Mercurial > repos > iuc > pygenometracks
changeset 11:7dd841a32245 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
line wrap: on
line diff
--- a/macros.xml Sun Feb 13 22:43:45 2022 +0000 +++ b/macros.xml Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.6</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.7</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement> @@ -61,6 +61,27 @@ <xml name="track_input_link_macro"> <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/> </xml> + <xml name="track_input_fasta_macro"> + <conditional name="fasta_source"> + <param name="fasta_source_selector" type="select" label="Choose the source for the fasta to display"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="fasta_cached" type="select" label="Fasta availables"> + <options from_data_table="fasta_indexes"> + <validator type="no_options" message="No cached fasta is available"/> + </options> + </param> + </when> + <when value="history"> + <param name="fasta_local" type="data" format="fasta" label="Fasta from history"/> + </when> + </conditional> + </xml> + <xml name="track_input_maf_macro"> + <param name="track_input_maf" type="data" format="maf" label="Track file for maf" multiple="False"/> + </xml> <!-- Common to nearly all tracks: --> <xml name="plot_title"> <param name="title" type="text" optional="true" label="Plot title" multiple="True"/> @@ -166,6 +187,20 @@ <when value="none" /> </conditional> </xml> + <xml name="backbone_color_bed_macro"> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" type="select" label="Define the color of the backbone:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="none">No border</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of the backbone"/> + </when> + <when value="bed_rgb" /> + <when value="none" /> + </conditional> + </xml> <xml name="bed_advanced_macro"> <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Global max rows" /> @@ -175,8 +210,17 @@ <section name ="gtf" title="When using gtf as input" expanded="False"> <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" help="Usually transcript_name or gene_name"/> - <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Merge all transcripts of each gene in a single entry" /> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry"> + <option value="false" selected="True">No</option> + <option value="true">Yes</option> + </param> + <when value="true"> + <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Merge overlapping exons" help="Usually it makes prettier plots" /> + </when> + <when value="false" /> + </conditional> </section> </xml> <xml name="utr_macro"> @@ -352,4 +396,21 @@ <option value="magma_r">magma reversed</option> <option value="cividis_r">cividis reversed</option> </xml> + <xml name="links_arcs_triangles_options"> + <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> + <option value="0" selected="True">default (proportional to distance)</option> + <option value="1">compacted (the height is proportional to the square root of the distance)</option> + <option value="2">highly compacted (the height is the same for all distances)</option> + </param> + <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops"> + <option value="false" selected="True">Extremities (start of first and end of second)</option> + <option value="true">Center (mean of start and end for each)</option> + </param> + </xml> + <xml name="region2_option"> + <param name="region2" type="text" label="Region of the genome that should be plotted on the y axis" optional="true" + value="" help="The format is chr:start-end, for example chr10:10-500. By default this is the region on the x-axis. Top is start and bottom is end. Use 'Invert the track' if you want the contrary."> + <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator> + </param> + </xml> </macros>
--- a/pyGenomeTracks.xml Sun Feb 13 22:43:45 2022 +0000 +++ b/pyGenomeTracks.xml Sat Oct 01 08:43:22 2022 +0000 @@ -7,14 +7,21 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ - ## First symlink data of hic to have the good extension + ## First symlink data + ## of hic to have the good extension + ## of fasta to have the index written in the working directory #for $counter, $track in enumerate($tracks): - #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": + #if $track.track_file_style_conditional.track_file_style_selector in ["hic_matrix_option", "hic_matrix_square_option"]: #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): #set ext = $data_matrix.extension ln -s $data_matrix ${counter}_${counter_matrix}.$ext && #end for #end if + #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option": + #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history": + ln -s $track.track_file_style_conditional.fasta_source.fasta_local fasta_${counter}.fa && + #end if + #end if #end for @@ -46,7 +53,7 @@ <configfile name="tracks_config"> ## Each track: #for $counter, $track in enumerate($tracks): - ## Hi-C Track + ## Hi-C Track triangle #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): [hic_section_${counter}_${counter_matrix}] @@ -106,6 +113,67 @@ #end for #end if + ## Hi-C Track square + #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_square_option": + #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): +[hic_section_${counter}_${counter_matrix}] + #set ext = $data_matrix.extension +file = ${counter}_${counter_matrix}.$ext +file_type = hic_matrix_square + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #else: +title = $data_matrix.element_identifier + #end if + #if $track.track_file_style_conditional.region2: +region2 = $track.track_file_style_conditional.region2 + #end if + #if $track.track_file_style_conditional.colormap: +colormap = $track.track_file_style_conditional.colormap + #end if + #if $track.track_file_style_conditional.min_value != "": +min_value = $track.track_file_style_conditional.min_value + #end if + #if $track.track_file_style_conditional.max_value != "": +max_value = $track.track_file_style_conditional.max_value + #end if +transform = $track.track_file_style_conditional.transform + #if $track.track_file_style_conditional.height_matrix != "": +height = $track.track_file_style_conditional.height_matrix + #end if + #if $track.track_file_style_conditional.show_masked_bins: +show_masked_bins = $track.track_file_style_conditional.show_masked_bins + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if + #if $track.track_file_style_conditional.scale_factor: +scale_factor = $track.track_file_style_conditional.scale_factor + #end if +rasterize = $track.track_file_style_conditional.rasterize + ## If a boundary file is given a new section needs to be written: + #if str($track.track_file_style_conditional.boundaries_file) != "None": + #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: + #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] + #else: + #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] + #end if +[tads_${counter}_${counter_matrix}] +file = $boundary_file +file_type = bed +display = squares +border_color = black +color = none +overlay_previous = share-y + #end if + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end for + #end if + ## Chrom_state track #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": #for $data_bed in $track.track_file_style_conditional.track_input_bed: @@ -148,7 +216,10 @@ file = $data_bed #if $ext == 'gtf': prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name -merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts + #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true': +merge_transcripts = true +merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons + #end if #end if #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title @@ -168,6 +239,11 @@ style = $track.track_file_style_conditional.bed_style.bed_style_select #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval + #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #else: height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': @@ -175,6 +251,7 @@ #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': color_utr = bed_rgb #else: + ## This is 'like' #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color_utr = bed_rgb #else: @@ -186,6 +263,12 @@ #end if #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included +arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction + #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #end if #end if display = $track.track_file_style_conditional.display @@ -196,11 +279,12 @@ #if $track.track_file_style_conditional.labels.plot_labels == 'true': all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin +fontstyle = $track.track_file_style_conditional.labels.fontstyle + #if $track.track_file_style_conditional.labels.fontsize: +fontsize = $track.track_file_style_conditional.labels.fontsize + #end if #end if file_type = $ext - #if $track.track_file_style_conditional.fontsize: -fontsize = $track.track_file_style_conditional.fontsize - #end if #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows #end if @@ -241,12 +325,17 @@ alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style -links_type = $track.track_file_style_conditional.links_type -compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level - #if $track.track_file_style_conditional.ylim != "": -ylim = $track.track_file_style_conditional.ylim +links_type = $track.track_file_style_conditional.display.links_type + #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: +compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level +use_middle = $track.track_file_style_conditional.display.use_middle #end if -use_middle = $track.track_file_style_conditional.use_middle + #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": +ylim = $track.track_file_style_conditional.display.ylim + #end if + #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": +region2 = $track.track_file_style_conditional.display.region2 + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -288,10 +377,12 @@ height = $track.track_file_style_conditional.height_narrow_peak #end if line_width = $track.track_file_style_conditional.line_width -show_labels = $track.track_file_style_conditional.show_labels file_type = narrow_peak - #if $track.track_file_style_conditional.fontsize: -fontsize = $track.track_file_style_conditional.fontsize +show_labels = $track.track_file_style_conditional.labels.show_labels + #if $track.track_file_style_conditional.labels.show_labels == 'true': + #if $track.track_file_style_conditional.labels.fontsize: +fontsize = $track.track_file_style_conditional.labels.fontsize + #end if #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted @@ -469,6 +560,8 @@ show_data_range = $track.track_file_style_conditional.type.show_data plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin +individual_color = $track.track_file_style_conditional.type.individual_color +summary_color = $track.track_file_style_conditional.type.summary_color #else colormap = $track.track_file_style_conditional.type.colormap #end if @@ -491,6 +584,15 @@ type = vlines #end if + ## Vhighlight: + #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option": +[vhighlight_$counter] +file = $track.track_file_style_conditional.track_input_bed_single +color = $track.track_file_style_conditional.color +alpha = $track.track_file_style_conditional.alpha +type = vhighlight + #end if + ## Hlines: #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": [hlines_$counter] @@ -579,6 +681,9 @@ #if $track.track_file_style_conditional.fontsize != "": fontsize = $track.track_file_style_conditional.fontsize #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if file_type = scalebar ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": @@ -586,12 +691,74 @@ height = $track.track_file_style_conditional.spacer_height #end if #end if + + ## Fasta: + #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option": +[Fasta_${counter}] + #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history": +file = fasta_${counter}.fa + #else: +file = $track.track_file_style_conditional.fasta_source.fasta_cached.fields.path + #end if + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +file_type = fasta + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if + + ## Maf: + #if $track.track_file_style_conditional.track_file_style_selector == "maf_option": +[Maf_${counter}] +file = $track.track_file_style_conditional.track_input_maf +file_index = $track.track_file_style_conditional.track_input_maf.metadata.maf_index +reference = $track.track_file_style_conditional.reference + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +line_width = $track.track_file_style_conditional.line_width +color_identical = $track.track_file_style_conditional.color_identical +color_mismatch = $track.track_file_style_conditional.color_mismatch +color_gap = $track.track_file_style_conditional.color_gap + #if $track.track_file_style_conditional.species_order != "": +species_order = $track.track_file_style_conditional.species_order + #if $track.track_file_style_conditional.species_labels != "": +species_labels = $track.track_file_style_conditional.species_labels + #end if +species_order_only = $track.track_file_style_conditional.species_order_only + #end if +display_ref_seq = $track.track_file_style_conditional.display_ref_seq +file_type = maf + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if #end for </configfile> </configfiles> <inputs> <!