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Posted By admin On 24/08/21
Program: beagle 5.1 (version: 18May20.d20)
Author: Brian Browning
Email: [email protected]
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Contents

Introduction

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beagle 5.1 is similar to version 5.0, but includes some additional improvements that increase accuracy and reduce computation time.

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Citation

If you use Beagle in a published analysis, please report the program version and cite the appropriate article.

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The Beagle 5.1 genotype imputation method is described in:

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B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed genome from next generation reference panels. Am J Hum Genet 103(3):338-348. doi:10.1016/j.ajhg.2018.07.015

The most recent reference for Beagle's phasing method is:

S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097. doi:10.1086/521987

This reference will be updated when the Beagle version 5 phasing method is published.

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Download Beagle 5.1

Beagle is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Sugars legacy stables. Beagle is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You can download a copy of the the GNU General Public License from http://www.gnu.org/licenses/.

Source files in the net/sf/samtools/ directory are from the Broad Institute and are used to perform BGZIP compression and decompression. Source files from the Broad Institute are licensed under the MIT license.

beagle.18May20.d20.jarBeagle 5.1 program file (requires Java version 8)
beagle_5.1_08Nov19.pdfBeagle 5.1 documentation
run.beagle.18May20.d20.examplea unix script which runs a short Beagle 5.1 analysis
beagle5_release_notesdescription of post-release changes in Beagle version 5
gpl_licenseGNU General Public License

The following resources are also available:

human genetic maps HapMap GrCh36, GrCh37, and GrCh38 genetic maps with cM units in PLINK format
human reference panel 1000 Genomes Project phase 3 reference panel
bref3.18May20.d20.jar Converts from VCF format to bref3 format. Enter 'java ‑jar bref3.18May20.d20.jar help' for usage instructions
unbref3.18May20.d20.jar Converts from bref3 format to VCF format. Enter 'java ‑jar unbref3.18May20.d20.jar help' for usage instructions
Variant Call Format An introduction to Variant Call Format (VCF)
conform-gt a program for making alleles in a VCF file to be consistent with a reference VCF file
Beagle Utilities a suite of utility programs
Beagle 5.0 the Beagle 5.0 web page
Beagle 4.1 the Beagle 4.1 web page
Beagle 4.0 the Beagle 4.0 web page
bref3.24May18.pdf The bref3 file format specification
beagle.200518.zipsource code for Beagle 5.1 (18May20.d20)

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Copyright: 2013-2020 Brian L. Browning
Last updated: May 18, 2020

Brown Note is a desktop notes application written in Python, using PyQt.

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Notes are implemented as decoration-less windows, which can be dragged around the desktop and edited at will. Details in the notes, and their position on the desktop, is stored in a SQLite file database, via SQLAlchemy, with note details and positions being restored on each session.

Introduction to the data model

Data model

The storage of user notes in the app is handled by a SQLite file database via SQLAlchemy, using the declarative_base interface. Each note stores its identifier (id , primary key), the text content with a maximum length of 1000 chars, and the x and y positions on the screen.

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The creation of database tables is handled automatically at startup, which also creates the database file `notes.db` if it does not exist. The created session is used for all subsequent database operations.

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Creating new notes

Python automatically removes objects from memory when there are no further references to them. If we create new objects, but don't assignment to a variable outside of the scope (e.g. a function) they will be deleted automatically when leaving the scope. However, while the Python object will be cleared up, Qt/C++ expects things to hang around until explicitly deleted. This can lead to some weird side effects and should be avoided.

The solution is simple: just ensure you always have a Python reference to any PyQt object you're creating. In the case of our notes, we do this using a _ACTIVE_NOTES dictionary. We add new notes to this dictionary as they are created.

The MainWindow itself handles adding itself to this list, so we don't need to worry about it anywhere else. This means when we create a callback function to trigger creation of a new note, the slot to do this can be as simple as creating the window.

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Starting up

When starting up we want to recreate all our existing notes on the desktop. We can do this by querying the database for all Note objects, and then creating a new MainWindow object for each one. If there aren't any we just create a blank note.

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The Note widget

The notes are implemented as QMainWindow objects. The main in the object name might be a bit of a misnomer, since you can actually have as many of them as you like.

The design of the windows was defined first in Qt Designer, so we import this and call self.setupUi(self) to intialize. We also need to add a couple of window hint flags to the window to get the style & behaviour we're looking for — Qt.FramelessWindowHint removes the window decorations and Qt.WindowStaysOnTopHint keeps the notes on top.

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To complete the setup for notes we need to either store the existing Note object (from the database) or create a new one. If we're starting with an existing note we load the settings into the current window, if we've created a new one we save it to the database.

This initial save just stores the position + an empty string. On a subsequent load we would have the default empty note.

We define a method to handle loading the content of a database Note object into the window, and a second to save the current settings back to the database.

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Both methods store to `_ACTIVE_NOTES` even though this is redundant once the first storage has occurred. This is to ensure we have a reference to the object whether we're loading from the database or saving to it.

The last step to a working notes application is to handle mouse interactions with our note windows. The interaction requirements are very basic — click to activate and drag to reposition.

The interaction is managed via three event handlers mousePressEvent, mouseMoveEvent and mouseReleaseEvent.

The press event detects a mouse down on the note window and registers the initial position.

The move event is only active while the mouse button is pressed and reports each movement, updating the current position of the note window on the screen.

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Finally release takes the end position of the dragged window and writes it to the database, by calling save().

The delete note handler shows a confirmation message, then handles the delete of the Note object from the database via db.session. Thefinal step is to close the window and delete the reference to it from_ACTIVE_NOTES. We do this by id, allowing us to delete the PyQt object reference after the Qt object has been deleted.

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Theming Notes

We want to add a bit of colour to our notes application and make them stand out on the desktop. While we could apply the colours to each element (e.g. using stylesheets) since we want to affect all windows there is a simpler way — setting the application palette.

First we create a new palette object with `QPalette()`, which will contain the current application palette defaults. Then we can override each colour in turn that we want to alter. The entries in a palette are identified by constants on `QPalette`, [see here for a full list]().