Roche 05434564001 Sequencing Solutions Signal Map User manual

Roche
Brand
Roche
Model
05434564001 Sequencing Solutions Signal Map
Category
Graphics software
Type
User manual
SignalMap v2.0.0 Software User’s Guide
Version 3.2
For Research Use Only.
Not for use in diagnostic procedures.
SignalMap v2.0.0 Software User’s Guide, v3.2
2
Copyright
© 2014-2019 Roche Sequencing Solutions, Inc. All Rights Reserved.
Edition
Version 1.0, Dec 2006. Version 2.0, March 2013. Version 3.0, January 2014. Version 3.1, September 2018. Version 3.2, May 2019.
Service Marks and Trademarks
All other product names and trademarks are the property of their respective owners.
Restrictions and Liabilities
This document is provided “as is” and Roche Sequencing Solutions, Inc. (“Roche”) assumes no responsibility for any
typographical, technical or other inaccuracies in this document. Roche reserves the right to periodically change information that
is contained in this document; however, Roche makes no commitment to provide any such changes, updates, enhancements or
other additions to this document to you in a timely manner or at all.
OTHER THAN THE LIMITED WARRANTY CONTAINED IN THIS USER GUIDE, ROCHE MAKES NO REPRESENTATIONS,
WARRANTIES, CONDITIONS OR COVENANTS, EITHER EXPRESS OR IMPLIED (INCLUDING WITHOUT LIMITATION, ANY
EXPRESS OR IMPLIED WARRANTIES OR CONDITIONS OF FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT,
MERCHANTABILITY, DURABILITY, TITLE, OR RELATED TO THE PERFORMANCE OR NON-PERFORMANCE OF ANY PRODUCT
REFERENCED HEREIN OR PERFORMANCE OF ANY SERVICES REFERENCED HEREIN).
This document might contain references to third party sources of information, hardware or software, products or services and/or
third party web sites (collectively the “Third-Party Information”). Roche does not control, and is not responsible for, any Third-
Party Information, including, without limitation the content, accuracy, copyright compliance, compatibility, performance,
trustworthiness, legality, decency, links, or any other aspect of Third-Party Information. The inclusion of Third-Party Information in
this document does not imply endorsement by Roche of the Third-Party Information or the third party in any way.
Roche does not in any way guarantee or represent that you will obtain satisfactory results from using Roche products as
described herein. The only warranties provided to you are included in the Limited Warranty enclosed with this guide. You assume
all risk in connection with your use of Roche products.
Roche is not responsible nor will not be liable in any way for your use of any of software or equipment that is not supplied by
Roche in connection with your use of the Roche products.
Conditions of Use
You are responsible for understanding and using the software described within. Roche does not guarantee any results you
may achieve.
Patent License Limitations
For patent license limitations for individual products, please refer to www.technical-support.roche.com.