--Arguments for pgt--> - <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" + <param argument="--region" type="text" label="Region of the genome to plot" optional="false" help="The format is chr:start-end, for example chr10:10-500"> <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator> </param> @@ -621,7 +788,8 @@ The order you add them represent the order they will be plotted from top to bottom."> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" type="select" label="Choose style of the track"> - <option value="hic_matrix_option">TAD visualization</option> + <option value="hic_matrix_option">TAD visualization (triangle)</option> + <option value="hic_matrix_square_option">TAD visualization (square)</option> <option value="chrom_states_option">Chromatine states</option> <option value="gene_track_option">Gene track / Bed track</option> <option value="link_track_option">Link track</option> @@ -630,10 +798,13 @@ <option value="bedgraph_track_option">Bedgraph track </option> <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option> <option value="vlines_track_option">Vlines track</option> + <option value="vhighlight_track_option">Vhighlight track</option> <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> <option value="xaxis_option">X-axis</option> <option value="scale_bar_option">Scale bar track</option> + <option value="fasta_option">Fasta track</option> + <option value="maf_option">Maf track</option> </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> @@ -644,8 +815,8 @@ <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> </param> + <expand macro="minmax_macro" /> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> - <expand macro="minmax_macro" /> <param name="transform" type="select" label="Plot the transformed value"> <option value="log1p" selected="True" >log1p</option> <option value="log">log</option> @@ -653,10 +824,40 @@ <option value="no">no transformation</option> </param> - <param name="height_matrix" type="float" value="" optional="True" label="height"/> + <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares rotated 45 degrees."/> <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Show masked bins" /> - <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> + label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." /> + <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display triangles on top of the heatmap"/> + <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> + <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Rasterize the heatmap" /> + <expand macro="inverted_macro" /> + <expand macro="spacer_macro" /> + + </when> + + <when value="hic_matrix_square_option"> + <expand macro="plot_title" /> + <expand macro="matrix_h5_cooler_multiple_macro" /> + + <param name="colormap" type="select" 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"> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> + </param> + <expand macro="minmax_macro" /> + <expand macro="region2_option" /> + <param name="transform" type="select" label="Plot the transformed value"> + <option value="log1p" selected="True" >log1p</option> + <option value="log">log</option> + <option value="-log">-log</option> + <option value="no">no transformation</option> + + </param> + <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares."/> + <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." /> + <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display squares on top of the heatmap"/> <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Rasterize the heatmap" /> @@ -729,6 +930,12 @@ <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to put labels in the right margin" help="Put labels in the margin if the region ends after the plotted region."/> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <param name="fontstyle" type="select" label="Fontstyle"> + <option value="normal" selected="True">normal</option> + <option value="italic">italic</option> + <option value="oblique">oblique</option> + </param> </when> <when value="false"/> </conditional> @@ -737,8 +944,8 @@ <option value="interleaved">interleaved (everything on 2 lines)</option> <option value="collapsed">collapsed (everything on 1 line)</option> <option value="triangles">triangles (plot triangles between start and end)</option> + <option value="squares">squares (plot squares on the diagonal)</option> </param> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> <conditional name="bed_style"> <param name="bed_style_select" type="select" label="Bed style"> <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> @@ -749,15 +956,20 @@ <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include the arrowhead in the bed interval:" help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> + <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1" + label="Size of arrowhead relative to the plotted region" + help="This size is also used to put space between the bed regions and their labels."/> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <expand macro="utr_macro" /> <expand macro="bed_advanced_macro" /> + <expand macro="backbone_color_bed_macro" /> </section> </when> <when value="UCSC"> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> <expand macro="bed_advanced_macro" /> + <expand macro="backbone_color_bed_macro" /> </section> </when> <when value="tssarrow"> @@ -793,21 +1005,28 @@ </when> </conditional> <expand macro="lines_macro" /> - <param name="links_type" type="select" label="Representation of the link:"> - <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> - <option value="triangles">triangles</option> - <option value="loops">loops (a rectangle highlighting the intersection)</option> - </param> - <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> - <option value="0" selected="True">default (proportional to distance)</option> - <option value="1">compacted (the height is proportional to the square root of the distance)</option> - <option value="2">highly compacted (the height is the same for all distances)</option> - </param> - <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> - <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops"> - <option value="false" selected="True">Extremities (start of first and end of second)</option> - <option value="true">Center (mean of start and end for each)</option> - </param> + <conditional name="display"> + <param name="links_type" type="select" label="Representation of the link:"> + <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> + <option value="triangles">triangles</option> + <option value="loops">loops (a diamond highlighting the intersection)</option> + <option value="squares">squares (a square highlighting the intersection symetrically to the diagonal)</option> + </param> + <when value="arcs"> + <expand macro="links_arcs_triangles_options" /> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="triangles"> + <expand macro="links_arcs_triangles_options" /> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="loops"> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="squares"> + <expand macro="region2_option" /> + </when> + </conditional> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> @@ -839,9 +1058,16 @@ </when> </conditional> <param name="line_width" type="float" value="1" label="width of lines" /> - <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" - label="Plot labels (name, p-val, q-val)" /> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <conditional name="labels"> + <param name="show_labels" type="select" label="Plot labels (name, p-val, q-val)"> + <option value="true" selected="True">yes</option> + <option value="false">no</option> + </param> + <when value="true"> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + </when> + <when value="false"/> + </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -939,6 +1165,8 @@ <option value="center" selected="True">Center</option> <option value="block">Block (draw a horizontal line between start and end)</option> </param> + <param name="individual_color" type="color" value="grey" label="Color of the individual lines" /> + <param name="summary_color" type="color" value="#1f77b4" label="Color of the summary line" /> </when> <when value="matrix"> <param name="colormap" type="select" label="colormap"> @@ -958,12 +1186,17 @@ <expand macro="track_input_bed_single_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines"/> </when> + <when value="vhighlight_track_option"> + <expand macro="track_input_bed_single_macro" /> + <param name="color" type="color" value="yellow" label="color of the highlight"/> + <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/> + </when> <when value="hlines_track_option"> <expand macro="plot_title" /> <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> <expand macro="lines_macro" /> - <param name="height" type="float" value="1.5" optional="True" label="height"/> + <param name="height" type="float" value="1.5" optional="True" label="height of the Hlines track"/> <expand macro="minmax_macro" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> @@ -1006,6 +1239,39 @@ </param> <param name="fontsize" type="float" optional="True" label="Fontsize of the size of the scale bar."/> + <param name="height" type="float" value="0.5" optional="True" label="height of the Scale bar track"/> + <expand macro="spacer_macro" /> + </when> + <when value="fasta_option"> + <expand macro="track_input_fasta_macro" /> + <expand macro="plot_title" /> + <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> + <expand macro="spacer_macro" /> + </when> + <when value="maf_option"> + <expand macro="track_input_maf_macro" /> + <expand macro="plot_title" /> + <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/> + <param name="reference" type="select" label="Reference"> + <options> + <filter type="data_meta" ref="track_input_maf" key="species" /> + </options> + </param> + <param name="line_width" type="float" value="0.5" label="width of lines"/> + <param name="color_identical" type="color" label="Color when bases are identical" value="black" /> + <param name="color_mismatch" type="color" label="Color when bases are different" value="grey" /> + <param name="color_gap" type="color" label="Color when bases corresponds to gap" value="lightgrey" /> + <param name="species_order" type="text" value="" label="[Optional] The order you want your species (space separated)" + help="checkout the choices for reference to see available species"/> + <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/> + <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Display only the species specified above"/> + <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Display the sequence of the reference"/> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> </conditional> @@ -1154,7 +1420,9 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes" /> <param name="height_bed" value="5" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1169,7 +1437,9 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> - <param name="fontsize" value="8" /> + <conditional name="labels"> + <param name="fontsize" value="8" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="gene_rows" value="3" /> @@ -1189,7 +1459,9 @@ <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> @@ -1416,7 +1688,9 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> @@ -1428,7 +1702,9 @@ <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> @@ -1446,7 +1722,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1466,7 +1741,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1485,7 +1759,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1591,7 +1864,6 @@ <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1606,7 +1878,6 @@ <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1623,7 +1894,9 @@ <param name="width_adjust" value="3" /> <param name="max_value" value="50" /> </conditional> - <param name="show_labels" value="false" /> + <conditional name="labels"> + <param name="show_labels" value="false" /> + </conditional> <param name="spacer_height" value="0.5"/> </conditional> </repeat> @@ -1639,7 +1912,6 @@ <param name="use_summit" value="false" /> <param name="show_data" value="false" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1663,8 +1935,8 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> - <param name="title" value="genes" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="gtf default" /> <param name="height_bed" value="10" /> </conditional> </repeat> @@ -1672,7 +1944,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="gtf" /> + <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> @@ -1683,7 +1955,34 @@ </conditional> <section name ="gtf"> <param name="prefered_name" value="gene_name"/> - <param name="merge_transcripts" value="true"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="false"/> + </conditional> + </section> + </section> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="same but merge overlapping exons" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="height_utr" value="0.75"/> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="#ff0000"/> + </conditional> + <section name ="gtf"> + <param name="prefered_name" value="gene_name"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="true"/> + </conditional> </section> </section> </conditional> @@ -1811,16 +2110,34 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="test" /> + <param name="title" value="defaut arrowhead fontstyle italic" /> <param name="height_bed" value="10" /> <param name="spacer_height" value="1"/> + <conditional name="labels"> + <param name="fontstyle" value="italic"/> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" /> + <param name="height_bed" value="10" /> + <param name="spacer_height" value="1"/> + <conditional name="labels"> + <param name="fontstyle" value="oblique"/> + </conditional> + <conditional name="bed_style"> + <param name="arrowhead_fraction" value="0.1"/> + </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> - <param name="title" value="test" /> + <param name="title" value="genes without orientation" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> @@ -1836,7 +2153,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="test" /> + <param name="title" value="arrowhead included" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> @@ -1938,7 +2255,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> - <param name="title" value="TAD separation score (Ramirez et al.)" /> + <param name="title" value="TAD separation score (Ramirez et al.) as block with horizontal lines and data range" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> @@ -1952,12 +2269,14 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> - <param name="title" value="TAD separation score (Ramirez et al.)" /> + <param name="title" value="TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> <param name="pos_score_in_bin" value="center" /> <param name="plot_horizontal_lines" value="false" /> + <param name="individual_color" value="blue"/> + <param name="summary_color" value="red"/> </conditional> </conditional> </repeat> @@ -1989,7 +2308,9 @@ <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="" /> <param name="line_width" value="10" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="red" /> @@ -2037,7 +2358,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="ylim" value="20000" /> + <conditional name="display"> + <param name="ylim" value="20000" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -2049,7 +2372,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="compact_arcs_level" value="1" /> + <conditional name="display"> + <param name="compact_arcs_level" value="1" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -2061,7 +2386,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="compact_arcs_level" value="2" /> + <conditional name="display"> + <param name="compact_arcs_level" value="2" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> @@ -2120,20 +2447,33 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> - <param name="title" value="flybase" /> + <param name="title" value="flybase backbone blue" /> <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="flybase"/> + <section name="bed_advanced"> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> + <param name="color" value="blue" /> + </conditional> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> - <param name="title" value="UCSC" /> + <param name="title" value="UCSC backbone blue" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> <section name="bed_advanced"> <param name="arrow_interval" value="10"/> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> + <param name="color" value="blue" /> + </conditional> </section> </conditional> </conditional> @@ -2573,7 +2913,9 @@ <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <param name="overlay_select" value="share-y" /> </conditional> </repeat> @@ -2615,7 +2957,9 @@ <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <param name="overlay_select" value="share-y" /> </conditional> </repeat> @@ -2628,7 +2972,9 @@ </conditional> <param name="line_width" value="3" /> <param name="invert_orientation" value="true" /> - <param name="use_middle" value="true" /> + <conditional name="display"> + <param name="use_middle" value="true" /> + </conditional> <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> <param name="height" value="3" /> </conditional> @@ -2655,7 +3001,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar where = right" /> - <param name="where" value="right" /> + <param name="sb_where" value="right"/> <param name="spacer_height" value="0.5"/> </conditional> </repeat> @@ -2675,7 +3021,7 @@ <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> - <param name="scalebar_start_position" value="3250000"/> + <param name="scalebar_end_position" value="3250000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> @@ -2710,7 +3056,6 @@ <param name="scalebar_end_position" value="3200000"/> <param name="size" value="50000"/> </section> - <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> @@ -2722,6 +3067,223 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> </test> + <!--test 22--> + <test> + <param name="region" value="chrM:10-30"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar height = 5" /> + <param name="sb_where" value="right"/> + <param name="height" value="5"/> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="fasta_option" /> + <param name="title" value="fasta from cached" /> + <conditional name="fasta_source"> + <param name="fasta_source_selector" value="cached"/> + <param name="fasta_cached" value="chrM"/> + </conditional> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="fasta_option" /> + <param name="title" value="fasta from history height = 5" /> + <conditional name="fasta_source"> + <param name="fasta_source_selector" value="history"/> + <param name="fasta_local" value="chrM.fa" ftype="fasta" /> + </conditional> + <param name="height" value="5"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="master_fasta.png" ftype="png" compare="sim_size" delta="100" /> + </test> + <!--test 23--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="spacer_option" /> + <param name="spacer_height" value="0.05" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="classical depth=300000 with arcs" /> + <param name="depth" value="300000" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with arcs" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="squares" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with arcs region2=chrX:3000000-3100000" /> + <param name="region2" value="chrX:3000000-3100000"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="squares" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000" /> + <param name="region2" value="chrX:3000000-3100000"/> + <param name="colormap" value="Blues"/> + <param name="transform" value="no" /> + <param name="boundaries_file" value="tad_classification.bed" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="sim_size" delta="1200" /> + </test> + <!--test 24--> + <test> + <param name="region" value="2:34704975-34705208"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="default" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="height = 3 show sequence" /> + <param name="height" value="3"/> + <param name="display_ref_seq" value="true"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="species_order = hg19 rn5, species_labels = Human Rat" /> + <param name="height" value="3"/> + <param name="species_order" value="hg19 rn5"/> + <param name="species_labels" value="Human Rat"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" /> + <param name="height" value="3"/> + <param name="species_order" value="hg19"/> + <param name="species_labels" value="Human"/> + <param name="species_order_only" value="true"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_maf.png" ftype="png" compare="sim_size" delta="1200" /> + </test> + <!--test 25--> + <test> + <param name="region" value="chr2:73,800,000-75,744,000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <param name="max_value" value="5" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="vhighlight_track_option" /> + <param name="track_input_bed_single" value="islands.bed" ftype="bed"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="sim_size" delta="1200" /> + </test> </tests> <help><![CDATA[ @@ -2738,6 +3300,8 @@ - narrow peaks - links - Hi-C matrices (cool or HiCExplorer h5) + - Fasta + - MAF (multiple alignment format) _________________ @@ -2757,10 +3321,13 @@ - **Bedgraph track:** generic bedgraph track plotting. - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). - **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``. + - **Vhighlight:** vertical rectangles drawn on top of all tracks following a bed file. It is used as a visual support to highlight some regions. - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks. - **Spacer:** Add some space between two tracks. - **X-axis:** Plot x-axis scale wherever you want. - **Scale bar track:** Plot scale bar. + - **Fasta track:** Display sequences from fasta. + - **Maf track:** Display alignments from maf. For each track, parameters for the color, the width or the font size can be defined.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,333 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT +TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG +GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC +CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA +AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT +GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT +TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT +ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC +CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA +ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA +GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT +AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA +ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC +ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT +AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC +GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA +GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT +CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC +TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC +CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG +AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC +AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA +GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG +GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC +TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC +AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA +GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA +CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA +ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT +TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG +AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT +GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA +CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT +CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC +CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA +AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT +AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA +GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA +ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG +TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA +TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC +AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA +CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA +GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata +atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc +agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg +ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT +GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT +ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC +AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT +ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA +GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT +AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT +ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT +ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt +aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt +aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT +CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC +AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC +TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG +CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC +AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC +AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG +CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC +ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT +TATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC +GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATA +CGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTA +TTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGAC +GCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACT +TCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCT +ACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCC +CCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTA +AATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaacc +catccctgagaatccaaaattctccgtgccacctatcacaccccatccta +AAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGG +TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT +CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCT +AACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCC +TCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAAC +AATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTC +ATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT +TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGC +CTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTAT +CCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAA +ATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCT +ACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC +TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACC +CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAAT +TCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATC +ATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCT +ACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG +TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCC +ACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACT +AATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGC +CCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAG +CCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT +AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAA +AAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAA +TTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGT +CTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCA +CTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC +TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGT +AACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAAT +CTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAG +TTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAAC +ATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGC +TATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCC +TTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCAC +AACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCC +TCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTC +CCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAA +CACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC +ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGA +ACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCC +TAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTA +GACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCAC +CGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA +AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACC +GTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAA +TAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTA +TTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTAT +CATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC +TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACA +TGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAAT +ATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCC +CCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaa +aaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcc +tccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTC +AAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCG +CAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCAC +CTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATC +TCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT +CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACG +AGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTAC +TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACAT +ACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTG +ACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC +AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGAC +CGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGT +TTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGG +GCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGT +AAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACA +CCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT +TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA +AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA +TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT +ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC +TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA +ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT +TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA +TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT +AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG +TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA +CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG +AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA +ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA +CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC +ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG +CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA +ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG +CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC +TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA +CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC +TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC +CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT +TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT +TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT +CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC +ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT +TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG +TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC +TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC +GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA +TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC +AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC +TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC +GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA +TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA +TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC +TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA +TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA +CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA +CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT +GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC +AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC +CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC +AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT +ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA +ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG +CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT +AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC +TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA +GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT +ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC +TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA +CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG +ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA +GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT +TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA +ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA +CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT +CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA +CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC +ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA +CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA +TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT +AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA +TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG +GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA +CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC +ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT +GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC +AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT +GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC +TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC +CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT +CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA +TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA +TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG +GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA +GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC +AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC +TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA +GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC +CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA +CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA +TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT +CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT +TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA +CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT +ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA +ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA +TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC +ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA +CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT +TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC +TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT +CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC +CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC +TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT +CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC +ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA +TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC +ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA +TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA +ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT +AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG +GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC +AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA +CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC +ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC +ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG +CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC +ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA +TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC +CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG +AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG +CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC +TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT +GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG +AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT +CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG +ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC +AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC +TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG +CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC +CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC +AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT +ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT +AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG +ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG +ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT +ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC +CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA +CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC +CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA +CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA +ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC +CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT +CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT +TAAATAAGACATCACGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,1 @@ +chrM 16569 6 50 51
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/first.maf Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,987 @@ +##maf version=1 +a score=41100.0 +s mm10.chr2 34705072 4 + 182113224 G-AAG +s rn5.chr3 19096925 4 + 183740530 G-AAG +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114691 4 - 141213431 G-ACA +i hg19.chr9 I 195 I 6 + +a score=423183.0 +s mm10.chr2 34705076 25 + 182113224 AGGTGGAGA-------ACTATAGAATTTGAAA +s rn5.chr3 19096929 25 + 183740530 AGGCAGAGA-------ACTGTGGAGTTTGAAA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114701 25 - 141213431 AAATAAAAG-------GCTGTAAATCTTGAAG +i hg19.chr9 I 6 C 0 + +a score=66158.0 +s mm10.chr2 34705101 4 + 182113224 GTCT +s rn5.chr3 19096954 4 + 183740530 GGCT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114726 4 - 141213431 TTCT +i hg19.chr9 C 0 C 0 + +a score=387811.0 +s mm10.chr2 34705105 18 + 182113224 AATATTGCTTTCA---GCAAA +s rn5.chr3 19096958 18 + 183740530 AATATTGCTTTCA---GCAAA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114730 18 - 141213431 AACACTGCTCTCA---GCAAA +i hg19.chr9 C 0 C 0 + +a score=10920.0 +s mm10.chr2 34705123 1 + 182113224 T +s rn5.chr3 19096976 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114748 1 - 141213431 T +i hg19.chr9 C 0 C 0 + +a score=-29032.0 +s mm10.chr2 34705124 7 + 182113224 GTCTTGA--- +s rn5.chr3 19096977 7 + 183740530 GTCCTAA--- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114749 2 - 141213431 -----AA--- +i hg19.chr9 C 0 C 0 + +a score=-6898.0 +s mm10.chr2 34705131 8 + 182113224 TTTA------AAAA +s rn5.chr3 19096984 8 + 183740530 TTTT------AAAA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114751 8 - 141213431 CTTT------AAAA +i hg19.chr9 C 0 I 1 + +a score=37882.0 +s mm10.chr2 34705139 24 + 182113224 AAAAATCTATGAGTGAAATG---AATA +s rn5.chr3 19096992 23 + 183740530 CGAATTC-ATGAATGAAATG---AATA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114760 24 - 141213431 AGATAAGTATGCAGAGGATG---GAAA +i hg19.chr9 I 1 C 0 + +a score=2589.0 +s mm10.chr2 34705163 1 + 182113224 T +s rn5.chr3 19097015 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114784 1 - 141213431 T +i hg19.chr9 C 0 C 0 + +a score=-36380.0 +s mm10.chr2 34705164 35 + 182113224 ATAATGCCATGAAAT--TGACTCTA-ATTTCT-AAATGT +s rn5.chr3 19097016 30 + 183740530 ATAATGCCACG-AAT--TAACTCTA-ATTTCT-AA---- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114785 32 - 141213431 -TTCAAACATAAAA---AAATTATT-A-ATCT-AAATGT +i hg19.chr9 C 0 C 0 + +a score=33050.0 +s mm10.chr2 34705199 17 + 182113224 ACTA-TTTTA--GACTACAG +s rn5.chr3 19097046 14 + 183740530 ---A-TCTTA--GACTACAG +i rn5.chr3 C 0 C 0 +s hg19.chr9 13114817 13 - 141213431 -----TTTTA--GTCTGAAG +i hg19.chr9 C 0 I 3470 + +a score=548.0 +s mm10.chr2 34705216 11 + 182113224 AACTCCCCCTC-- +s rn5.chr3 19097060 11 + 183740530 AACCCCCACTC-- +i rn5.chr3 C 0 C 0 + +a score=-4856.0 +s mm10.chr2 34705227 6 + 182113224 CCCAAA- +s rn5.chr3 19097071 6 + 183740530 CCAAAA- +i rn5.chr3 C 0 C 0 + +a score=87104.0 +s mm10.chr2 34705233 20 + 182113224 AGATAACCCTAACTAAGCAT +s rn5.chr3 19097077 16 + 183740530 AGATACCC----CTAAGCAC +i rn5.chr3 C 0 C 0 + +a score=1769.0 +s mm10.chr2 34705253 1 + 182113224 G +s rn5.chr3 19097093 1 + 183740530 G +i rn5.chr3 C 0 C 0 + +a score=-7449.0 +s mm10.chr2 34705254 3 + 182113224 TCT-- +s rn5.chr3 19097094 3 + 183740530 TCT-- +i rn5.chr3 C 0 C 0 + +a score=-9682.0 +s mm10.chr2 34705257 3 + 182113224 TAA +s rn5.chr3 19097097 3 + 183740530 TAA +i rn5.chr3 C 0 C 0 + +a score=45039.0 +s mm10.chr2 34705260 9 + 182113224 CACAACTAG +s rn5.chr3 19097100 9 + 183740530 CACAATTAG +i rn5.chr3 C 0 C 0 + +a score=4300.0 +s mm10.chr2 34705269 1 + 182113224 A +s rn5.chr3 19097109 1 + 183740530 A +i rn5.chr3 C 0 C 0 + +a score=135112.0 +s mm10.chr2 34705270 16 + 182113224 AA-T------ATTAAAATAG----GTA +s rn5.chr3 19097110 16 + 183740530 AA-T------ATTAAAATAG----GTA +i rn5.chr3 C 0 C 0 + +a score=171803.0 +s mm10.chr2 34705286 14 + 182113224 AGTATACAGAGACT +s rn5.chr3 19097126 14 + 183740530 AGTATAAAGATACC +i rn5.chr3 C 0 C 0 + +a score=59500.0 +s mm10.chr2 34705300 4 + 182113224 AAAA +s rn5.chr3 19097140 4 + 183740530 AAAA +i rn5.chr3 C 0 I 99 +s hg19.chr9 13118300 4 - 141213431 ggac +i hg19.chr9 I 3470 C 0 + +a score=26234.0 +s mm10.chr2 34705304 2 + 182113224 CT +s rn5.chr3 19097243 2 + 183740530 CT +i rn5.chr3 I 99 C 0 +s hg19.chr9 13118304 2 - 141213431 tt +i hg19.chr9 C 0 C 0 + +a score=4664.0 +s mm10.chr2 34705306 1 + 182113224 T +s rn5.chr3 19097245 1 + 183740530 T +i rn5.chr3 C 0 C 0 + +a score=10920.0 +s mm10.chr2 34705307 1 + 182113224 T +s rn5.chr3 19097246 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118306 1 - 141213431 t +i hg19.chr9 C 0 C 0 + +a score=10500.0 +s mm10.chr2 34705308 1 + 182113224 C +s rn5.chr3 19097247 1 + 183740530 C +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118307 1 - 141213431 c +i hg19.chr9 C 0 C 0 + +a score=1320.0 +s mm10.chr2 34705309 14 + 182113224 TCCACTCACGGATT---- +s rn5.chr3 19097248 14 + 183740530 TCCATTCATGGatt---- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118308 18 - 141213431 tctacacatggaattttt +i hg19.chr9 C 0 C 0 + +a score=8456.0 +s mm10.chr2 34705323 15 + 182113224 TCCTTATAACAGATT +s rn5.chr3 19097262 15 + 183740530 tcattatgacagatt +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118326 15 - 141213431 tcattatgactgaca +i hg19.chr9 C 0 C 0 + +a score=352.0 +s mm10.chr2 34705338 11 + 182113224 TCTAGAAGTAG--- +s hg19.chr9 13118341 11 - 141213431 cctagaagtgg--- +i hg19.chr9 C 0 C 0 + +a score=25195.0 +s mm10.chr2 34705349 194 + 182113224 TTCT-------------------TTTTTTTCCCCGCCTtttttttgagacagggtttctctgtgtagatcttg-------gctgtcctggaactcact--ctgtagac-caggctggccttgaactcagaaatccgcctgcctctgcctctgcctctgcctcccaagtgctgggattaaaggcttgcagcaccactgcctggcCtttttt-------ttttttttaaaga + +a score=0.0 +s mm10.chr2 34705543 173 + 182113224 tttattattatttatatgtaagtacactgtagctatcctcagacacaccagtagagggcatcagatgtcatttcagatggttgtaaaccaccatgtggttgctaggatttgaactcaggaccttcattagaacagtcagtgctcttaaccgctgaaccatctctccagccccC + +a score=1419.0 +s mm10.chr2 34705716 5 + 182113224 TCTAG +s rn5.chr3 19097277 5 + 183740530 tctag +i rn5.chr3 C 0 C 0 + +a score=23757.0 +s mm10.chr2 34705721 71 + 182113224 AAGTAGTTCTAACTGATCCAAATTTAGAATATGATCATCTAAGTCCCCAAGAACACATTGACAAGTTATGC +s rn5.chr3 19097282 71 + 183740530 aagtagttctaactgaaccaaatttagaatatgaacatttaagtccccacgtacacactgacaagttatgc +i rn5.chr3 C 0 I 271 +s hg19.chr9 13118352 65 - 141213431 ------aactaacctgactaaatttagaatgtgaacatttaagaccttaaatagatactgacaaagtatgt +i hg19.chr9 C 0 C 0 + +a score=1587.0 +s mm10.chr2 34705792 4 + 182113224 CCCA +s rn5.chr3 19097624 4 + 183740530 CCTG +i rn5.chr3 I 271 C 0 +s hg19.chr9 13118417 4 - 141213431 ccca +i hg19.chr9 C 0 I 76 + +a score=1744.0 +s mm10.chr2 34705796 49 + 182113224 CTTTGATTTTTAGGGCTTTGTTTT--GGTTGTTTTAGGATTTTTTTTTCTC +s rn5.chr3 19097628 51 + 183740530 CTTTGTTTTGTAGGAttttgcttttgggttttttcttctcttttttctttc +i rn5.chr3 C 0 C 0 + +a score=-3038.0 +s mm10.chr2 34705845 83 + 182113224 CTTTTT----CTTTCGTttttggttttttggatcaggactcactatgtagact-tggctgacctagaactcactatgtagaccaggca +s rn5.chr3 19097679 83 + 183740530 tttttt----gttttttttttttttttttggataaaggctcactctacagact-tggctgacttggaactcactatgtaagccaggca +i rn5.chr3 C 0 C 0 + +a score=-8755.0 +s mm10.chr2 34705928 42 + 182113224 agtctcaaactcatagatattccctg----gcctctatct---gagttc +s rn5.chr3 19097762 45 + 183740530 aatcttaaactcacagataatcccct----gcctccacctcctgagtgc +i rn5.chr3 C 0 C 0 + +a score=1299.0 +s mm10.chr2 34705970 3 + 182113224 tga +s rn5.chr3 19097807 3 + 183740530 tga +i rn5.chr3 C 0 C 0 + +a score=-2713.0 +s mm10.chr2 34705973 5 + 182113224 cattC +s rn5.chr3 19097810 5 + 183740530 tacaa +i rn5.chr3 C 0 C 0 + +a score=6695.0 +s mm10.chr2 34705978 1 + 182113224 T +s rn5.chr3 19097815 1 + 183740530 t +i rn5.chr3 C 0 C 0 + +a score=395.0 +s mm10.chr2 34705979 1 + 182113224 A +s rn5.chr3 19097816 1 + 183740530 a +i rn5.chr3 C 0 C 0 + +a score=28965.0 +s mm10.chr2 34705980 8 + 182113224 TAATTACC +s rn5.chr3 19097817 8 + 183740530 tgaTTACC +i rn5.chr3 C 0 C 0 + +a score=12376.0 +s mm10.chr2 34705988 1 + 182113224 T +s rn5.chr3 19097825 1 + 183740530 T +i rn5.chr3 C 0 C 0 + +a score=12907.0 +s mm10.chr2 34705989 1 + 182113224 T +s rn5.chr3 19097826 1 + 183740530 T +i rn5.chr3 C 0 C 0 + +a score=258.0 +s mm10.chr2 34705990 1 + 182113224 A +s rn5.chr3 19097827 1 + 183740530 A +i rn5.chr3 C 0 C 0 + +a score=29575.0 +s mm10.chr2 34705991 1 + 182113224 A +s rn5.chr3 19097828 1 + 183740530 A +i rn5.chr3 C 0 C 0 + +a score=18893.0 +s mm10.chr2 34705992 1 + 182113224 A +s rn5.chr3 19097829 1 + 183740530 A +i rn5.chr3 C 0 C 0 + +a score=395908.0 +s mm10.chr2 34705993 19 + 182113224 A-------AGCCATTCT------CACTCCTAC +s rn5.chr3 19097830 19 + 183740530 A-------GGTCATTCT------CACCCCCAC +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118497 19 - 141213431 A-------AGTCATCCT------CATTTCCCC +i hg19.chr9 I 76 C 0 +s sorAra1.scaffold_258498 5366 18 + 196505 A-------AGCCcctct------ttttcca-t +i sorAra1.scaffold_258498 N 0 C 0 + +a score=11678.0 +s mm10.chr2 34706012 1 + 182113224 A +s rn5.chr3 19097849 1 + 183740530 A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118516 1 - 141213431 C +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5384 1 + 196505 t +i sorAra1.scaffold_258498 C 0 C 0 + +a score=41513.0 +s mm10.chr2 34706013 1 + 182113224 A +s rn5.chr3 19097850 1 + 183740530 A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118517 1 - 141213431 T +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5385 1 + 196505 t +i sorAra1.scaffold_258498 C 0 C 0 + +a score=154000.0 +s mm10.chr2 34706014 1 + 182113224 C +s rn5.chr3 19097851 1 + 183740530 C +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118518 1 - 141213431 C +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5386 1 + 196505 c +i sorAra1.scaffold_258498 C 0 C 0 + +a score=98483.0 +s mm10.chr2 34706015 1 + 182113224 T +s rn5.chr3 19097852 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118519 1 - 141213431 T +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5387 1 + 196505 t +i sorAra1.scaffold_258498 C 0 C 0 + +a score=13020051.0 +s mm10.chr2 34706016 111 + 182113224 T--ACCATGGGCTATGTCATCCATATCT--GGACTAGTTACA-GAATCTTTGCCCCC-AAAATCA-GAGCTGCACTCAGA-TCTCAGGTCTTCGATCTTATTGGGAATATCCTCCGATG +s rn5.chr3 19097853 111 + 183740530 T--ACCATGGGCTATGTCATCCACATCT--GGACTAGTTACA-GAATCTTTACCCCC-AAAATCA-GAGCTGCACTCAGA-TCGCAGGTCTTCGATCTTATTGGGAATATCCTCCGATG +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118520 111 - 141213431 T--ACCGTGAGTTATTTCATCCATGTCT--GGACTAGTGACA-GAATCTTTACCCCC-AAAATCA-GAGCTGCACTCAGA-TCTCAGGTCTTCAATCTTATTGGGAATATCCTCAGAGG +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5388 111 + 196505 t--accATGAGTTACTTCATCCATGTCT--GGGCTAGTGACA-GAGTCTTTACCCCC-AAAGTCA-GAGCTGCACTCAGA-TCTCAGGTCTTCTATCTTATTAGGAATATCCTCAGAGG +i sorAra1.scaffold_258498 C 0 C 0 + +a score=1769347.0 +s mm10.chr2 34706127 14 + 182113224 TAGCACTTATACCT +s rn5.chr3 19097964 14 + 183740530 TAGCGCTTATGCCT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118631 14 - 141213431 TTGCACTTATGCCT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5499 14 + 196505 TTGCACTTATgcct +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-78567.0 +s mm10.chr2 34706141 7 + 182113224 TTAAA-------------------AA----- +s rn5.chr3 19097978 7 + 183740530 TTGAA-------------------AA----- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118645 7 - 141213431 TTAAA-------------------AA----- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5513 6 + 196505 tt-aa-------------------ag----- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-435240.0 +s mm10.chr2 34706148 8 + 182113224 ATACAGCA-------------------------------------- +s rn5.chr3 19097985 7 + 183740530 -TACAGCA-------------------------------------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118652 1 - 141213431 -------A-------------------------------------- +i hg19.chr9 C 0 C 0 + +a score=-126692.0 +s mm10.chr2 34706156 2 + 182113224 A-A- +s rn5.chr3 19097992 2 + 183740530 A-A- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118653 2 - 141213431 C-A- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5519 2 + 196505 a-t- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-311071.0 +s mm10.chr2 34706158 6 + 182113224 A-A----TACA-- +s rn5.chr3 19097994 5 + 183740530 A------TACA-- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118655 3 - 141213431 A--------TA-- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5521 3 + 196505 a--------aa-- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-651211.0 +s mm10.chr2 34706164 10 + 182113224 TA--A--G----------------------------------------------------------------------------------------------TAAA--TA +s rn5.chr3 19097999 10 + 183740530 GA--A--G----------------------------------------------------------------------------------------------TAAA--TA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118658 10 - 141213431 GT--A--A----------------------------------------------------------------------------------------------AAAA--TA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5524 12 + 196505 at--a--a--------------------------------------------------------------------------------------------ttaaaa--ct +i sorAra1.scaffold_258498 C 0 C 0 + +a score=165149.0 +s mm10.chr2 34706174 5 + 182113224 AATAA +s rn5.chr3 19098009 4 + 183740530 AACA- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118668 4 - 141213431 AACA- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5536 2 + 196505 a--a- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=386714.0 +s mm10.chr2 34706179 12 + 182113224 GCTGCAAG----AAGA-------- +s rn5.chr3 19098013 9 + 183740530 ---GCAAG----AAGA-------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118672 9 - 141213431 ---GGAAG----AAGA-------- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5538 13 + 196505 ---gcAAACTGGAACA-------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=224266.0 +s mm10.chr2 34706191 6 + 182113224 CCAAAG-- +s rn5.chr3 19098022 6 + 183740530 ACAAAG-- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118681 6 - 141213431 ACAAAA-- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5551 6 + 196505 ACAAAA-- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=584015.0 +s mm10.chr2 34706197 35 + 182113224 TAGTTACAC-------AA---------------------------------------------------------------------------------A--ATTT--TATG---------AAG--TT-------------------------------T-GGAGAAA----------------------------------------------------TT-- +s rn5.chr3 19098028 36 + 183740530 CAGTTACAC-------AA---------------------------------------------------------------------------------A--ATTC--TACT---------AAG--TT-------------------------------TTGGATAAA----------------------------------------------------TC-- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118687 36 - 141213431 TATCCACAC-A-----AA---------------------------------------------------------------------------------A--AGTA--TATG---------AAA--TT-------------------------------T-GGAGAAA----------------------------------------------------CT-- +i hg19.chr9 C 0 I 4 +s sorAra1.scaffold_258498 5557 36 + 196505 TAAGCACAC-A-----GA---------------------------------------------------------------------------------A--AGTT--TATG---------AAG--TC-------------------------------T-GGAGAAA----------------------------------------------------GT-- +i sorAra1.scaffold_258498 C 0 I 4 + +a score=-1110372.0 +s mm10.chr2 34706232 43 + 182113224 CCTTTTC-------------------------------------------------AAA---CT--A---TC--CAC-------------------------------------------------------------------------------------------------------------------------------------------------------------CTACAC------ATGTGA-GTTGCTGAGTGCT-------- +s rn5.chr3 19098064 37 + 183740530 CCTCCTC-------------------------------------------------GAG---CT--G---TC--CAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGTGA-GCTGCCGAGTGCT-------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118727 47 - 141213431 CATTCTC-------------------------------------------------GAA---TT--T---TG--T----------------------------GTCCCAGT--TC------------------------------------------------------------------------------------------------------------------------TATAC------ATGTGA----GTTTAGTATT-------- +i hg19.chr9 I 4 C 0 +s sorAra1.scaffold_258498 5597 51 + 196505 TACCCTC-------------------------------------------------AATT--GT--T---TG--T----------------------------GTCCAGTTC-TA------------------------------------------------------------------------------------------------------------------------CACAC------AAGGGA-GCTG-CCGGTGTT-------- +i sorAra1.scaffold_258498 I 4 C 0 + +a score=-57305.0 +s mm10.chr2 34706275 9 + 182113224 G-------------------GCAAGTTA +s rn5.chr3 19098101 9 + 183740530 G-------------------CCACCTCA +i rn5.chr3 C 0 C 0 + +a score=-785463.0 +s mm10.chr2 34706284 23 + 182113224 CCAC--------------------------------------------------------------------------TGTTA----TTCAAACACACT----TA----------- +s rn5.chr3 19098110 23 + 183740530 CCAC--------------------------------------------------------------------------TGCTG----TCCAAGTACACT----TA----------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118774 35 - 141213431 -------------------------------------------------------ATATCCTT---TA-T-GGTA--CTACTG----CTTAAATATACT----TA----------- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5648 36 + 196505 -------------------------------------------------------TCGGCTTT---TATC-AGTA--CTACTG----CTTAAATATGAT----TA----------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=38342.0 +s mm10.chr2 34706307 6 + 182113224 TCTTGC- +s rn5.chr3 19098133 6 + 183740530 TCTTGC- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118809 6 - 141213431 CCTTGC- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5684 5 + 196505 C-CCGA- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=173064.0 +s mm10.chr2 34706313 10 + 182113224 T-TTATACAAT +s rn5.chr3 19098139 8 + 183740530 T---ATACAGC +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118815 10 - 141213431 T-TTACACAAC +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5689 7 + 196505 T-GTGTGC--- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=110922.0 +s mm10.chr2 34706323 13 + 182113224 ATCATC------------------------------------------AGA---ATT-A +s rn5.chr3 19098147 13 + 183740530 AGCATC------------------------------------------AAA---AGT-T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118825 13 - 141213431 ATAATC------------------------------------------AGA---ATC-G +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5696 12 + 196505 -AAAAT------------------------------------------ATC---CAA-G +i sorAra1.scaffold_258498 C 0 I 1 + +a score=-155855.0 +s mm10.chr2 34706336 16 + 182113224 CACGC----T----ATAC-----CTAAAT +s rn5.chr3 19098160 15 + 183740530 CATGC----T----GTAC-----CTAA-T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118838 14 - 141213431 --TAC----A----ATTC-----TAAAGT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5709 16 + 196505 TACAT----G----CTCT-----GTACAC +i sorAra1.scaffold_258498 I 1 I 5 + +a score=5448.0 +s mm10.chr2 34706352 3 + 182113224 ATC +s rn5.chr3 19098175 3 + 183740530 ATT +i rn5.chr3 C 0 C 0 + +a score=-7915.0 +s mm10.chr2 34706355 2 + 182113224 GT- +s rn5.chr3 19098178 2 + 183740530 GT- +i rn5.chr3 C 0 C 0 + +a score=592160.0 +s mm10.chr2 34706357 20 + 182113224 AGCAAAAGC-----TAT-CAAAAA----TA +s rn5.chr3 