js │ │ │ ├── breadcrumbs.js │ │ │ ├── fontsize.js │ │ │ ├── getBlank.js │ │ │ ├── getMenu.js │ │ │ ├── images │ │ │ │ ├── README.txt │ │ │ │ ├── add.jpg │ │ │ │ ├── built-with-forrest-button.png │ │ │ │ ├── chapter.gif │ │ │ │ ├── chapter_open.gif │ │ │ │ ├── current.gif │ │ │ │ ├── error.png │ │ │ │ ├── external-link.gif │ │ │ │ ├── fix.jpg │ │ │ │ ├── forrest-credit-logo.png │ │ │ │ ├── hack.jpg │ │ │ │ ├── header_white_line.gif │ │ │ │ ├── info.png │ │ │ │ ├── instruction_arrow.png │ │ │ │ ├── label.gif │ │ │ │ ├── page.gif │ │ │ │ ├── pdfdoc.gif │ │ │ │ ├── poddoc.png │ │ │ │ ├── printer.gif │ │ │ │ ├── rc-b-l-15-1body-2menu-3menu.png │ │ │ │ ├── rc-b-r-15-1body-2menu-3menu.png │ │ │ │ ├── rc-b-r-5-1header-2tab-selected-3tab-selected.png │ │ │ │ ├── rc-t-l-5-1header-2searchbox-3searchbox.png │ │ │ │ ├── rc-t-l-5-1header-2tab-selected-3tab-selected.png │ │ │ │ ├── rc-t-l-5-1header-2tab-unselected-3tab-unselected.png │ │ │ │ ├── rc-t-r-15-1body-2menu-3menu.png │ │ │ │ ├── rc-t-r-5-1header-2searchbox-3searchbox.png │ │ │ │ ├── rc-t-r-5-1header-2tab-selected-3tab-selected.png │ │ │ │ ├── rc-t-r-5-1header-2tab-unselected-3tab-unselected.png │ │ │ │ ├── remove.jpg │ │ │ │ ├── rss.png │ │ │ │ ├── spacer.gif │ │ │ │ ├── success.png │ │ │ │ ├── txtdoc.png │ │ │ │ ├── update.jpg │ │ │ │ ├── valid-html401.png │ │ │ │ ├── vcss.png │ │ │ │ ├── warning.png │ │ │ │ └── xmldoc.gif │ │ │ ├── menu.js │ │ │ ├── note.txt │ │ │ ├── print.css │ │ │ ├── profile.css │ │ │ ├── prototype.js │ │ │ └── screen.css │ │ ├── status.html │ │ ├── tools │ │ │ ├── browser.html │ │ │ ├── font-converter.html │ │ │ ├── images │ │ │ │ ├── svgviewerAOI.png │ │ │ │ ├── svgviewerBrowsing.png │ │ │ │ ├── svgviewerDefaultRegular.png │ │ │ │ ├── svgviewerFileOpen.png │ │ │ │ ├── svgviewerLocationBar.png │ │ │ │ ├── svgviewerMultipleFiles.png │ │ │ │ ├── svgviewerOpenPage.png │ │ │ │ ├── svgviewerPan.png │ │ │ │ ├── svgviewerPreferences.png │ │ │ │ ├── svgviewerThumbnail.png │ │ │ │ ├── svgviewerViewSource.png │ │ │ │ ├── svgviewerViewTree.png │ │ │ │ └── svgviewerZoomin.png │ │ │ ├── index.html │ │ │ ├── pretty-printer.html │ │ │ └── rasterizer.html │ │ ├── uses.html │ │ └── using │ │ │ ├── architecture.html │ │ │ ├── dom-api.html │ │ │ ├── extending.html │ │ │ ├── images │ │ │ ├── HighLevelArchitecture.png │ │ │ ├── svgapplication.png │ │ │ ├── svggen.jpg │ │ │ └── svggenHighLevelArchi.jpg │ │ │ ├── index.html │ │ │ ├── parsers.html │ │ │ ├── scripting │ │ │ ├── ecmascript.html │ │ │ ├── java.html │ │ │ └── security.html │ │ │ ├── svg-generator.html │ │ │ ├── swing.html │ │ │ └── transcoder.html │ ├── extensions │ │ ├── README.txt │ │ ├── batik-rasterizer-ext.jar │ │ └── batik-squiggle-ext.jar │ └── lib │ │ ├── LICENSE.dom-documentation.txt │ │ ├── LICENSE.dom-software.txt │ │ ├── LICENSE.js.txt │ │ ├── LICENSE.pdf-transcoder.txt │ │ ├── LICENSE.sax.txt │ │ ├── LICENSE.xalan-2.6.0.txt │ │ ├── LICENSE.xerces_2_5_0.txt │ │ ├── README.js.txt │ │ ├── README.pdf-transcoder.txt │ │ ├── README.xalan-2.6.0.txt │ │ ├── README.xerces_2_5_0.txt │ │ ├── README.xml-apis-ext.txt │ │ ├── README.xml-apis.txt │ │ ├── Squiggle.icns │ │ ├── batik-anim.jar │ │ ├── batik-awt-util.jar │ │ ├── batik-bridge.jar │ │ ├── batik-codec.jar │ │ ├── batik-css.jar │ │ ├── batik-dom.jar │ │ ├── batik-ext.jar │ │ ├── batik-extension.jar │ │ ├── batik-gui-util.jar │ │ ├── batik-gvt.jar │ │ ├── batik-parser.jar │ │ ├── batik-script.jar │ │ ├── batik-svg-dom.jar │ │ ├── batik-svggen.jar │ │ ├── batik-swing.jar │ │ ├── batik-transcoder.jar │ │ ├── batik-util.jar │ │ ├── batik-xml.jar │ │ ├── js.jar │ │ ├── make-squiggle-app.sh │ │ ├── pdf-transcoder.jar │ │ ├── xalan-2.6.0.jar │ │ ├── xerces_2_5_0.jar │ │ ├── xml-apis-ext.jar │ │ └── xml-apis.jar │ ├── buildInFont.pl │ ├── generate_font_embed_defs.pl │ ├── 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