SignalMap v2.0.0Software User’s Guide, v3.2
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Table of Contents
Preface ........................................................................................................................................... 5
Intended Use ................................................................................................................................................. 5
Contact Information .................................................................................................................................... 5
Technical Support............................................................................................................................... 5
Conventions Used in This Guide ........................................................................................................... 5
Symbols ................................................................................................................................................... 5
Text ........................................................................................................................................................... 5
Chapter 1. Before You Begin.................................................................................................... 6
What is SignalMap Software? ................................................................................................................ 6
Recommended System Requirements ................................................................................................ 6
Installing SignalMap Software ............................................................................................................... 6
Checking for Updates ................................................................................................................................ 7
Chapter 2. Understanding Basic Concepts .......................................................................... 8
SignalMap Workflow .................................................................................................................................. 8
Navigating the SignalMap Software Interface ................................................................................ 8
Toolbar .................................................................................................................................................... 9
Panes and Pane Selector ................................................................................................................. 9
Information and Attributes ............................................................................................................ 10
Position Scale ..................................................................................................................................... 11
Tracks .................................................................................................................................................... 11
Status Bar ............................................................................................................................................. 12
Printing Data ................................................................................................................................................ 12
Viewing or Changing Print Settings .......................................................................................... 12
Previewing Data Before Printing ................................................................................................ 13
Printing Data as Shown on the Screen .................................................................................... 13
Chapter 3. Importing Data ...................................................................................................... 14
Recognized File Types ............................................................................................................................. 14
GFF Files ............................................................................................................................................... 14
BED Files .............................................................................................................................................. 14
Importing Data ............................................................................................................................................ 14
Annotation .................................................................................................................................................... 15
Hyperlinks ..................................................................................................................................................... 16
Chapter 4. Browsing Data ....................................................................................................... 18
Viewing Panes and Tracks ..................................................................................................................... 18
Viewing Tracks on a Particular Pane ........................................................................................ 19
Viewing All Tracks ............................................................................................................................ 19
Going To a Specific Location ....................................................................................................... 20
Reorganizing Panes .................................................................................................................................. 20
Reordering Panes ............................................................................................................................. 20
Deleting Panes ................................................................................................................................... 20
Reorganizing Tracks ................................................................................................................................. 21
Selecting Tracks ................................................................................................................................ 21
Moving Tracks.................................................................................................................................... 21
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Deleting Tracks .................................................................................................................................. 21
Searching ...................................................................................................................................................... 22
Magnifying Regions of Data ................................................................................................................. 22
Zooming In (Increasing Magnification)................................................................................... 23
Zooming Out (Decreasing Magnification) ............................................................................. 24
Changing the Track Height ................................................................................................................... 24
Changing the Y Axis ................................................................................................................................. 25
Manually Setting the Y-Axis Scale ............................................................................................ 25
Automatically Setting the Y-Axis Scale ................................................................................... 25
Changing the Track Style ....................................................................................................................... 25
Changing the Track Color ...................................................................................................................... 26
Highlighting Tracks ................................................................................................................................... 27
Selecting a Cursor Track ............................................................................................................... 27
Highlighting a Data Point .............................................................................................................. 27
Jumping to the Next or Previous Data Point ......................................................................... 28
Using Hyperlinks ........................................................................................................................................ 28
Chapter 5. Exporting Data ....................................................................................................... 30
Selecting Data ............................................................................................................................................. 30
Selecting One Region ..................................................................................................................... 30
Selecting Multiple Regions ........................................................................................................... 30
Exporting Selections to a GFF File ...................................................................................................... 31
Exporting a Screen Capture .................................................................................................................. 31
Exporting a Screen Capture as a Windows Metafile ......................................................... 32
Exporting a Screen Capture as a BMP, GIF, PNG or TIFF ................................................ 32
Appendix A. GFF Files ............................................................................................................... 34
Understanding GFF Files ........................................................................................................................ 34
Examples in Text File Format ................................................................................................................ 35
Appendix B. BED Files .............................................................................................................. 36
Understanding BED Files ....................................................................................................................... 36
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Preface
Intended Use
The SignalMap software is intended for research use only. Not for use in diagnostic
procedures.
The SignalMap software is a visualization tool for Roche design data.
Contact Information
Technical Support
If you have technical questions, contact your local Roche Technical Support. Go to
www.roche.com/support for contact information.
Conventions Used in This Guide
Symbols
Symbol Description
Important Note. Information critical to the success of the procedure or use of the product. Failure
to follow these instructions could result in compromised data.
Information Note: Designates a note that provides additional information concerning the current
topic or procedure.
Text
Conventions Description
Numbered listing
Indicates steps in a procedure that must be performed in the order listed.
Italic type, blue
Identifies a resource in a different area of this manual or on a web site.
Italic type
Identifies the names of dialog boxes, windows, tabs, panels, views, or message
boxes in the software.
Bold type
Identifies names of menus and controls (buttons, checkboxes, etc.) in the
software.
SignalMap v2.0.0 Software User’s Guide, v3.2
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Chapter 1. Before You Begin
What is SignalMap Software?
The SignalMap software enables you to visualize Roche design data. It provides the ability to:
• Import one or more GFF (General Feature Format) or BED files.