19098180 20 + 183740530 AGCAGAAGC-----TAC-CAAAAG----TA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118852 20 - 141213431 AGGACAGGC-----TAC-TAAGAA----CA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5730 20 + 196505 AGCAGAAGC-----TAT-GCAGTA----CA +i sorAra1.scaffold_258498 I 5 C 0 + +a score=-246926.0 +s mm10.chr2 34706377 6 + 182113224 TCA-----A--------GA +s rn5.chr3 19098200 6 + 183740530 TCG-----A--------AA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118872 6 - 141213431 GAA-----A--------CA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5750 4 + 196505 GAT-----A---------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-935672.0 +s mm10.chr2 34706383 18 + 182113224 GCTG------------------AA--------AG---AGGAG-----------------------CAGCA +s rn5.chr3 19098206 17 + 183740530 GCTG------------------AA---------G---AAGAA-----------------------CAGTT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118878 17 - 141213431 GTTG------------------TA---------G---AGAGA-----------------------CTGTT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5754 20 + 196505 ----------------------GT---------C---AGGGAA---CA---CAC-----A-----TGAGC +i sorAra1.scaffold_258498 C 0 C 0 + +a score=499767.0 +s mm10.chr2 34706401 25 + 182113224 CGTCCA--TTATTTT----AACAGGCTGTA--A +s rn5.chr3 19098223 23 + 183740530 CGTCAG--TTATC------AATAGGCTGTG--A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118895 26 - 141213431 TGCCAA--TTACTTC----AACAGGCTCCAT-A +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5774 26 + 196505 TGCAAA--TTACTTT----AATGAGCTCTGC-G +i sorAra1.scaffold_258498 C 0 C 0 + +a score=767553.0 +s mm10.chr2 34706426 54 + 182113224 A----AGC------CACATATT--AAGTT----CTCAAAGA----TTAT------------G-AAG-GCATAAAATTAAT-TTTTTTCC +s rn5.chr3 19098246 54 + 183740530 A----AGC------TACACATT--AGGTT----CTCAAAGA----TTAT------------G-AAA-GCGTAAAATTGAT-TTTGTTCC +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118921 55 - 141213431 A----GGC------CACACATT--AAGTT----CTCAAAGAT---TTCA------------G-GTG-CAATGGAAATAAG-TTTGTTTT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5800 55 + 196505 A----AGC------CGCACATT--AAGCT----CTCATAGCT---ATTT------------G-GTA-CCCTAGAAATAAT-TTCATTCC +i sorAra1.scaffold_258498 C 0 C 0 + +a score=512662.0 +s mm10.chr2 34706480 12 + 182113224 CTGG-GGACTACT +s rn5.chr3 19098300 12 + 183740530 CTGG-AGACTACT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118976 12 - 141213431 CTGG-AAATTACT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5855 12 + 196505 CTGG-AAATCACC +i sorAra1.scaffold_258498 C 0 C 0 + +a score=266794.0 +s mm10.chr2 34706492 19 + 182113224 GAG-AACTTAAATAA-CATA--T +s rn5.chr3 19098312 19 + 183740530 GAG-CTCTTAAATAA-CACA--T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13118988 19 - 141213431 CAG-CTCTTAAATAT-AACA--T +i hg19.chr9 C 0 I 2 +s sorAra1.scaffold_258498 5867 1 + 196505 C---------------------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=43661.0 +s mm10.chr2 34706511 4 + 182113224 CT--CT +s rn5.chr3 19098331 4 + 183740530 CT--CT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119009 4 - 141213431 CT--TT +i hg19.chr9 I 2 C 0 + +a score=10868.0 +s mm10.chr2 34706515 1 + 182113224 T +s rn5.chr3 19098335 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119013 1 - 141213431 T +i hg19.chr9 C 0 C 0 + +a score=-67977.0 +s mm10.chr2 34706516 23 + 182113224 gggggtggagatacagctcag----------------tg +s rn5.chr3 19098336 23 + 183740530 ggggacaaagctacagctcag----------------tg +i rn5.chr3 C 0 C 0 + +a score=-16667.0 +s mm10.chr2 34706539 4 + 182113224 at---ga +s rn5.chr3 19098359 5 + 183740530 ac--aga +i rn5.chr3 C 0 C 0 + +a score=-47800.0 +s mm10.chr2 34706543 9 + 182113224 acacatgac +s rn5.chr3 19098364 9 + 183740530 gcacatgac +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 5868 9 + 196505 GCTGGTAAT +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-120172.0 +s mm10.chr2 34706552 20 + 182113224 taacatgtcccaagtt--------------------ctgg +s rn5.chr3 19098373 20 + 183740530 taacatgtcccgagtt--------------------ctga +i rn5.chr3 C 0 C 0 + +a score=-60366.0 +s mm10.chr2 34706572 21 + 182113224 gttcaacagatagtacca-------------------------------------------------------tac +s rn5.chr3 19098393 18 + 183740530 gttcaacagccagcacca---------------------------------------------------------- +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 5877 5 + 196505 -------------TATCA---------------------------------------------------------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-3306.0 +s mm10.chr2 34706593 3 + 182113224 cat-- + +a score=-199980.0 +s mm10.chr2 34706596 23 + 182113224 aa------aacAGCCAACAAAACCC-AGTT-------------- +s rn5.chr3 19098411 18 + 183740530 ----------gcagcaacaaaaCCC-AGT--------------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119014 7 - 141213431 ------------------TGTATCA------------------- +i hg19.chr9 C 0 C 0 + +a score=21021.0 +s mm10.chr2 34706619 1 + 182113224 A +s rn5.chr3 19098429 1 + 183740530 A +i rn5.chr3 C 0 C 0 + +a score=28151.0 +s mm10.chr2 34706620 3 + 182113224 TCT +s rn5.chr3 19098430 3 + 183740530 TCT +i rn5.chr3 C 0 C 0 + +a score=21179.0 +s mm10.chr2 34706623 3 + 182113224 CTT- +s rn5.chr3 19098433 3 + 183740530 CTT- +i rn5.chr3 C 0 C 0 + +a score=-542671.0 +s mm10.chr2 34706626 14 + 182113224 TGG-TAAC-----AC------------T--------TTAT-------- +s rn5.chr3 19098436 14 + 183740530 TGG-TAAC-----AC------------T--------TTAT-------- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119021 7 - 141213431 -------------AC------------T--------TTAT-------- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5882 7 + 196505 -------------AC------------A--------TTAT-------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-12000.0 +s mm10.chr2 34706640 5 + 182113224 AAAC-A +s rn5.chr3 19098450 5 + 183740530 AAAC-A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119028 5 - 141213431 AAAT-A +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5889 5 + 196505 ACAC-G +i sorAra1.scaffold_258498 C 0 C 0 + +a score=112347.0 +s mm10.chr2 34706645 2 + 182113224 GA +s rn5.chr3 19098455 2 + 183740530 GA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119033 2 - 141213431 GG +i hg19.chr9 C 0 I 7 +s sorAra1.scaffold_258498 5894 2 + 196505 GG +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-75428.0 +s mm10.chr2 34706647 10 + 182113224 AAGA-AGGGGA +s rn5.chr3 19098457 10 + 183740530 AAGA-AGGGGA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119042 10 - 141213431 AGGG-GGTGAA +i hg19.chr9 I 7 C 0 +s sorAra1.scaffold_258498 5896 10 + 196505 GTGG-TAGGAA +i sorAra1.scaffold_258498 C 0 C 0 + +a score=26690.0 +s mm10.chr2 34706657 1 + 182113224 T +s rn5.chr3 19098467 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119052 1 - 141213431 C +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5906 1 + 196505 C +i sorAra1.scaffold_258498 C 0 I 2 + +a score=582929.0 +s mm10.chr2 34706658 21 + 182113224 GCCTTCAAA--------------------TTCCTAGC----CCTT +s rn5.chr3 19098468 21 + 183740530 GCCTTCAAA--------------------TTCCTAGT----CCTT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119053 21 - 141213431 ACCTTCAAA--------------------TCCCTACT----CCTT +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5909 21 + 196505 ACCTTCCAA--------------------TCCTTATT----CCTT +i sorAra1.scaffold_258498 I 2 C 0 + +a score=357258.0 +s mm10.chr2 34706679 6 + 182113224 AAAAC---------------------------------A--- +s rn5.chr3 19098489 6 + 183740530 AAAAC---------------------------------A--- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119074 6 - 141213431 AAAAC---------------------------------A--- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5930 6 + 196505 AAAAC---------------------------------A--- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=522064.0 +s mm10.chr2 34706685 8 + 182113224 AGA-C-AGAC +s rn5.chr3 19098495 8 + 183740530 AGA-C-AGAC +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119080 8 - 141213431 AGA-C-AGAC +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5936 8 + 196505 AGA-C-AGAC +i sorAra1.scaffold_258498 C 0 C 0 + +a score=75873.0 +s mm10.chr2 34706693 1 + 182113224 A +s rn5.chr3 19098503 1 + 183740530 A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119088 1 - 141213431 A +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5944 1 + 196505 A +i sorAra1.scaffold_258498 C 0 C 0 + +a score=117040.0 +s mm10.chr2 34706694 1 + 182113224 T +s rn5.chr3 19098504 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119089 1 - 141213431 T +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5945 1 + 196505 T +i sorAra1.scaffold_258498 C 0 C 0 + +a score=18601995.0 +s mm10.chr2 34706695 141 + 182113224 A-CCGGACACAAC-ACTGAGG--CCTGGT-GTGC-TGGGGC-GGGAA--CTGACCTCCCTGAC-ATCCGTATCATCA-GATGTGCTG-CCCAGTCCAGAACAG---CTCT-CCAGCTCTTGGAGGCGCTCTTCCTGCTTTAAGTCTGGAGCCTCTGA +s rn5.chr3 19098505 141 + 183740530 A-CCGGACACAAC-ACTGAGG--CCTGGT-GTGC-TGGGGC-GGGAA--CTGACCTCCCTGAC-ATCCGTATCATCA-GATGTACTG-CCCAGTCCAGAACAG---CTCT-CCAGCTCTTGGAGGCGCTCTTCCTGCTTTAAGTCTGGAGCCTCTGC +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119090 141 - 141213431 A-CCGGACACAAC-ACTGAGG--CCTGGT-GTGC-TGGGGC-GGGAA--CTGACCTCCCTGAC-ATCCGTATCATCA-GATGTGCTA-CCCAGTCCAGAACAG---CTCT-CCAGTTCTTGCAGACGCTCCTCCTGCTTTAGGTCTGGGGCCTCTAA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 5946 141 + 196505 A-CCCGACACAAC-ACTGAGG--CCTGGT-GTGC-TGGGGC-GGGAA--CTGACCTCCCTGAC-ATCCGTGTCGTCA-GAGGTGCTG-CCCAGGCCGGAACAG---CTCT-CCAGCTCCTGCAGACGCTCCTCCTGCTTCAGGTCTGGGGCTTCTAG +i sorAra1.scaffold_258498 C 0 C 0 + +a score=93544.0 +s mm10.chr2 34706836 1 + 182113224 A +s rn5.chr3 19098646 1 + 183740530 A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119231 1 - 141213431 A +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6087 1 + 196505 G +i sorAra1.scaffold_258498 C 0 C 0 + +a score=265691.0 +s mm10.chr2 34706837 6 + 182113224 CAGAAA- +s rn5.chr3 19098647 6 + 183740530 CAGAGA- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119232 6 - 141213431 TAGAAG- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6088 6 + 196505 GAAAGA- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=100475.0 +s mm10.chr2 34706843 1 + 182113224 A +s rn5.chr3 19098653 1 + 183740530 A +i rn5.chr3 C 0 I 41 +s hg19.chr9 13119238 1 - 141213431 A +i hg19.chr9 C 0 I 45 +s sorAra1.scaffold_258498 6094 1 + 196505 G +i sorAra1.scaffold_258498 C 0 I 41 + +a score=123198.0 +s mm10.chr2 34706844 2 + 182113224 CA +s rn5.chr3 19098695 2 + 183740530 CA +i rn5.chr3 I 41 C 0 +s hg19.chr9 13119284 2 - 141213431 CA +i hg19.chr9 I 45 C 0 +s sorAra1.scaffold_258498 6136 2 + 196505 CC +i sorAra1.scaffold_258498 I 41 C 0 + +a score=83667.0 +s mm10.chr2 34706846 1 + 182113224 G +s rn5.chr3 19098697 1 + 183740530 G +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119286 1 - 141213431 G +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6138 1 + 196505 A +i sorAra1.scaffold_258498 C 0 C 0 + +a score=30972.0 +s mm10.chr2 34706847 1 + 182113224 C +s rn5.chr3 19098698 1 + 183740530 C +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119287 1 - 141213431 C +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6139 1 + 196505 C +i sorAra1.scaffold_258498 C 0 C 0 + +a score=74745.0 +s mm10.chr2 34706848 1 + 182113224 T +s rn5.chr3 19098699 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119288 1 - 141213431 T +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6140 1 + 196505 T +i sorAra1.scaffold_258498 C 0 C 0 + +a score=223036.0 +s mm10.chr2 34706849 11 + 182113224 TT------TG-TG--ACT-TA +s rn5.chr3 19098700 11 + 183740530 TT------TG-TG--ACT-TA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119289 11 - 141213431 TT------TG-TG--ACC-CA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6141 11 + 196505 TC------CG-TG--ACC-CA +i sorAra1.scaffold_258498 C 0 C 0 + +a score=3047381.0 +s mm10.chr2 34706860 139 + 182113224 GACATACAAG---C-------G-ATT-GGGG----AATAAA-GAGAT---TT----------A-------TAAG------CCTAAGCTACTT-AGC-AAAG-CTAGTTAG---ATCA---TAGTTTAAAGAAGAT-A---AGGTTATGA--TTTC-CTCCTGATA-----TACACACT---AGTTTGT----------TATGTACAG-ATGTCAAC---T +s rn5.chr3 19098711 134 + 183740530 G----AGAAG---C-------C-ACT-GGGG----AATACC-TAGCT---TT----------A-------TAAG------TCTAAGTTACTC-ACC-AAAA-CTTGTTAG---ATCA---TAGATT-AAGAAGGC-A---AGGTTATAA--TTTC-CCCCTGATA-----TACACACT---AATTTGC----------TATGCACAG-ACGACAAC---T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119300 149 - 141213431 G----ATAAA---CAAAG--CT-ACC-AGGG----CATGAA-TAAAA---TCAGTG-CAAATACATGTG-TAAG------TCTGGACTAGTT-----AATG-CTAGTTAG---ATTA---AGTGTT----AAGTC-A---AAGTTGTGAT-TTTC-ATCCCAATA-----TAAGC--C---AGTTCAC----------TGTGCACAG-ATGAAAAC-GTG +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6152 151 + 196505 G----CTGAA---GAAAA--CTGAAC-AGGG----CTT--A-CGGAAGGGTCAGTG-TAAATAGATTTC-TAGG------TCTCGGCCAGTT-AGT-AAGG-CTGGTT-G---AAGA---AACGCCAAGGAAGTC-ATATCAACTCTGAT-TTTC--CCCCAGCA-----TAGGC--C---AGT----------------TGTACAG-ATAAAAAC-T-- +i sorAra1.scaffold_258498 C 0 I 2 + +a score=-43731.0 +s mm10.chr2 34706999 2 + 182113224 AT- +s rn5.chr3 19098845 2 + 183740530 GT- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119449 1 - 141213431 G-- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6305 2 + 196505 GG- +i sorAra1.scaffold_258498 I 2 C 0 + +a score=126153.0 +s mm10.chr2 34707001 4 + 182113224 TTCT- +s rn5.chr3 19098847 4 + 183740530 TTCT- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119450 4 - 141213431 TTCT- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6307 4 + 196505 TTTT- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=311713.0 +s mm10.chr2 34707005 8 + 182113224 AGAATACT +s rn5.chr3 19098851 8 + 183740530 AGACTACT +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119454 8 - 141213431 AGATCACT +i hg19.chr9 C 0 I 4 +s sorAra1.scaffold_258498 6311 8 + 196505 AGATCACT +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-2161.0 +s mm10.chr2 34707013 2 + 182113224 TT +s rn5.chr3 19098859 2 + 183740530 CT +i rn5.chr3 C 0 I 199 +s hg19.chr9 13119466 1 - 141213431 -T +i hg19.chr9 I 4 I 1 + +a score=-432190.0 +s mm10.chr2 34707015 20 + 182113224 AAAGAAAAAAAAAAGCG------------AT----------T--------------- +s rn5.chr3 19099060 26 + 183740530 aaacaaaacaaaacaaa------------acTGTA----CAT--------------- +i rn5.chr3 I 199 C 0 +s hg19.chr9 13119468 11 - 141213431 ---------------------------ACAGAGTA----TGC--------------- +i hg19.chr9 I 1 C 0 +s sorAra1.scaffold_258498 6319 17 + 196505 -------------------ATT--CTCAATGAGTG----TGC--------------- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=221858.0 +s mm10.chr2 34707035 6 + 182113224 TCTTGG +s rn5.chr3 19099086 6 + 183740530 TCTTGG +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119479 6 - 141213431 TATTGA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6336 5 + 196505 TAC-GG +i sorAra1.scaffold_258498 C 0 C 0 + +a score=458493.0 +s mm10.chr2 34707041 12 + 182113224 TTAACACGTAAA- +s rn5.chr3 19099092 12 + 183740530 TTAACACATAAA- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119485 12 - 141213431 TTAACATGTGAA- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6341 12 + 196505 CTAACATGAAAA- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=67988.0 +s mm10.chr2 34707053 8 + 182113224 CTA---ATCAA +s rn5.chr3 19099104 5 + 183740530 CTG------AA +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119497 5 - 141213431 CTG------GA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6353 5 + 196505 CTG------AA +i sorAra1.scaffold_258498 C 0 C 0 + +a score=123485.0 +s mm10.chr2 34707061 3 + 182113224 TAG +s rn5.chr3 19099109 3 + 183740530 CAG +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119502 3 - 141213431 CAA +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6358 3 + 196505 CAA +i sorAra1.scaffold_258498 C 0 C 0 + +a score=33526.0 +s mm10.chr2 34707064 4 + 182113224 GA--GC-- +s rn5.chr3 19099112 4 + 183740530 GA--GC-- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119505 6 - 141213431 GAGAGT-- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6361 6 + 196505 GAACGC-- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=167903.0 +s mm10.chr2 34707068 8 + 182113224 A-CAGAAT--A +s rn5.chr3 19099116 8 + 183740530 A-CAGAAT--A +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119511 8 - 141213431 A-TGGAAT--A +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6367 7 + 196505 A-GAGAAG--- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=2760.0 +s mm10.chr2 34707076 1 + 182113224 A +s rn5.chr3 19099124 1 + 183740530 G +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119519 1 - 141213431 G +i hg19.chr9 C 0 C 0 + +a score=-203.0 +s mm10.chr2 34707077 4 + 182113224 TATA--- +s rn5.chr3 19099125 3 + 183740530 TGT---- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119520 3 - 141213431 CCT---- +i hg19.chr9 C 0 C 0 + +a score=73448.0 +s mm10.chr2 34707081 10 + 182113224 CAACACTGTA--- +s rn5.chr3 19099128 9 + 183740530 -AACACTGTA--- +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119523 9 - 141213431 -GGTATTAAA--- +i hg19.chr9 C 0 C 0 +s sorAra1.scaffold_258498 6374 1 + 196505 ---------A--- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-28287.0 +s mm10.chr2 34707091 5 + 182113224 TCAA---C +s rn5.chr3 19099137 7 + 183740530 TCCACT-C +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 6375 5 + 196505 TCAAC--- +i sorAra1.scaffold_258498 C 0 C 0 + +a score=4831.0 +s mm10.chr2 34707096 1 + 182113224 T +s rn5.chr3 19099144 1 + 183740530 T +i rn5.chr3 C 0 C 0 +s hg19.chr9 13119532 1 - 141213431 T +i hg19.chr9 C 0 I 709 +s sorAra1.scaffold_258498 6380 1 + 196505 T +i sorAra1.scaffold_258498 C 0 I 1 + +a score=555.0 +s mm10.chr2 34707097 1 + 182113224 C +s rn5.chr3 19099145 1 + 183740530 C +i rn5.chr3 C 0 C 0 + +a score=18165.0 +s mm10.chr2 34707098 3 + 182113224 TCT +s rn5.chr3 19099146 3 + 183740530 TCT +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 6382 2 + 196505 -TT +i sorAra1.scaffold_258498 I 1 C 0 + +a score=32760.0 +s mm10.chr2 34707101 3 + 182113224 AAA +s rn5.chr3 19099149 3 + 183740530 AAA +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 6384 3 + 196505 AAA +i sorAra1.scaffold_258498 C 0 C 0 + +a score=-12377.0 +s mm10.chr2 34707104 8 + 182113224 TCTCAATG +s rn5.chr3 19099152 8 + 183740530 GTTCAATG +i rn5.chr3 C 0 C 0 +s sorAra1.scaffold_258498 6387 6 + 196505 --TTTAAA +i sorAra1.scaffold_258498 C 0 I 672 + +a score=13142.0 +s mm10.chr2 34707112 17 + 182113224 ttctcaaaagcacttaa--- +s rn5.chr3 19099160 17 + 183740530 TTTTCAAAAGCACTTAC--- +i rn5.chr3 C 0 C 0 + +a score=2730.0 +s mm10.chr2 34707129 2 + 182113224 aa +s rn5.chr3 19099177 2 + 183740530 AA +i rn5.chr3 C 0 C 0 + +a score=1746.0 +s mm10.chr2 34707131 3 + 182113224 tgg +s rn5.chr3 19099179 3 + 183740530 Tgg +i rn5.chr3 C 0 C 0 + +a score=1998.0 +s mm10.chr2 34707134 22 + 182113224 gcat------gaca--gcagggcaatctca +s rn5.chr3 19099182 24 + 183740530 gcat------gatattgcagggcactctca +i rn5.chr3 C 0 C 0 + +a score=452.0 +s mm10.chr2 34707156 4 + 182113224 acac +s rn5.chr3 19099206 4 + 183740530 gcac +i rn5.chr3 C 0 C 0 + +a score=8445.0 +s mm10.chr2 34707160 152 + 182113224 tcaataagcagaggcaggtggatctctgtgagtttgagtccagcctaaaatacactggcagttccatgaatagcctgagctacatgacgagatcctgtctcaaaCTAGCTCCAAAAAGGAAGACAGG-AAAATCATTTCTTTACTTAATACTT +s rn5.chr3 19099210 147 + 183740530 tcaagaggcagaggcaggtgga--tctgtaagtctgaggccagcctgaggttcactggcagttcca-gcatagcctgagctacatgatgagaccctggctcaaaccaa---aagaaaGAAAGAAAGGAAAAATGATTTCTTTATCTAATATTT +i rn5.chr3 C 0 I 1 + +a score=0.0 +s mm10.chr2 34707312 6 + 182113224 TACCTA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/islands.bed Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,5 @@ +chr2 73970064 73983434 islandI +chr2 74060473 74082287 islandII +chr2 74201443 74221207 islandIII +chr2 74264930 74274051 islandIV +chr2 74290763 74304478 islandV
--- a/test-data/test11.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test11.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ [x-axis] where = top -[hic_section_0_0] +[hic_section_1_0] file = test-data/Li_et_al_2015.h5 file_type = hic_matrix title = Kc DpnII (Li et al. 2015) @@ -12,21 +12,25 @@ rasterize = true [spacer] height = 0.05 -[bedgraph_matrix_2] +[bedgraph_matrix_3] file = test-data/tad_score.gz -title = TAD separation score (Ramirez et al.) +title = TAD separation score (Ramirez et al.) as block with horizontal lines and data range height = 10.0 type = lines file_type = bedgraph_matrix show_data_range = true plot_horizontal_lines = true pos_score_in_bin = block -[bedgraph_matrix_3] +individual_color = grey +summary_color = #1f77b4 +[bedgraph_matrix_4] file = test-data/tad_score.gz -title = TAD separation score (Ramirez et al.) +title = TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue height = 10.0 type = lines file_type = bedgraph_matrix show_data_range = false plot_horizontal_lines = false -pos_score_in_bin = center \ No newline at end of file +pos_score_in_bin = center +individual_color = blue +summary_color = red \ No newline at end of file
--- a/test-data/test12.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test12.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ [x-axis] where = top -[hic_section_0_0] +[hic_section_1_0] file = Li_et_al_2015.h5 file_type = hic_matrix title = Kc DpnII (Li et al. 2015) @@ -9,7 +9,7 @@ transform = no scale_factor = 1.0 rasterize = true -[links_1] +[links_2] file = test.arcs height = 1.5 color = red @@ -19,7 +19,7 @@ links_type = loops overlay_previous = share-y file_type = links -[links_2] +[links_3] file = test.arcs title = test.arcs height = 5.0 @@ -29,6 +29,8 @@ line_width = 0.5 line_style = solid links_type = arcs +compact_arcs_level = 0 +use_middle = false orientation = inverted overlay_previous = no file_type = links \ No newline at end of file
--- a/test-data/test15.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test15.ini Sat Oct 01 08:43:22 2022 +0000 @@ -2,16 +2,21 @@ where = bottom [genes_1_0] file = dm3_genes.bed.gz -title = flybase +title = flybase backbone blue color = #000000 border_color = #000000 style = flybase height_utr = 1.0 color_utr = grey arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = blue display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 @@ -19,14 +24,18 @@ overlay_previous = no [genes_2_0] file = dm3_genes.bed.gz -title = UCSC +title = UCSC backbone blue color = #000000 border_color = #000000 style = UCSC arrow_interval = 10 +color_backbone = blue display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 @@ -43,6 +52,9 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 @@ -60,6 +72,9 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60
--- a/test-data/test17.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test17.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,67 +1,129 @@ -[test bedgraph] +[bedgraph_0] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = blue -height = 5 title = bedgraph color = blue transform = no -transform = no - -[test bedgraph] +color = blue +alpha = 1.0 +height = 5.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +[bedgraph_1] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +title = bedgraph color = blue transform = log color = blue -height = 5 -title = bedgraph color = blue transform = log +alpha = 1.0 +height = 5.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill transform = log - -[test bedgraph] +y_axis_values = transformed +log_pseudocount = 0.0 +overlay_previous = no +[bedgraph_2] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +title = bedgraph color = red transform = log min_value = 1 color = red -height = 5 -title = bedgraph color = red transform = log min_value = 1 -min_value = 1 +alpha = 1.0 +height = 5.0 +min_value = 1.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill transform = log - -[test bedgraph] +y_axis_values = transformed +log_pseudocount = 0.0 +overlay_previous = no +[bedgraph_3] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = green -height = 5 title = bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 -transform = log -log_pseudocount = 2 -min_value = 0 - -[test bedgraph with operation] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = green -height = 5 -title = bedgraph color = green operation = log(2+file) min_value = 0.7 -operation = log(2+file) -min_value = 0.7 - -[test bedgraph] +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +transform = log +y_axis_values = transformed +log_pseudocount = 2.0 +overlay_previous = no +[bedgraph_4] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = black -height = 5 +title = bedgraph color = green operation = log(2+file) min_value = 0.7 +color = green +alpha = 1.0 +height = 5.0 +min_value = 0.7 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +operation = log(2+file) +overlay_previous = no +[bedgraph_5] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 -transform = log2 -log_pseudocount = 1 -min_value = 0 - -[test bedgraph] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = black -height = 5 +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +transform = log2 +y_axis_values = transformed +log_pseudocount = 1.0 +overlay_previous = no +[bedgraph_6] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black operation = log2(1+file) min_value = 0 -operation = log2(1+file) -min_value = 0 - -[test bedgraph] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = black -height = 5 +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +operation = log2(1+file) +overlay_previous = no +[bedgraph_7] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original +color = black +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill transform = log2 -log_pseudocount = 1 -min_value = 0 y_axis_values = original - -[x-axis] \ No newline at end of file +log_pseudocount = 1.0 +overlay_previous = no +[x-axis] +where = bottom \ No newline at end of file
--- a/test-data/test19.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test19.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,75 +1,129 @@ -[test bedgraph] +[bedgraph_0] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +title = bedgraph color = blue transform = no color = blue -height = 5 -title = bedgraph color = blue transform = no -transform = no +alpha = 1.0 +height = 5.0 +show_data_range = true grid = true - -[test bedgraph] +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +[bedgraph_1] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = blue -height = 5 title = bedgraph color = blue transform = log -transform = log +color = blue +alpha = 1.0 +height = 5.0 +show_data_range = true grid = true - -[test bedgraph] +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +transform = log +y_axis_values = transformed +log_pseudocount = 0.0 +overlay_previous = no +[bedgraph_2] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +title = bedgraph color = red transform = log min_value = 1 color = red -height = 5 -title = bedgraph color = red transform = log min_value = 1 -min_value = 1 +alpha = 1.0 +height = 5.0 +min_value = 1.0 +show_data_range = true +grid = true +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill transform = log -grid = true - -[test bedgraph] +y_axis_values = transformed +log_pseudocount = 0.0 +overlay_previous = no +[bedgraph_3] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = green -height = 5 title = bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 -transform = log -log_pseudocount = 2 -min_value = 0 -grid = true - -[test bedgraph with operation] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = green -height = 5 -title = bedgraph color = green operation = log(2+file) min_value = 0.7 -operation = log(2+file) -min_value = 0.7 +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true grid = true - -[test bedgraph] +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +transform = log +y_axis_values = transformed +log_pseudocount = 2.0 +overlay_previous = no +[bedgraph_4] file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz -color = black -height = 5 +title = bedgraph color = green operation = log(2+file) min_value = 0.7 +color = green +alpha = 1.0 +height = 5.0 +min_value = 0.7 +show_data_range = true +grid = true +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +operation = log(2+file) +overlay_previous = no +[bedgraph_5] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 -transform = log2 -log_pseudocount = 1 -min_value = 0 -grid = true - -[test bedgraph] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = black -height = 5 +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = true +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +transform = log2 +y_axis_values = transformed +log_pseudocount = 1.0 +overlay_previous = no +[bedgraph_6] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black operation = log2(1+file) min_value = 0 -operation = log2(1+file) -min_value = 0 -grid = true - -[test bedgraph] -file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz color = black -height = 5 +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = true +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +operation = log2(1+file) +overlay_previous = no +[bedgraph_7] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original +color = black +alpha = 1.0 +height = 5.0 +min_value = 0.0 +show_data_range = true +grid = true +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill transform = log2 -log_pseudocount = 1 -min_value = 0 y_axis_values = original -grid = true - -[x-axis] \ No newline at end of file +log_pseudocount = 1.0 +overlay_previous = no +[x-axis] +where = bottom \ No newline at end of file