• Visualize tracks of data organized into panes and tracks.
• Link to a web site with detailed information for a selected gene.
• Export a subset of your data.
• Print and export screen captures.
Recommended System Requirements
Specification
Memory 512 MB
Processor Pentium III 600 MHz or equivalent
Hard Drive Disk 10 MB
Operating System Microsoft Windows XP, Windows 7
Monitor SXGA 1280x1024 with 16-bit colors
Hardware Graphics Driver Recommended
Keyboard Standard
Software Java 6
Installing SignalMap Software
You must install the SignalMap software from files downloaded from the Roche website at
https://sequencing.roche.com/en/products-solutions/by-category/target-
enrichment/software/signal-map-software.html.
1. Click on the Download link.
2. Select Open to run the installer or Save to save the installer file to your computer.
3. Unzip the downloaded file.
4. Double-click SignalMap_install.exe.
5. Follow the on-screen installer instructions (Figure 1).
By installing the SignalMap software, you agree to the terms and conditions of the relevant
software license agreement(s).
Chapter 1. Before You Begin
SignalMap v2.0.0 Software User’s Guide, v3.2
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Figure 1: SignalMap Installer
Checking for Updates
To verify that you are using the most up-to-date version of this guide to view your designs, go
to https://sequencing.roche.com/en/products-solutions/by-category/target-
enrichment/software/signal-map-software.html
.
SignalMap v2.0.0 Software User’s Guide, v3.2
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Chapter 2. Understanding Basic
Concepts
This chapter describes the basic concepts underlying the software to enable you to use
SignalMap software effectively and efficiently.
SignalMap Workflow
The following is a broad overview of a typical session using SignalMap software:
1. Start the SignalMap software. The SignalMap program window appears.
2. Choose File -> New to create a new document window.
3. Import your data files. For more information, see the Importing Data section in Chapter
3. Importing Data.
4. Explore your data.
- Browse your data. For more information, see the
Viewing Panes and Tracks
section in
Chapter 4. Browsing Data.
- Export your data or screen capture. For more information, see the Exporting Your
Data section in Chapter 5. Exporting Data.
- Print a screen. For more information, see the Printing Data section in this chapter.
Navigating the SignalMap Software Interface
When you import files into SignalMap software, a navigation window similar to Figure 2
appears:
Figure 2. SignalMap software Navigation Window
Chapter 2. Understanding Basic Concepts
SignalMap v2.0.0 Software User’s Guide, v3.2
9
Toolbar
Use the buttons on the toolbar to quickly access SignalMap features. A description of each
icon is provided in Table 1 below.
You can display or hide the toolbar by choosing View -> Toolbar.
You can move the pane selector by dragging it with the mouse.
Icon Name Description
Create a New
Document
Creates a new document (or window) in which to import data. The first new
document window is called GFF1. Subsequent windows opened in the same
session are named sequentially, GFF2, GFF3, and so on.
Import Files
Imports existing GFF/BED files, saved with either .gff, .bed, or .txt filename
extension. You can import several files at a time.
Print Preview Displays a preview of the current display before you print.
Print Prints the current display to the selected printer.
Pointer Click to select data or genes.
For locations on the gene track annotated with web addresses, double-click to
activate the hyperlink.
Magnifier Use to zoom in or out of the display in the selected pane. Be aware your
magnification selections will not affect other panes.
• Click in the display to double the magnification around the center of
the click.
• Press the Ctrl key then click to halve the magnification.
• Click and drag to magnify an area.
Ruler Click and drag within a pane to display the Width and Position of the selection in
the header, when the header is displayed.
Autoscale Enables the automatic scaling of the y axis for the selected tracks.
Manual Scale Displays the Manual Scale dialog box, from which you can change the minimum
and maximum y-axis scale for the selected tracks.
Increase
Point Size
Increases the height of the data to make it more visible.
Decrease
Point Size
Decreases the height of the data.
Table 1. Icon Names and Descriptions
Panes and Pane Selector
SignalMap software displays the data from a GFF or BED file in panes. Each pane contains
information corresponding to one seqname defined in the imported file. Typically, a seqname
will be the chromosome or region name for Roche-supplied data.
You can select individual panes from the selection box in the pane selector. Choosing the All
Tracks button displays all tracks.
SignalMap software replaces an empty seqname with a space.
Chapter 2. Understanding Basic Concepts
SignalMap v2.0.0 Software User’s Guide, v3.2
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Icon Name Description
Back (Pane
History)
Displays the previous pane in your browsing history.
Forward
(Pane
History)
Displays the next pane in your browsing history.
Information and Attributes
SignalMap software can optionally display information about the dataset and the attributes of
features.
Display Header
Displays the enabled information and attributes, and the Roche logo at the top of the pane.
You can display or hide the header by choosing View -> Display Header.
Loaded Files
Displays information about loaded files:
• Files: An alphanumeric listing of all loaded files.
• Load Time: The total time it took to import data from all files.
You can display or hide the loaded files information by choosing View -> Loaded Files.
Track Statistics
Displays statistics about tracks:
• Rows loaded: The total number of rows from all of the tracks in all of the loaded files.
• Positions Displayed: The exact range of positions currently displayed.
• Total Positions: The exact range of positions from all of the tracks in the pane.
You can display or hide the track statistics by choosing View -> Track Statistics.
Pointer Info
Displays information that corresponds to the feature under the pointer:
• Score: The score for the feature.
• Pos: The first and last position of the feature.
• Attr: The contents of an optional column in a GFF file. Attribute information could
include web site links and annotation.
You can display or hide the pointer info by choosing View -> Pointer Info.
Pointer info is not displayed if there is no feature under the pointer.
Chapter 2. Understanding Basic Concepts
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Cursor Info
Displays information that corresponds to the feature highlighted by the cursor:
• Score: The score for the feature.
• Pos: The first and last position for the feature.
• Attr: The contents of an optional column in a GFF file. Attribute information could
include web site links and annotation.
You can display the cursor info by choosing Cursor -> Attach Cursor.
You can hide the cursor info by choosing Cursor -> Detach Cursor.
Selection Info
Displays information that corresponds to the selected region:
• Width: The width of the region.
• Position: The first and last position of the region.
The selection info is displayed when either the pointer or the ruler is selected
in the Toolbar.
Select a region by clicking in the pane and dragging the mouse.
Position Scale
Displays the x-axis scale for all tracks in the pane. This scale corresponds to the start and end
column in the GFF file.
Tracks
Figure 3: Tracks
Chapter 2. Understanding Basic Concepts
SignalMap v2.0.0 Software User’s Guide, v3.2
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Each track displays data for different types of features in the imported file (Figure 3).
• Y-Axis Scale: Displays the y-axis scale information.
• Track Information: Displays the feature, number of rows, and other information
about the track.
• Highlighted Gene: A transparent gray bar is displayed over the track at the location of
the selected gene.
Status Bar
The status of various lock keys is displayed in the lower right corner of the screen, to the right
hand side of the status bar.
• Caps Lock: Displays CAPS when the Caps Lock key is set on your keyboard.
• Num Lock: Displays NUM when the Num Lock key is set on your keyboard.
• Scroll Lock: Displays SCRL when the Scroll Lock key is set on your keyboard.
Printing Data
SignalMap software prints your data based on the magnification of the display. That is, the
Print command prints exactly what you see on your screen. Therefore, zoom in to the region
before using the Print command. (See the Magnifying Regions of Data section in Chapter 4.
Browsing Data for details.) Data always print to a single page.
Before you print your data, check your print settings. You may need to change the
print orientation from portrait to landscape.
Viewing or Changing Print Settings
1. Choose File -> Print Setup.
The Print Setup dialog box appears.
2. Select your printer and print properties.
For example, you may want to change the orientation from portrait to landscape.
3. Click OK to print.
Your data prints onto one page.
Chapter 2. Understanding Basic Concepts
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Previewing Data Before Printing
1. Choose File -> Print Preview or click the Print Preview button on the toolbar.
A preview of what will print displays in the window, as shown in Figure 4.
2. Click Print… at the top of the preview window to print the data.
Figure 4: Print Preview
Printing Data as Shown on the Screen
1. Choose File -> Print or click the Print button on the toolbar.
The Print dialog box appears.
2. Select your printing preferences.
3. Click OK.
Your data prints onto one page.
Notes
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Chapter 3. Importing Data
SignalMap software organizes imported data by seqname, one per pane, then by feature, one
per track, and then by position. This chapter describes the process to:
• Import data
• Import annotation
• Include hyperlinks
Although SignalMap software easily imports very large files (hundreds of
megabytes), it requires significant amounts of memory to do so. Roche
recommends you close other memory-intensive software, such as graphics
programs, when working with SignalMap software to avoid losing information
should those programs stop responding. If SignalMap software stops responding,
try splitting large files by chromosome or region into two or more files and import
those into SignalMap software. If SignalMap software continues to be unresponsive,
report the problem to Roche.
Recognized File Types
GFF Files
The SignalMap software can import and export GFF files with either GFF or TXT filename
extensions. For more information about GFF files, see -
www.sanger.ac.uk/resources/software/gff/spec.html or see the
Understanding GFF Files
section in
Appendix A. GFF Files
.
BED Files
The SignalMap software can import BED files with either BED or TXT filename extensions.
For more information about BED files, see genome.ucsc.edu/FAQ/FAQformat.html#format1 or
see the
Understanding BED Files
section in
Appendix B. BED Files
Importing Data
You can import any GFF file with a GFF or TXT filename extension, or any BED file with a
BED or TXT filename extension, into SignalMap software.
1. Choose between the following:
- To import data into your current document, choose File -> Import or click the
Import Files button on the toolbar.
- To import data into a new document, choose File -> New or click the New button on
the toolbar.
A new document window opens, and the Import Files dialog box appears.
Drag and drop GFF/BED files into the current document to import them.
Chapter 3. Importing Data
SignalMap v2.0.0 Software User’s Guide, v3.2
15
2. Select the files to import. Hold down the Ctrl key while clicking to select multiple files.
3. Click Open.
The SignalMap software imports the files into the document.
The Import Files window (Figure 5) provides status information that shows the progress of the
import. In this example, SignalMap software has loaded 31% of the third file, representing
46% progress towards the time required to import all files.
Figure 5: Import Files Window
Figure 6 shows an example of data-only GFF files.
Figure 6: Data-Only GFF Files
Each data track imported is assigned to a unique color unless a color is specified as an
attribute of a feature.
BED files without a trackname header, will be placed in tracks named the same as the
filename, with the filename extension removed.
Annotation
The SignalMap software imports annotation (any feature other than data) in the same way as
any other GFF file.
The SignalMap software can display certain tracks with specific colors to enable you to more
easily identify them in the pane. This is achieved by defining the color of each data point or
annotation feature in the attribute column of the GFF file using the color tag (see the
Understanding GFF Files section in Appendix A. GFF Files). Table 2 shows acceptable color
tags.
Chapter 3. Importing Data
SignalMap v2.0.0 Software User’s Guide, v3.2
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chr21 hg19_snp137Common snp 33031974 33031974 1
+
. color 00FFFF; snp_id "rs7277748";
chr21 hg19_snp137Common snp 33032287 33032287
1
+
. color=FF0000; snp_id "rs17881180"
Table 2: Acceptable Color Tags
Figure 7 shows a typical example of the use of color tags.
Figure 7: Colored Tracks
Example track color assignments for annotation:
• gene: This track contains information about the start and end of genes. You can click
a gene to highlight all data in the same position as that gene. If web hyperlinks were
specified in the GFF file, you can double-click their location on the gene track to
open your computer’s default web browser and access the specified web site.
Displays with a blue color in Figure 7.
• exon: This track contains exon data. Displays with a brown color in Figure 7.
• data: This track contains user data. Displays with a green color in Figure 7.
Hyperlinks
The SignalMap software treats any http hyperlink in the GFF file’s attribute field as a
hyperlink. URLs can also be specified using the GFF3 tag format url=someurl. You can
separate multiple items in the attribute field with a semicolon (;).
Placing the pointer over a data point containing a hyperlink allows you to view the web
address. Double-clicking data with a hyperlink opens your computer’s default web browser
and accesses the specified web site.
A common use for hyperlinks is to link to web site information about specific genes. This
would be accomplished by adding URL links in the attribute fields for gene feature records.
Table 3 provides acceptable hyperlinks.
chr 1 NGS track1 20 30 30.0 . . chr info; http://www.roche.com
chr1 NGS track1 30 40 40.0 . . url='http://www.roche.com'
chrX NGS track1 10 15 20.0 . . http://www.ncbi.nlm.nih.gov/gene/?term=NM_001412
Table 3: Acceptable Hyperlinks
Chapter 3. Importing Data
SignalMap v2.0.0 Software User’s Guide, v3.2
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Notes
SignalMap v2.0.0 Software User’s Guide, v3.2
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Chapter 4. Browsing Data
The SignalMap software allows you to quickly browse your GFF (General Feature Format) or
BED data. In this chapter, you learn to:
• View panes and tracks
• Reorganize tracks
• Search data
• Magnify regions of data
• Change the track height
• Change the y-axis scale
• Change the track style
• Change the color
• Highlight track data
• Use hyperlinks
Viewing Panes and Tracks
The SignalMap software organizes data into panes and tracks. Each SignalMap document can
contain up to 32,768 panes.
Each pane can contain an unlimited number of tracks. A pane contains data tracks
corresponding to one seqname. Roche-supplied data will usually be organized to display one
chromosome or region per pane. The name of the pane (seqname) appears above the first
track selected, as shown in Figure 8.
Typically, each individual track contains only one data or annotation feature. The feature
name and other details are printed below the graphical representation of the data on the track.
When a new file is imported, the first pane is selected by default.
Chapter 4. Browsing Data
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Viewing Tracks on a Particular Pane
1. Use the pane selector to select to a pane of interest or browse through panes using the
history buttons and the up/down buttons.
2. The SignalMap software displays the data tracks for the selected pane (seqname), as
shown in Figure 8.
Figure 8: Tracks on a Selected Pane
Viewing All Tracks
1. Select All Tracks (the top selection in the pane selector drop-down list).
All tracks appear in the All Tracks pane, as shown in Figure 9.
Figure 9: All Tracks Pane
Chapter 4. Browsing Data
SignalMap v2.0.0 Software User’s Guide, v3.2
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2. The tracks for each seqname appear with alternating color backgrounds (white and lime
green) to separate the seqname data visually.
3. Use the window’s vertical scroll bar keys to scroll to the tracks to view in this pane.
Going To a Specific Location
1. Choose View -> Go to Position or press Ctrl + G.
The Go to Position dialog box appears (Figure 10), displaying the current pane and its
Start and End Positions.
Figure 10: Go To Position Dialog Box
2. Select the pane edit the position, and click OK.
The SignalMap software displays the pane and positions selected.
Reorganizing Panes
The SignalMap software sorts newly imported panes in the order that they were in the file.
You can change the sort preference in the Pane menu. You can also delete panes you do not
want.
Reordering Panes
1. Choose Pane -> Sort.
2. Choose from the following options:
- Unsorted: Panes are displayed in the order they were loaded.
- Alphanumeric: Panes are sorted alphabetically (case-insensitive). If the pane starts
with “chr”, the pane is sorted numerically using the number following “chr”.
Deleting Panes
1. Select the pane to delete.
2. Choose Pane -> Delete.
The SignalMap software deletes the pane.
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Roche 05434564001 Sequencing Solutions Signal Map User manual

Roche
Brand
Roche
Model
05434564001 Sequencing Solutions Signal Map
Category
Graphics software
Type
User manual
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