--- a/test-data/test2.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test2.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ [x-axis] where = top -[bigwig_0] +[bigwig_1] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test line color = red @@ -10,9 +10,10 @@ nans_to_zeros = false type = line:1.0 show_data_range = false +grid = false file_type = bigwig overlay_previous = no -[bigwig_0] +[bigwig_1] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test line color = red @@ -22,9 +23,10 @@ nans_to_zeros = false type = line:1.0 show_data_range = false +grid = false file_type = bigwig overlay_previous = no -[bigwig_1] +[bigwig_2] file = test-data/bigwig_chrx_2e6_5e6.bw title = nans_to_zeros color = blue @@ -34,9 +36,10 @@ nans_to_zeros = true type = line:1.0 show_data_range = true +grid = false file_type = bigwig overlay_previous = no -[hlines_2] +[hlines_3] height = 1.5 y_values = 50 show_data_range = false @@ -46,7 +49,7 @@ line_style = dashed overlay_previous = share-y file_type = hlines -[hlines_3] +[hlines_4] title = hlines height = 1.5 min_value = 12.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test22.ini Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,21 @@ + +[scale bar] +file_type = scalebar +title = scalebar height = 5 +where = right +height = 5 + +[spacer] + +[fasta_1] +file_type = fasta +title = fasta from cached +file = chrM.fa + +[spacer] + +[fasta_2] +file_type = fasta +title = fasta from history height = 5 +file = chrM.fa +height = 5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test23.ini Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,61 @@ +[x-axis] +where = top + +[spacer] +height = 0.05 + +[hic matrix] +file = Li_et_al_2015.h5 +title = classical depth=300000 with arcs +depth = 300000 +transform = log1p +file_type = hic_matrix + +[test arcs overlay] +file = test_wide.arcs +color = red +line_width = 5 +links_type = loops +overlay_previous = share-y + +[hic matrix square] +file = Li_et_al_2015.h5 +title = square with arcs +transform = log1p +file_type = hic_matrix_square + +[test arcs overlay] +file = test_wide.arcs +color = red +line_width = 5 +links_type = squares +overlay_previous = share-y + +[hic matrix square] +file = Li_et_al_2015.h5 +title = square with arcs region2=chrX:3000000-3100000 +transform = log1p +file_type = hic_matrix_square +region2 = chrX:3000000-3100000 + +[test arcs overlay] +file = test_wide.arcs +color = red +line_width = 5 +links_type = squares +overlay_previous = share-y + +[hic matrix square] +file = Li_et_al_2015.h5 +title = square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000 +file_type = hic_matrix_square +region2 = chrX:3000000-3100000 +colormap = Blues +transform = no + +[test domains] +file = tad_classification.bed +color = none +border_color = black +display = squares +overlay_previous = share-y
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test24.ini Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,44 @@ +[maf] +file = first.maf +reference = mm10 +file_index = /tmp/first.maf.index +title = default + +[spacer] +height = 1 + +[maf] +file = first.maf +reference = mm10 +file_index = /tmp/first.maf.index +title = height = 3 show sequence +display_ref_seq = true +height = 3 + +[spacer] +height = 1 + +[maf] +file = first.maf +reference = mm10 +file_index = /tmp/first.maf.index +title = species_order = hg19 rn5, species_labels = Human Rat +species_order = hg19 rn5 +species_labels = Human Rat +height = 3 + +[spacer] +height = 1 + +[maf] +file = first.maf +reference = mm10 +file_index = /tmp/first.maf.index +title = species_order = hg19, species_labels = Human, species_order_only = true +species_order = hg19 +species_labels = Human +species_order_only = true +height = 3 + +[x-axis] +where = bottom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test25.ini Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,21 @@ +[bedgraph_0] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +title = bedgraph color = blue +color = blue +alpha = 1.0 +height = 5.0 +show_data_range = true +grid = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +max_value = 5 + +[islands as highlight] +file = islands.bed +type = vhighlight + +[x-axis] +where = bottom
--- a/test-data/test4.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test4.ini Sat Oct 01 08:43:22 2022 +0000 @@ -9,6 +9,7 @@ number_of_bins = 2000 type = fill show_data_range = false +grid = false file_type = bigwig overlay_previous = no [bigwig_1] @@ -21,6 +22,7 @@ number_of_bins = 300 type = fill show_data_range = false +grid = false file_type = bigwig overlay_previous = share-y [x-axis]
--- a/test-data/test5.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test5.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ [x-axis] where = top -[genes_0_0] +[genes_1_0] file = dm3_subset_BDGP5.78.gtf.gz prefered_name = transcript_name merge_transcripts = false @@ -12,15 +12,16 @@ display = stacked height = 10.0 labels = true -file_type = bed +all_labels_inside = false +labels_in_margin = false +file_type = gtf global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no [spacer] height = 1.0 -[genes_1_0] +[genes_2_0] file = dm3_subset_BDGP5.78_asbed4.bed.gz title = test color = #000000 @@ -30,11 +31,12 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no [spacer] height = 1.0 \ No newline at end of file
--- a/test-data/test6.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test6.ini Sat Oct 01 08:43:22 2022 +0000 @@ -5,6 +5,7 @@ type = box use_summit = true height = 4.0 +line_width = 1.0 show_labels = true file_type = narrow_peak overlay_previous = no @@ -15,8 +16,8 @@ type = box use_summit = true height = 4.0 +line_width = 2.0 show_labels = true -line_width = 2 file_type = narrow_peak overlay_previous = no [narrow_peak_2_0] @@ -29,6 +30,7 @@ width_adjust = 3.0 max_value = 50.0 height = 4.0 +line_width = 1.0 show_labels = false file_type = narrow_peak overlay_previous = no @@ -43,6 +45,7 @@ show_data_range = false width_adjust = 1.5 height = 4.0 +line_width = 1.0 show_labels = true file_type = narrow_peak overlay_previous = no
--- a/test-data/test7.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test7.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,42 +1,79 @@ [x-axis] where = top -[genes_0_0] -file = test-data/dm3_genes.bed.gz -title = genes +[genes_1_0] +file = test-data/dm3_subset_BDGP5.78.gtf.gz +prefered_name = transcript_name +title = gtf default color = #000000 border_color = #000000 style = flybase height_utr = 1.0 color_utr = grey +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true -file_type = bed +all_labels_inside = false +labels_in_margin = false +fontstyle = normal +file_type = gtf global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_1_0] +[genes_2_0] file = test-data/dm3_subset_BDGP5.78.gtf.gz prefered_name = gene_name merge_transcripts = true -title = gtf +merge_overlapping_exons = false +title = gtf merge transcripts, use gene_name, red 0.75 UTR color = #000000 border_color = #000000 style = flybase height_utr = 0.75 color_utr = #ff0000 +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true -file_type = bed +all_labels_inside = false +labels_in_margin = false +fontstyle = normal +file_type = gtf global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_2_0] +[genes_3_0] +file = test-data/dm3_subset_BDGP5.78.gtf.gz +prefered_name = gene_name +merge_transcripts = true +merge_overlapping_exons = true +title = same but merge overlapping exons +color = #000000 +border_color = #000000 +style = flybase +height_utr = 0.75 +color_utr = #ff0000 +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 +display = stacked +height = 10.0 +labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal +file_type = gtf +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_4_0] file = test-data/dm3_genes_withrgbandscore.bed.gz title = genes with scores color = cool_r @@ -44,33 +81,43 @@ style = flybase height_utr = 1.0 color_utr = grey +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_3_0] +[genes_5_0] file = test-data/dm3_genes_withrgbandscore.bed.gz title = genes with utr as bed_rgb -color = black +color = #000000 border_color = #000000 style = flybase height_utr = 1.0 color_utr = bed_rgb +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_3_0] +[genes_6_0] file = test-data/dm3_genes_withrgbandscore.bed.gz title = genes with coding as bed_rgb - labels_in_margin color = bed_rgb @@ -78,17 +125,21 @@ style = flybase height_utr = 1.0 color_utr = grey +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true +all_labels_inside = false labels_in_margin = true +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_4_0] +[genes_7_0] file = test-data/dm3_genes_withrgbandscore.bed.gz title = genes bed_rgb like - all_labels_inside color = bed_rgb @@ -96,13 +147,17 @@ style = flybase height_utr = 1.0 color_utr = bed_rgb +arrowhead_included = false +arrowhead_fraction = 0.004 +color_backbone = #000000 display = stacked height = 10.0 labels = true all_labels_inside = true +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no \ No newline at end of file
--- a/test-data/test8.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test8.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,6 +1,6 @@ [x-axis] where = top -[genes_0_0] +[genes_1_0] file = test-data/dm3_genes.bed.gz title = dm3_genes.bed color = #000000 @@ -10,13 +10,14 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false file_type = bed global_max_row = true max_labels = 15 line_width = 0.5 -arrowhead_included = false overlay_previous = no -[genes_1_0] +[genes_2_0] file = test-data/dm3_genes.bed.gz title = genes.bed.gz color = #000000 @@ -26,9 +27,10 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false file_type = bed global_max_row = false max_labels = 60 line_width = 2.0 -arrowhead_included = false overlay_previous = no \ No newline at end of file
--- a/test-data/test9.ini Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/test9.ini Sat Oct 01 08:43:22 2022 +0000 @@ -1,29 +1,58 @@ [x-axis] where = top -[genes_0_0] +[genes_1_0] file = dm3_subset_BDGP5.78.gtf.gz prefered_name = transcript_name merge_transcripts = false -title = test +title = defaut arrowhead fontstyle italic color = #000000 border_color = #000000 style = flybase height_utr = 1.0 color_utr = grey +arrowhead_included = false +arrowhead_fraction = 0.004 display = stacked height = 10.0 labels = true -file_type = bed +all_labels_inside = false +labels_in_margin = false +fontstyle = italic +file_type = gtf global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no [spacer] height = 1.0 -[genes_1_0] +[genes_2_0] +file = dm3_subset_BDGP5.78.gtf.gz +prefered_name = transcript_name +merge_transcripts = false +title = arrowhead_fraction 0.1 fontstyle oblique +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +arrowhead_included = false +arrowhead_fraction = 0.1 +display = stacked +height = 10.0 +labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = oblique +file_type = gtf +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[spacer] +height = 1.0 +[genes_3_0] file = dm3_subset_BDGP5.78_asbed4.bed.gz -title = test +title = genes without orientation color = red border_color = #000000 style = UCSC @@ -31,35 +60,42 @@ display = stacked height = 10.0 labels = true +all_labels_inside = false +labels_in_margin = false +fontstyle = normal file_type = bed global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = false overlay_previous = no [spacer] height = 1.0 -[genes_2_0] +[genes_4_0] file = dm3_subset_BDGP5.78.gtf.gz prefered_name = transcript_name merge_transcripts = false -title = test +title = arrowhead included color = red border_color = #000000 style = flybase height_utr = 1.0 color_utr = grey +arrowhead_included = true +arrowhead_fraction = 0.004 display = stacked height = 10.0 labels = true -file_type = bed +all_labels_inside = false +labels_in_margin = false +fontstyle = normal +file_type = gtf global_max_row = false max_labels = 60 line_width = 0.5 -arrowhead_included = true overlay_previous = no [spacer] height = 1.0 -[vlines_3] +[vlines_5] file = dm3_subset_BDGP5.78_asbed4.bed.gz +line_width = 0.5 type = vlines \ No newline at end of file
--- a/test-data/testpyGT.sh Sun Feb 13 22:43:45 2022 +0000 +++ b/test-data/testpyGT.sh Sat Oct 01 08:43:22 2022 +0000 @@ -20,5 +20,9 @@ pgt --tracks test-data/test19.ini --region chr2:73,800,000-75,744,000 --fontSize 12 -o test-data/test_log_grid.png pgt --tracks test-data/test20.ini --region chrX:3000000-3300000 --fontSize 12 -o test-data/test_arcs_use_middle.png pgt --tracks test-data/test21.ini --region X:3000000-3600000 --fontSize 12 --trackLabelFraction 0.3 --plotWidth 12 --dpi 20 -o test-data/master_scale_bar_startend.png +pgt --tracks test-data/test22.ini --region chrM:10-30 --fontSize 12 -o test-data/master_fasta.png +pgt --tracks test-data/test23.ini --region chrX:3000000-3300000 --fontSize 12 -o test-data/test_matrix_square.png +pgt --tracks test-data/test24.ini --region 2:34704975-34705208 --fontSize 12 -o test-data/test_maf.png +pgt --tracks test-data/test25.ini --region chr2:73,800,000-75,744,000 --fontSize 12 -o test-data/test_vhighlight.png conda_env_deactivate
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat Oct 01 08:43:22 2022 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables>