Nyzo version 492 (commit on GitHub) corrects issues with creation of the first cycle of the new blockchain. It also adds a script for generating a new Genesis block to start a new blockchain.
This version affects neither the sentinel nor the verifier in a significant way for the main Nyzo blockchain. It is only of interest to those wishing to start a testnet or a new blockchain.
In versions 475 and 476, various mechanisms were added to divide communication between in-cycle and out-of-cycle verifiers. These mechanisms were preventing processing of the first cycle of a new blockchain, as there is not yet a defined cycle until the first cycle is completed. This version adds some special conditions for the first cycle of a blockchain to allow for proper message passing during that cycle.
In the BlacklistManager class, a condition was added to bypass blacklisting for the Genesis cycle. The “Genesis cycle” is the first cycle of the blockchain, the cycle starting at the Genesis cycle. The “Genesis cycle” is the first cycle of the blockchain, the cycle starting at the Genesis block.
In the calculateCycleInformation() method of the Block class, a check on the value of primaryCycleIndex was added. While this section of code is important and not especially simple to understand, this change is quite safe. Values of 4 or greater would throw an exception at line 281, because primaryCycleLengths is an array that always has a length of 4. So, it is easy to see that there is no situation where the code would have worked correctly before this change but will not work correctly after this change. The condition eliminated at line 290 was correct, but it is no longer necessary due to the addition of the earlier condition.
In both the verifierInCurrentCycle() and verifierInOrNearCurrentCycle() methods of BlockManager, conditions have been added to consider all verifiers as in-cycle verifiers during creation of the Genesis cycle. These changes will not affect any current verifiers of the current Nyzo blockchain, but it is necessary to allow proper communication in a new blockchain. When the current Nyzo blockchain was started, there was no separation of messaging between in-cycle and out-of-cycle verifiers, so this was not a concern.
In the Message class, the broadcast() method now uses the newly modified verifierInOrNearCurrentCycle() method to determine whether each verifier should receive a message. This causes messages to be broadcast to the entire mesh in the Genesis cycle, and it causes no change in behavior for later cycles.
The TestnetGenesisBlockCreator class, as its name indicates, generates a Genesis block for a new blockchain for a testnet. The use of a hardcoded verifier private seed and rounding of timestamps allows this script to generate identical Genesis blocks on multiple systems if run at similar times. This script should not be used unmodified for starting anything other than a disposable testnet blockchain, but it could serve as a basis for a script that could generate a Genesis block for other production blockchains.
In UnfrozenBlockManager, a special case was added to always vote for the lowest-scored block available in the Genesis cycle. When the first cycle has not yet completed, the standard scoring system does not yet apply. The current code assigns large negative values, derived from the verifier identifier, to each block. When establishing a new blockchain that is not intended to be discarded, this logic should be modified to establish a Genesis cycle that suits your specific purposes.
In later logic for determining block vote, the Genesis-cycle case has been removed, as it is now handled in the newly added logic above.
In the only change that will affect operation of verifiers in the current Nyzo blockchain (though in a negligible way), node-join messages are now sent to all trusted entry points when the mesh is requested from those entry points. This improves connectivity of a new mesh, and it adds minimal overhead to the existing mesh.
To start your own testnet, start two or more cloud instances. The lowest-spec instances on most providers should be sufficient. No more than 512MB or RAM and 8GB of storage is necessary. Incoming port 9444 TCP should be open on all instances. The easiest option is to open 9444 to all IPs, but it can also be opened to just the other IPs of the testnet.
Clone the repository (https://github.com/n-y-z-o/nyzoVerifier) on your instances.
Follow the instructions to install the repository, except for the following line, which should be skipped:
sudo cp trusted_entry_points /var/lib/nyzo/production
Instead, create your own file with your testnet verifiers. For simplicity, all verifiers can contain references to all verifiers in the mesh, including self-references. Eliminating self-references (a verifier listing itself as a trusted entry point) will provide a slight startup benefit by eliminating a single null bootstrap response from each verifier's initialization sequence.
The /var/lib/nyzo/production/trusted_entry_points file should look similar to the following:
<IP_ADDRESS>:9444 # IP or FQDN of your first verifier <IP_ADDRESS>:9444 # second verifier
Both IPs and FQDNs are supported for the first component. The second component is the port. This can be changed in the code, but the default incoming port for the Nyzo verifier is 9444.
The trusted_entry_points file is how verifiers find each other and establish the mesh. They tell a new verifier what the current state of the blockchain is, and they tell the verifier where the other nodes are. A democratic process is typically used to combine the information from all trusted entry points when joining, but only one trusted entry point is necessary as long as you actually trust the information from that entry point fully.
While there is an option for “testnet” in the code, it is not required for running a testnet. It adds some extra complication and slightly different behaviors, so it's best to build a first testnet without activating the testnet option.
Put the following identifier in the private-seed file of one instance. This is the same seed used in the script for the Genesis block, and using it allows use of a smaller mesh. Without this, three or more verifiers would be needed for the testnet. This file is /var/lib/nyzo/production/verifier_private_seed, and the following line should be the only line in the file:
0101010101010101-0101010101010101-0101010101010101-0101010101010101
If you do not provide this, a cryptographically secure random-number generator will generate a seed for your verifier the first time it starts.
After completing the setup, but before starting the verifier with sudo supervisorctl reload, run the script on each instance at approximately the same time by running this command from the nyzoVerifier directory:
sudo java -jar build/libs/nyzoVerifier-1.0.jar co.nyzo.verifier.TestnetGenesisBlockCreator
In the output, look for a line similar to this:
next increment is in 84.4 seconds (1.4 minutes) at<PHONE_NUMBER>000
Ensure that the timestamp<PHONE_NUMBER>000, in this example) is the same on all of your instances. When the timestamp is the same, the blocks will be identical, as the script has all the other parameters hard-coded for consistency. This script is a shortcut for generating a single Genesis block and distributing it from a central location.
If the timestamp is not the same, run the script again on all verifiers. If you have trouble getting the timestamp to match, generate a block on a single verifier and copy it to the other verifiers. The file location is /var/lib/nyzo/production/blocks/individual/i_000000000.nyzoblock.
If you do not use the script to create a new Genesis block, your verifiers will download the Genesis block from September 13 and begin creating a new blockchain from it. While your verifiers will have no problem processing this blockchain, it is more than 1.85 million blocks behind as of the date of this release, so the verifiers will take some time to catch up to the current open edge.
Next, start the verifiers. So you can watch the verifiers process the first few blocks, the recommended way to start the verifiers the first time is:
sudo java -jar build/libs/nyzoVerifier-1.0.jar
The verifiers have several recovery mechanisms, so the order in which you start them doesn't matter. The first verifier will, naturally, fail to reach any other verifiers in its initialization process, but the verifiers will quickly find one another and begin exchanging messages after the second verifier is started.
If you start the verifiers immediately after generating the Genesis block, they will just sit and do nothing for a little while after initialization, waiting for the blockchain to begin. Then, you'll see regular activity. When you see lines like this, you know the blockchain has started processing:
freezing block [Block: height=1, hash=69a4...2e3a] with standard mechanism
You can stop the verifiers at any time, then load them in the background with the following command:
sudo supervisorctl reload


This script will show a little popup when you mouse over a link, like a tooltip. The popups can have any html content that you want. It features
automatic detection of the window size, so it won't float offscreen when you move near the edges. You can have a
fading effect for windows internet explorer 5+, and on all platforms in ns6.
Fade
Animation
Detectiontype
|


| parse_markdown_comments | index /home/nik/git/fvafrcu/documentation/inst/python/parse_markdown_comments.py |
#% markdown comments for various source files
#%
#% extract markdown like comments from (source code) file, convert them to
#% valid markdown and run pandoc on it.
#% Since the comment characters for different languagues change, this program
#% can be adjusted to use the comment character used in your file by command
#% line arguments.
#%
#% author: Dominik Cullmann
#% copyright: 2014, Dominik Cullmann
#% license: GPL v3.0
#% version: 0.1-2
#% maintainer: Dominik cullmann
#% email<EMAIL_ADDRESS>#% status: prototype
usage: pydoc.py [-h] [-o NAME_POSTFIX] [-e NAME_PREFIX] [-c COMMENT_CHARACTER]
[-m MAGIC_CHARACTER] [--example] [-p HEADER_PATTERN] [-l]
file
convert markdown-style from a file to markdown and html via pandoc.
positional arguments:
file the name of the file to convert comments from
optional arguments:
-h, --help show this help message and exit
-o NAME_POSTFIX, --postfix NAME_POSTFIX
change the postfix added to the files created
(default: _markdown)
-e NAME_PREFIX, --prefix NAME_PREFIX
change the prefix added to the files created (default:
)
-c COMMENT_CHARACTER, --comment COMMENT_CHARACTER
change the comment character (default: #)
-m MAGIC_CHARACTER, --magic MAGIC_CHARACTER
change the magic character (default: %)
--example show program's version number and exit
-p HEADER_PATTERN, --header-pattern HEADER_PATTERN
give the regex pattern to find the line determining a
header. If you give an empty string, any header will
be parsedas if it were a markdown-style comment.
(default: ^$)
-l, --latex
markdown style comments are headed by one or more comment characters giving
the markdown heading level and a magic character marking it as
markdown.
try --example for an example
| Modules | ||||||
|
| Classes | ||||||||||
|
| Functions | ||
|


Outstanding diplomat of the Philippine revolution.
Born in Taal, Batangas, on May 26, 1859.
Gen. Emilio Aguinaldo appointed him as Minister Plenipotentiary to the peace conference in Washington and Paris.
Died on September 29, 1941, at the Manila Doctor's Hospital.


django-elections 0.2 documentation
Each RaceCounty object contains either the information associated with a particular race in a particular county of a state, or the statewide county summary for that race. In New England states, the reporting units are town or city, and statewide town or city summary.
Required CharField(1)
Single character flag indicating test (t) vs. live (l) election results data.
Required BigIntegerField Primary Key
The race_county_id value is for use as a unique identifier for reference from the CountyResult model.
Required IntegerField
AP-assigned race number. Race numbers are guaranteed to be unique only within a state.
Required DateField
Date of the election.
Required CharField(2)
Two character state abbreviation (e.g., IA, LA, ).
IntegerField()
AP-assigned county number. For the statewide total, the “county” number is one (1). County numbers are guaranteed to be unique ONLY within a state.
IntegerField
Federal Information Processing Standard code. This is zero (0), for the statewide summary total.
Required CharField(64)
Name of the state’s county. This is the state’s name for the statewide total.
Required CharField(1)
Single character office type ID. Only Top-of-the-ticket races (President [P], Governor [G], US Senate [S], and US House [H]) are guaranteed to be unique on a national level. All other office types are guaranteed to be unique only within a state. There are other characters used, depending on the state and local races.
Required CharField(1)
National, state or local race type identifier. National identifiers are:
Other characters may be used, depending on the state and local races.
Required IntegerField
Integer indicating district number or an initiative number. This may be zero (0) for a statewide race.
CharField(64)
Name of the office (e.g., U.S. House, Governor, etc.).
CharField(64)
The district or initiative name (e.g., District 46, 1A-Gay Marriage, etc.) This may be empty for a statewide race (e.g., a Governor race).
CharField(16)
Party abbreviation for the race (e.g., Dem, GOP, Lib, etc.). This may be empty for a General Election.
CharField(32)
Description of the type of race (e.g., Primary, Runoff, General).
CharField(64)
Further description of the office type.
Required IntegerField()
The maximum number of winners.
IntegerField
Number of candidates in a runoff race.
Required IntegerField
The number of precincts currently reporting during the election.
Required IntegerField
The total number of precincts.


@* * Copyright 2010-2017 Artima, Inc. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. *@ @(selectedStyle: examples.StyleTraitExamples)
import org.scalatest.Matchers._ val result = "hai" result should have length 3 // Works for any type T for which an implicit Length[T] is available, including String, // Array, scala.collection.GenSeq, java.util.List, and any object with length field or // method or getLength method; the length value can be Int or Long. result should have size 3 // Works for any type T for which an implicit Size[T] is available, including String, Array, // scala.collection.GenTraversable, java.util.Collection, java.util.Map, and any object with // size field or method or getSize method; the size value can be Int or Long.


We define ‘coders’ as anyone who has written a line of code (HTML, CSS, JavaScript, Ruby, Python, Java, SQL whatever) and can explain what it does.
Three airports are accessible to our NYC venue: John F Kennedy International Airport, Laguardia Airport, or Newark Liberty International Airport.
To contact the Write/Speak/Code organizers please email<EMAIL_ADDRESS>While we don't offer refunds, you can transfer your ticket to another person free of charge. Please reach out to<EMAIL_ADDRESS>before transferring the ticket for verification.
Sponsor representatives will get to network with attendees during lunch breaks, extended snack breaks, and conference parties.
The deadline for sponsorship depends upon the type and level of sponsorship. To sponsor the conference & conference related events, sponsors must commit by end of July. The sponsorship deadline for the local Own Your Expertise events will vary based on the local schedules.
Check out our 2018 Sponsorship Prospectus for information on sponsorship levels and benefits then email us at<EMAIL_ADDRESS>Write/Speak/Code is proud to offer childcare and eldercare for all of our full-day events. Childcare will be available for the entire duration of the conference (4 days). In addition to noting childcare and/or eldercare on your registration when you purchase your ticket, please email<EMAIL_ADDRESS>with the following information:
Childcare and Eldercare will take place on the premises unless specifically instructed otherwise.
We will once again be offering a private Lactation Room for attendees during the conference. More information on room scheduling will be released leading up to the conference for those who request it. Please email<EMAIL_ADDRESS>Write/Speak/Code 2018 will be held in an ADA accessible venue. ASL interpreters and/or CART services will be made available as needed. In addition to noting your needs on your registration, please also email<EMAIL_ADDRESS>if you require other accommodations. We're happy to do whatever we can to make your experience comfortable, safe, and welcoming.


After almost 4 months of development I've uploaded the first release of Soya yesterday night =)
Please feel free to browse through the web site, download the latest release, check out the source repository, join the mailing list, report bugs, request new features, ...


Image Rule 5: Verify Decorative Images
Group 1: Image with a empty alt
Image 1:
Group 2: Image with a empty aria-label
Image 2:
Group 3: Image with a empty aria-labelledby
Group 4: Image with no accessible tag
Image 4:
Group 5: Image with HTML 5 hidden
Image 5:
Group 6: Image with a short text alternative
Image 6:
Group 7: Image with a empty aria-label
Image 7:
Group 8: Image with a short text alternative using aria-labelledby
Image text description 8
Group 9: Image with a short text alternative using aria-labelledby
Image text description 3
Group 10: Hidden image with alst=""
Image 10:


THE SHAWSHANK REDEMPTION A film review by James Berardinelli Copyright 1994 James Berardinelli
Rating (0 to 10): 8.5
Date Released: 9/23/94 (limited) Running Length: 2:22 Rated: R (Violence, language, mature themes)
Starring: Tim Robbins, Morgan Freeman, Bob Gunton, William Sadler, Clancy Brown, Gil Bellows Director: Frank Darabont Producer: Niki Marvin Screenplay: Frank Darabont, based on "Rita Hayworth and the Shawshank Redemption" by Stephen King Cinematography: Roger Deakins Music: Thomas Newman Released by Columbia Pictures
With a legion of titles like PET SEMATARY, FIREWALKER, SLEEPWALKERS, MAXIMUM OVERDRIVE, and CHILDREN OF THE CORN, it's reasonable not to expect much from Stephen King-inspired motion pictures. Adaptations of the prolific author's work typically vary from mildly entertaining to virtually unwatchable. There are a few notable exceptions, however; two of which (STAND BY ME, MISERY) were crafted by widely-respected director Rob Reiner. While THE SHAWSHANK REDEMPTION is not a Reiner movie per se, it is a production of Castle Rock Pictures (Reiner's film company), and ranks among the best filmed versions of any King stories to date.
Spanning the years from 1947 through 1966, THE SHAWSHANK REDEMPTION takes the "innocent man in prison" theme and bends it at a different angle. Instead of focusing on crusades for freedom, the movie ventures down the less-traveled road of concentrating on the personal cost of adapting to prison life and how some convicts, once they conform, lose the ability to survive beyond the barbed wire and iron bars. As one of the characters puts it: "These [prison] walls are funny. First you hate them, then you get used to them, then you start to depend on them."
Filmed on location in a disused Ohio prison, THE SHAWSHANK REDEMPTION is set in a place of perpetual dreariness. What little color there is, is drab and lifeless (lots of grays and muted greens and blues), and there are times when the film is a shade away from black-and-white (give credit to cinematographer Roger Deakins, a longtime Cohen brothers collaborator). It's ironic, therefore, that the central messages are of hope, redemption, and salvation.
First time feature director Frank Darabont helms a fleet of impressive performances. Tim Robbins, as Andrew Dufresne, plays the wrongly convicted man with quiet dignity. Andy's ire is internal; he doesn't rant about his situation or the corruptness of the system that has imprisoned him. His unwillingness to surrender hope wins him the admiration of some and the contempt of others, and allows the audience to identify with him that much more strongly.
Ellis Boyd Redding (Morgan Freeman), or "Red" as his friends call him, is the self-proclaimed "Sears and Roebuck" of the Shawshank Prison (for a price, he can get just about anything from the outside). His is the narrative voice and, for once, the disembodied words aid, rather than intrude upon, the story. Serving a life sentence for murder, Red is a mixture of cynicism and sincerity - a man with a good soul who has done a vile deed. His friendship with Andy is one of THE SHAWSHANK REDEMPTION's highlights.
William Sadler (as a fellow prisoner), Clancy Brown (as a sadistic guard), and Bob Gunton (as the corrupt warden) all give fine supporting performances. Newcomer Gil Bellows, in a small-but-crucial role (that was originally intended for Brad Pitt), brings the poise of a veteran to his portrayal of Tommy Williams, Andy's protege.
Ultimately, the stand-out actor is the venerable James Whitmore, doing his finest work in years. Whitmore's Brooks is a brilliantly-realized character, and the scenes with him attempting to cope with life outside of Shawshank represents one of the film's most moving--and effective--sequences.
Unfortunately, following a solid two hours of thought-provoking drama, the movie deflates like a punctured balloon during its overlong denouement.
"Salvation lies within," advises Warden Norton at one point. It is the presentation of this theme that makes THE SHAWSHANK REDEMPTION unique. Prison movies often focus on the violence and hopelessness of a life behind bars. While this film includes those elements, it makes them peripheral. THE SHAWSHANK REDEMPTION is all about hope and, because of that, watching it is both uplifting and cathartic.
- James Berardinelli<EMAIL_ADDRESS>.
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


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| Version | Changes |
| v9.0.0 | The Error names and messages are now properly compared |
| v8.0.0 | The Set and Map content is also compared |
| v6.4.0, v4.7.1 | Typed array slices are handled correctly now. |
| v6.1.0, v4.5.0 | Objects with circular references can be used as inputs now. |
| v5.10.1, v4.4.3 | Handle non-Uint8Array typed arrays correctly. |
| v0.1.21 | Added in: v0.1.21 |
| Version | Changes |
| v9.0.0 | Enumerable symbol properties are now compared. |
| v9.0.0 | The NaN is now compared using the SameValueZero comparison. |
| v8.5.0 | The Error names and messages are now properly compared |
| v8.0.0 | The Set and Map content is also compared |
| v6.4.0, v4.7.1 | Typed array slices are handled correctly now. |
| v6.1.0 | Objects with circular references can be used as inputs now. |
| v5.10.1, v4.4.3 | Handle non-Uint8Array typed arrays correctly. |
| v1.2.0 | Added in: v1.2.0 |
| Version | Changes |
| v5.11.0, v4.4.5 | The message parameter is respected now. |
| v4.2.0 | The error parameter can now be an arrow function. |
| Version | Changes |
| v10.0.0 | Calling assert.fail() with more than one argument is deprecated and emits a warning. |
| v0.1.21 | Added in: v0.1.21 |
| History | Changes |
| v10.0.0 | Instead of throwing the original error it is now wrapped into an AssertionError that contains the full stack trace. |
| v10.0.0 | Value may now only be undefined or null. Before any truthy input was accepted. |
| v0.1.97 | Added in: v0.1.97 |
| Version | Changes |
| v9.0.0 | The Error names and messages are now properly compared |
| v8.0.0 | The Set and Map content is also compared |
| v6.4.0, v4.7.1 | Typed array slices are handled correctly now. |
| v6.1.0, v4.5.0 | Objects with circular references can be used as inputs now. |
| v5.10.1, v4.4.3 | Handle non-Uint8Array typed arrays correctly. |
| v0.1.21 | Added in: v0.1.21 |
| History | Changes |
| v9.0.0 | The -0 and +0 are not considered equal anymore. |
| v9.0.0 | The NaN is now compared using the SameValueZero comparison. |
| v9.0.0 | The Error names and messages are now properly compared |
| v8.0.0 | The Set and Map content is also compared |
| v6.4.0, v4.7.1 | Typed array slices are handled correctly now. |
| v6.1.0 | Objects with circular references can be used as inputs now. |
| v5.10.1, v4.4.3 | Handle non-Uint8Array typed arrays correctly. |
| v1.2.0 | Added in: v1.2.0 |


Inserting a Document
How to insert a document using the DotNetNuke.RadEditorProvider RTE.
- Click the Insert Media button and select Document Manager from the drop down list. This will open the Document Manager.
- Navigate to and select the required document. See "Using the Resource Manager"
- Optional. In the Link Text text box, modify the text associated with this document. The filename is used by default.
- Optional. At Target select the target window for this link.
- Optional. In the Tooltip text box, enter a tool tip to be displayed when a user places their mouse over this link.
- Optional. At CSS Class, select a class for the document link.
- Click the Insert button.
Tip: Additional document properties are available. See "Setting Document Properties"
The Document Manager


PLANET SICK-BOY: http://www.sick-boy.com
Phillip Noyce's (The Saint) adaptation of Jeffrey Deaver's bestseller is a clunky effort that could have been much better under a decent director's care. Denzel Washington stars as a decorated cop that became paralyzed in the line of duty. Bedridden, he tries to catch a serial killer using an inexperienced female officer as his vessel to catch the murderer in this sloppy whodunit.
Washington (The Siege) plays Lincoln Rhyme, who is not only a successful New York City police officer but the author of several true-crime books as well. The film opens with Rhyme bravely trying to rescue a trapped citizen, only to be hit with a falling hunk of metal that nearly cuts him in half. Four years later, Rhyme is still technically a member of the police force, although he can move only his head, one shoulder and, for some reason, the index finger of his right hand, which he uses to operate several computers and televisions while he is confined to his bed. He also has seizures with increasing frequency and is terrified that a big one could leave him like a vegetable. Apparently he hasn't seen himself act lately.
Meanwhile, the killer is a cabbie and each fare is a potential victim. We see him pick up a ritzy white couple at the airport. They want to go to 5th Avenue, but instead he takes them into a desolate neighborhood while they desperately try to escape from the backseat. Couldn't they call for help? I'm thinking that the odds of picking up New Yorkers without a cell phone are staggering, as is the likelihood of the existence of that perfectly straight road he sped down with no lights, stop signs, traffic or pedestrians.
The man's body is discovered by Amelia Donaghy (Angelina Jolie, Pushing Tin), a child-model-turned-beat-cop that plans to be transferred to the less-exciting Youth Services Division. The evidence she finds - white powder, a newspaper clipping, a large bolt and a page number torn from a book – are taken to Rhyme, where he is able to quickly determine the exact time and place of the murderer's next act. Unlikely? You bet. This is explained away by having Rhyme well-versed in the history of the city. Right.
While confined to bed, Rhyme sends Donaghy to each crime scene as they try to gain ground on the killer. He instructs her in what evidence to look for, relying on her eyes and ears as he tries to avoid having control of the investigation wrestled away by Captain Howard Cheney (Michael Rooker, The Replacement Killers). At one point, Cheney is kept at bay by Rhyme's live-in nurse Thelma (Queen Latifah, Living out Loud). Nurse Latifah is actually the acting high-point of Collector.
Washington is better than he has been lately, which isn't saying much. I hear he's very good in The Hurricane, which arrives in theaters in January, but I'll believe it when I see it. Jolie isn't bad in her role, but her attractiveness is almost distracting. Other than her, the other highlights are the dazzling overhead shots of New York City. The bland cast of co-stars include Ed O'Neill (Married with Children), Luis Guzmán (OZ), Leland Orser (Very Bad Things) and Mike McGlone (She's the One). I'm sure the book was much better.
Comparisons to Silence of the Lambs will be inevitable, as the experienced but immobile Washington guides the still-wet-behind-the-ears Jolie to the murderer. Instead, Collector seems more like See No Evil, Hear No Evil, where a blind guy (Richard Pryor) and a deaf guy (Gene Wilder) try to solve a murder. Collector will likely be compared to Se7en as well, but its staged murder scenes are not nearly as disturbing as David Fincher's serial-killer benchmark. Neither of these films offered a red herring as poorly as in Collector.
1:58 - R for strong violent content including grisly images, and for language
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


Avoid the following common mistakes when you use automatic indicators.
Indicators can provide inaccurate output values before they are warmed up. To avoid issues, always check the IsReady
flag before you use indicator output values.
if (_indicator.IsReady) { var value = _indicator.Current.Value; }
if self.indicator.IsReady: value = self.indicator.Current.Value
If you create an automatic indicator and then register it for automatics updates or call the Update
method, the indicator receives multiple input values during each update cycle. To avoid issues, create automatic indicators but don't register them for automatic updates or call the Update
method.


|
| float | random () |
| | random values in the range ( 0.0f ... 1.0f ) More...
|
| |
| bool | compare (float a, float b, float epsilon) |
| |
| bool | check (float f) |
| | Check the value the correct value. More...
|
| |
| bool | check (double d) |
| | Check the value the correct value. More...
|
| |
| float | sqr (float x) |
| | x*x More...
|
| |
| float | abs (float val) |
| |
| template<typename T > |
| T | lerp (float alpha, const T &v0, const T &v1) throw () |
| | Calculate the linear interpolation. More...
|
| |
| template<class T > |
| T | clamp (const T &v, const T &l, const T &u) throw () |
| | reduction in the range between More...
|
| |
| template<typename T > |
| void | fill (T *dest, const T val, const int num) throw () |
| | fill the buffer dest value val number num. More...
|
| |
| float | sign (const float val) |
| | Returns the sign of
x>0 : 1
x=0 : 0
x<0 : -1. More...
|
| |
| int | sign2 (float x) |
| | Returns the sign of
x>0 : 1
x=0 : 0
x<0 : -1. More...
|
| |
| float | clump (float value, float _min, float _max) |
| | Clipping values in a range between minimum and maximum inclusive. More...
|
| |
| void | sincos (const float a, float &outSin, float &outCos) |
| | sine and cosine. More...
|
| |
| float | arccot (float f) |
| | Calculate the arc cotangent. More...
|
| |
| float | arctg (float y, float x) |
| | Calculate the arc tangent. More...
|
| |
| float | safeAcos (float x) |
| | Same as acos(x), but if x is out of range, it is "clamped" to the nearest valid value. The value returned is in range 0...pi, the same as the standard C acos() function. More...
|
| |
| float | cotan (const float f) |
| | cotangent More...
|
| |
| float | radiansToDegree (float rad) |
| | Angle in radians to degrees. More...
|
| |
| float | degreeToRadians (float dgr) |
| | Angle in degrees to radians. More...
|
| |
| float | normalize_angle (float angle) |
| | Normalization of the angle of rotation angle. Cast the value in the range -PI ... + PI . More...
|
| |
| float | lerp (const float f1, const float f2, const float k) |
| | Linear interpolation. More...
|
| |
| int | round (float f) |
| | rounding . More...
|
| |
| float | max3 (float a, float b, float c) |
| | Get an average of 3 values. More...
|
| |
| float | aver_a (const float *pf, const unsigned int num) |
| | Compute and return the average (arithmetic) More...
|
| |
| float | aver_g (const float *pf, const unsigned int num) |
| | Compute and return the geometric mean. More...
|
| |
static math functions(float/double).


GitLOC - Git Lines of Code
Page Not Found: Error 404
The requested URL could not be found. Please return to the
home page
.


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Forest fires causes immediate damage and extreme health risks due to smoke pollution.
Increasing due to increased drought, increased temperatures, and human-driven changes.
Data from people on the ground near areas of concern, to help firefighters.
Origin of fire, Path of fire.
See the entire landscape and help with valuable information.
Best paths for rescue, Best paths to help people evacuate.
Get the latest news of the affected areas.
Awareness towards forest fire.


- Author
- Johannes M. Schmitt schmi.nosp@m.ttjo.nosp@m.h@gma.nosp<EMAIL_ADDRESS>Definition at line 14855 of file compiled.php.
| __construct |
( |
|
$name, |
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$value = null , |
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$expire = 0 , |
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$path = '/' , |
|
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$domain = null , |
|
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|
$secure = false , |
|
|
|
$httpOnly = true |
|
) |
| |
| __construct |
( |
|
$name, |
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$value = null , |
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$expire = 0 , |
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$path = '/' , |
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$domain = null , |
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$secure = false , |
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$httpOnly = true |
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) |
| |
Constructor.
- Parameters
-
| string | $name | The name of the cookie |
| string | $value | The value of the cookie |
| int | string | \DateTime | $expire | The time the cookie expires |
| string | $path | The path on the server in which the cookie will be available on |
| string | $domain | The domain that the cookie is available to |
| bool | $secure | Whether the cookie should only be transmitted over a secure HTTPS connection from the client |
| bool | $httpOnly | Whether the cookie will be made accessible only through the HTTP protocol |
- Exceptions
-
Definition at line 46 of file Cookie.php.
Returns the cookie as a string.
- Returns
- string The cookie
Definition at line 82 of file Cookie.php.
Gets the domain that the cookie is available to.
- Returns
- string
Definition at line 146 of file Cookie.php.
Gets the time the cookie expires.
- Returns
- int
Definition at line 158 of file Cookie.php.
Gets the name of the cookie.
- Returns
- string
Definition at line 122 of file Cookie.php.
Gets the path on the server in which the cookie will be available on.
- Returns
- string
Definition at line 170 of file Cookie.php.
Gets the value of the cookie.
- Returns
- string
Definition at line 134 of file Cookie.php.
Whether this cookie is about to be cleared.
- Returns
- bool
Definition at line 206 of file Cookie.php.
Checks whether the cookie will be made accessible only through the HTTP protocol.
- Returns
- bool
Definition at line 194 of file Cookie.php.
Checks whether the cookie should only be transmitted over a secure HTTPS connection from the client.
- Returns
- bool
Definition at line 182 of file Cookie.php.
The documentation for this class was generated from the following files:


The class LevelMatchFilter allows logging events with a specified level. More...
#include <levelmatchfilter.h>
Public Member Functions | |
| LevelMatchFilter (QObject *pParent=0) | |
| bool | acceptOnMatch () const |
| Level | levelToMatch () const |
| void | setAcceptOnMatch (bool accept) |
| void | setLevelToMatch (Level level) |
| virtual Decision | decide (const LoggingEvent &rEvent) const |
Protected Member Functions | |
| virtual QDebug | debug (QDebug &rDebug) const |
Properties | |
| bool | acceptOnMatch |
| Level | levelToMatch |
The class LevelMatchFilter allows logging events with a specified level.
| Log4Qt::LevelMatchFilter::LevelMatchFilter | ( | QObject * | pParent = 0 |
) |
| bool Log4Qt::LevelMatchFilter::acceptOnMatch | ( | ) | const |
| virtual QDebug Log4Qt::LevelMatchFilter::debug | ( | QDebug & | rDebug | ) | const [protected, virtual] |
Writes all object member variables to the given debug stream rDebug and returns the stream.
LevelMatchFilter(acceptonmatch:true leveltomatch:"WARN" next:Log4Qt::DenyAllFilter(0x3bce3a8) referencecount:1 )
Implements Log4Qt::LogObject.
| virtual Decision Log4Qt::LevelMatchFilter::decide | ( | const LoggingEvent & | rEvent | ) | const [virtual] |
Implements Log4Qt::Filter.
| Level Log4Qt::LevelMatchFilter::levelToMatch | ( | ) | const |
| void Log4Qt::LevelMatchFilter::setAcceptOnMatch | ( | bool | accept | ) | [inline] |
| void Log4Qt::LevelMatchFilter::setLevelToMatch | ( | Level | level | ) | [inline] |
bool Log4Qt::LevelMatchFilter::acceptOnMatch [inline, read, write] |
The property holds if an event is accpeted on a match.
The default is true.
Level Log4Qt::LevelMatchFilter::levelToMatch [inline, read, write] |
The property holds the level to match for this filter.
The default is Level::NULL_INT.


Preparation time
less than 30 mins
Cooking time
10 to 30 mins
Serves
Serves 4
A speedy supper for 4, with a few special touches thrown in.
For the Dover sole, dust the fish in the seasoned flour. Heat a large frying pan and add the oil. Once hot, add the fish skin-side down and cook for a couple of minutes. Turn over and cook for a further minute.
Remove the fish from the pan and set aside to rest.
Heat the butter in a separate frying pan, add the shallot and fry for a few minutes. One it has reached the nut brown stage (or beurre noisette), add the lemon juice, parsley and shrimps and cook for a couple of minutes.
For the beans and potatoes, place the potatoes in a steamer above a large saucepan of salted water. Cook for 15-20 minutes, until done.
Just before serving add the butter, parsley and season with salt and pepper.
Cook the French beans in a separate pan of boiling salted water for 4-5 minutes. Drain and just before serving add the butter and season with salt and pepper.
Heat a small frying pan and add the almonds, toast on a low heat for 2-3 minutes or until golden-brown.
To serve, place the dover sole onto a serving plate, along with the new potatoes and French beans. Top the beans with the toasted almonds.


PokéSprite Spinda Painter proof of concept, by dada78641. View the code on Github.
This is a proof of concept for displaying Spinda's spots on its box sprite.
Spinda is a Pokémon with four spots on its face, whose coordinates are determined by either its personality value (Gen 3–5) or its encryption constant (Gen 6 and up), two hidden numbers inside its data. In the game itself, each Spinda has the same generic box sprite (its custom spots are only visible in battle), but by using a blank sprite and a masked overlay sprite we're able to show its spots on its box sprite as well.
You can view your own Spinda's personality value and encryption constant using a save editor like PKHeX.
Example values
Related links
MIT license.


Administrator User Administrator List User ID Services Account Namespaces Authority Roles Created Time more 생성


--- layout: default ---
Trizbort.io is a browser-based tool that lets you easily map adventure games. Drag rooms into your map and link them up using connections in all compass directions. Add a list of objects present in each room. Finally, export your map straight to your adventure game toolkit of choice: TADS, Inform, Quest or Alan.
Trizbort.io lets you edit the properties of your rooms using a quick and intuitive editor. Room name and description, room colors, room borders, elliptical or octagonal rooms - we got it.
Add named objects with descriptions to your rooms, and even create containment relationships - which will be included in your code generation later.
Trizbort.io can export your map to various adventure game development system. It supports TADS, Inform, Quest and Alan, among others. Code is generated for your rooms, connections and objects, and you can feed it straight into your compiler.
subscribe via RSS
{%- endif -%}


WITNESS LIST Elections Committee March 11, 1997-2:00P HB 324Committee Substitute (days/hours for vote) For: Rep. Glen Maxey (author) Registering, but not testifying: For: Bill Bilyeu (Collin Cty -Tx Ass EA) On: Melinda Nickless (SOS) HB 674 For: Bill Bilyeu (CollinCtyEA) Mary Ann Collins (Repub Pty Tx) On: Andrea Gibbud (BeeCtyTaxAss(f) TACA(a)) Ranette Wood (City of Garland) Steve McDonald (Tx Dem Pty) Tony Sirvello III (EA Harris Cty) Registering, but not testifying: On: Cindy Stapper (Secy of State) HB 753 For: Bill Bilyeu (Collin Cty EA TAEA) Tony Sirvello III (EA Harris Cty) Registering, but not testifying: For: Dana DeBeauvoir (Travis Cty Clerk) HB 927Committee Substitute (early voting proced.) For: Andrea Gibbud (Herself) Bruce Sherbet (TAEA) On: Tom Krampitz (TxDist&Cty Att Ass) Tony Sirvello III (EA Harris Cty Clerk Off) Registering, but not testifying: For: John W. Holtermann (TxSilverHairLege) On: Cindy Stapper (Secy of State) Steve McDonald (Tx Dem Pty) HB 1253 For: Bill Bilyeu (CollinCtyEA) Rep. Henry Cuellar (author) On: Ann McGeehan (Secy of State) Registering, but not testifying: For: Andrea Gibbud (herself TaxAssCollASS) Steve McDonald (Tx Dem Pty) HB 1257 Committee Substitute (early voting proc.) For: Rep. Henry Cuellar (author) On: Andrea Gibbud (Tax Assessor/coll.Ass) Tony Sirvello III (HarrisCtyEA) Registering, but not testifying: For: Edward Martin (Himself) John Holtermann (TxSilverHairLeg) Steve McDonald (Tx Dem Pty) On: Cindy Stapper (Secy of State) HB 1350 Committee Substitute (elig reqrmt clerks) Registering, but not testifying: For: Dana DeBeauvoir (Travis Cty/CtyClrksAss) Tony Sirvello III (Harris Cty Clrk off) On: Elizabeth Hanshaw-Ross (Secy of State) HB 1351 Registering, but not testifying: For: Steve McDonald (Tx Dem Pty) On: Elizabeth Hanshaw-Ross (Secy of State) HB 1400 Amendment (sign declare winner) For: Bill Bilyeu (Collin Cty Elect.TAEA) Jerry Meadows (Hart Info. Serv.) Rep. Barry Telford (author) Robert Parten (Himself) Registering, but not testifying: For: Tony J. Sirvello III (Harris Cty. EA) HB 1483 Against: Bruce Sherbet (Dallas Cty Elect Adm) On: Andrea Gibbud (TaxAssCollAss) Mary Ann Collins (Repub Pty Tx) Robert Parten (himself) Tony Sirvello III (Harris Cty Elect Adm) Registering, but not testifying: For: Steve McDonald (Tx Dem Pty) On: Barbara Brinkmeyer (Tax Asses Coll. Ass.) Cindy Stapper (Secy of State) HB 1645 For: Bruce Sherbet (TAEA) Tony Sirvello (EA Harris Cty Clerk off) On: Melinda Nickless (Secy of State) HB 1652 Committee Substitute (conduct/fin primary) For: Bill Bilyeu (Tx Ass EA) Rep. Bill Siebert (author) On: Mary Ann Collins (Repub Pty Tx) Steve McDonald (Tx Dem Pty) Tony Sirvello III (CtyClerk/(f) Kaufman(a)) Registering, but not testifying: On: Ann McGeehan (Secy of State) Elizabeth Hanshaw-Ross (Secy of State) HB 1852 On: Andrea Gibbud (Bee Cty Tax Ass/Coll) Melinda Nickless (Secy of State) Registering, but not testifying: For: Bruce Sherbet (TAEA) On: Barbara Brinkmeyer (Bee Cty Tax Ass/Coll) HB 1966 For: Andrea Gibbud (TACA - Bee CtyTaxCl/ass) Betty Brown (herself) Mary Ann Collins (Repub Pty Tx) Ranette Wood (Garland- City Secretary) Robert Parten (himself) On: Steve McDonald (Tx Dem Pty) Tony Sirvello III (Harris Cty EA) Registering, but not testifying: For: Linda Sue Winn (City of West Lake Hills)


Thomas Opiyo Okumu is a graduate student studying international developmental studies, and he is originally from Kenya. He explained that he came to OU for the International Development Studies Program, one only offered at a few universities. He also chose OU because he found the school had a good reputation.
“One of the things I used to look at when I was trying to find a university was the ranking of the university, the worldwide ranking,” Opiyo Okumu said. “When I looked at Ohio University in the U.S., it was really a good ranking, around 146 – number 146 out of all the universities in America. And so, to me, it means a lot because it puts me on the map in my country.”
Now in Athens, Opiyo Okumu has thrown himself into OU. He is vice president of the African Students’ Union, and he explained he has been able to find a sense of belonging through extracurriculars.
“The African Students’ Union is a large organization here, and they're part of the Bobcat community – when I'm here I feel home,” Opiyo Okumu said.
Namrata Jain is an OU alumna, who graduated in May 2020 with a masters in Asian studies. Jain is originally from India, and she was an ally of many student organizations while working with the Indian Student Association and the International Student Union. She helped to host Diwali and the Holy Nights festivals for students, participated in conferences and helped give food lectures for classes.
Jain was heavily involved during her time here, and she is excited to recall it.
“Athens was home for four years, so I still miss it,” Jain said.
Jain said she felt welcome at OU, listing a number of teachers who were always available to help, which she appreciated. She talked about how she felt many professors went above and beyond the limits of their profession to help her.
Coming from tropical India, Jain said she was unprepared for the winter weather and fondly recalled a time a professor helped her adjust.
“Professor Julie White actually gave me a parka,” Jain said. “She was like, ‘You will need this, I don't know if you've been in [cold weather].’ But I think that was extremely heart-warming and such a beautiful welcome.”
Tithi Patel, a sophomore studying nursing, explained she was born in India as well and, like Opiyo Okumu, has found serenity through her classes and extracurriculars.
She advised fellow students, especially international, to get involved wherever possible.
“Try to connect as much as you can, like in class or just go and meet new people,” Patel said. “Try to get involved in as many organizations as you can. Try to get in contact with more people.”
Omar Kurdi was born in Saudi Arabia and graduated from OU in 2015. He now works as the associate humanitarian affairs officer at the United Nations Office for the Coordination of Humanitarian Affairs. Kurdi said his time at OU helped him get where he is today.
“The different time and people management skills gained through being active on and off campus, in academics and in student life, are skills I still draw upon today,” Kurdi said in an email.
Like Jain, he looked back fondly at his time at OU.
“The first thing that comes to mind when I think about OU is the intangible atmosphere at the university,” Kurdi recalled in an email. “It's a wonderful combination of desire, curiosity, willingness to learn and grow and a bit of stress mixed in during finals week. But also when you think OU, you can't ignore the tangible feel of college green and all the experiences one has traversing those bricks.”
Kurdi said that the lessons learned at OU will help students much past their time in Athens, just like they have helped him.
“The 'real-word' isn't much different than a classroom, a group project,” Kurdi said in an email. “Working with people to achieve common goals, dealing with conflict and different opinions, challenging our own beliefs – these are all topics that are explored daily at OU.”
Jain agreed with Kurdi, explaining how her education at OU continues to help her today.
“I think Ohio prepared me for … anywhere in the world, in the sense that I understand a lot of interpersonal relations because of the kind of exposure that I got at OU,” Jain said.
Although Athens is a long way from home, all four students and alumni spoke of the people at OU helping to make them feel settled in a new place.
“The very fact that people were very, very nice and very helpful made it so much easier being international here,” Jain said.


{% extends 'other.html' %} {% block more_css %} .display-open-badge { display: block; float: left; height: 80px; width: 300px; background-image: url({{ url_for('static', filename="img/open-badge-logo.png") }}); background-repeat: no-repeat; background-position: 0px 0px; } {% endblock %} {% block main %}
Upon completion of this webinar, you have the opportunity to earn either a Gold, Silver, or Bronze Open Badge indicating your competency and familiarity with using Linked Data with MARC records. By registering and attending this webinar you automatically earned your Bronze Badge that you can receive by sending an email to Jeremy Nelson and creating an Mozilla Open Badge Backpack Account.
You need to answer correctly 60% of the badge assessments for a silver. To earn a Gold Badge you need to answer correctly 87% of the badge assessments. All badge assessments are in the webinar's IPython notebook, url down below.
Please see directions on the downloads page.
If you wish to earn a Silver Badge or Gold Badge, follow these steps
The Bronze Badge is earned by attending the Coding Experiments with MARC and Linked Data in the LITA Linked Data Webinar Series.
The Silver Badge is earned by scoring over 60% on the badge assessments.
Earn your Gold Badge by scoring over 87% on the badge assessments.


Getting started
To run regenie, use the command ./regenie
on the command line,
followed by options and flags as needed.
To get a full list of options use
./regenie --help
The directory examples/
contains some small example files that are
useful when getting started. A test run on a set of binary traits can be achieved by the
following 2 commands.
In Step 1, the whole genome regression model is fit to the traits, and a set of genomic predictions are produced as output
./regenie \
--step 1 \
--bed example/example \
--exclude example/snplist_rm.txt \
--covarFile example/covariates.txt \
--phenoFile example/phenotype_bin.txt \
--remove example/fid_iid_to_remove.txt \
--bsize 100 \
--bt --lowmem \
--lowmem-prefix tmp_rg \
--out fit_bin_out
In Step 2, a set of imputed SNPs are tested for association using a Firth logistic regression model
./regenie \
--step 2 \
--bgen example/example.bgen \
--covarFile example/covariates.txt \
--phenoFile example/phenotype_bin.txt \
--remove example/fid_iid_to_remove.txt \
--bsize 200 \
--bt \
--firth --approx \
--pThresh 0.01 \
--pred fit_bin_out_pred.list \
--out test_bin_out_firth
One of the output files from these two commands is included in example/test_bin_out_firth_Y1.regenie
.
Basic options
Input
| Option | Argument | Type | Description |
|---|---|---|---|
--bgen, --bed, --pgen |
FILE | Required | Input genetic data file. Either BGEN file eg. file.bgen , or bed/bim/fam prefix that assumesfile.bed , file.bim , file.fam exist, or pgen/pvar/psam prefix that assumesfile.pgen , file.pvar , file.psam exist |
--sample |
FILE | Optional | Sample file corresponding to input BGEN file |
--bgi |
FILE | Optional | Index bgi file corresponding to input BGEN file |
--ref-first |
FLAG | Optional | Specify to use the first allele as the reference allele for BGEN or PLINK bed/bim/fam file input [default is to use the last allele as the reference] |
--keep |
FILE | Optional | Inclusion file that lists individuals to retain in the analysis |
--remove |
FILE | Optional | Exclusion file that lists individuals to remove from the analysis |
--extract |
FILE | Optional | Inclusion file that lists IDs of variants to keep |
--exclude |
FILE | Optional | Exclusion file that lists IDs of variants to remove |
--extract-or |
FILE | Optional | Inclusion file that lists IDs of variants to keep regardless of minimum MAC filter |
--exclude-or |
FILE | Optional | Exclusion file that lists IDs of variants to remove unless MAC is above threshold |
--phenoFile |
FILE | Required | Phenotypes file |
--phenoCol |
STRING | Optional | Use for each phenotype you want to include in the analysis |
--phenoColList |
STRING | Optional | Comma separated list of phenotypes to include in the analysis |
--phenoExcludeList |
STRING | Optional | Comma separated list of phenotypes to ignore from the analysis |
--covarFile |
FILE | Optional | Covariates file |
--covarCol |
STRING | Optional | Use for each covariate you want to include in the analysis |
--covarColList |
STRING | Optional | Comma separated list of covariates to include in the analysis |
--catCovarList |
STRING | Optional | Comma separated list of categorical covariates to include in the analysis |
--covarExcludeList |
STRING | Optional | Comma separated list of covariates to ignore |
--pred |
FILE | Optional | File containing predictions from Step 1 (see Overview). This is required for --step 2 |
--tpheno-file |
STRING | Optional | to use a phenotype file in transposed format (e.g. BED format) |
--tpheno-indexCol |
INT | Optional | index of phenotype name column in transposed phenotype file |
--tpheno-ignoreCols |
INT | Optional | indexes of columns to ignore in transposed phenotype file |
--iid-only |
FLAG | Optional | to specify if header in transposed phenotype file only contains sample IID (assume FID=IID) |
Note: Parameter expansion can be used when specifying phenotypes/covariates (e.g. --covarCol PC{1:10}
).
Also, multiple files can be specified for --extract/--exclude/--keep/--remove
by using a comma-separated list.
Genetic data file format
regenie can read BGEN files, bed/bim/fam files or pgen/psam/pvar files in Step 1 and Step 2.
The BGEN file format is described here.
The bed/bim/fam file format is described here.
The pgen/pvar/psam file format is described here.
Tools useful for genetic data file format conversion are : PLINK, QCTOOL, BCFTOOLS.
Step 2 of regenie can be sped up by using BGEN files using v1.2 format with 8 bits encoding
(genotype file can be generated with PLINK2 using
option --export bgen-1.2 'bits=8'
) as well as having an accompanying .bgi index file
(a useful tool to create such file is bgenix which is part of the BGEN library).
To include X chromosome genotypes in step 1 and/or step 2, males should be coded as diploid so that their genotypes are 0/2 (this is done automatically for BED and PGEN file formats with haploid genotypes). Chromosome values of 23 (for human analyses), X, Y, XY, PAR1 and PAR2 are all acceptable and will be collapsed into a single chromosome.
Sample inclusion/exclusion file format
2 2
7 7
.
No header. Each line starts with individual FID IID. Space/tab separated.
Samples listed in the file that are not in bgen/bed/pgen file are ignored.
Variant inclusion/exclusion file format
20
31
.
No header. Each line must start with variant ID (if there are additional columns, file must be space/tab separated).
Variants listed in this file that are not in bgen/bed/pgen file are ignored.
Covariate file format
FID IID V1 V2 V3
1 1 1.46837294454993 1.93779743016325 0.152887004505393
2 2 -1.2234390803815 -1.63408619199948 -0.190201446835255
3 3 0.0711531925667286 0.0863906292357564 0.14254739715665
.
Line 1 : Header with FID, IID and covariate names.
Followed by lines of values. Space/tab separated.
Each line contains individual FID and IID followed by covariate values.
Samples listed in this file that are not in bgen/bed/pgen file are ignored. Genotyped samples that are not in this file are removed from the analysis as well as samples with missing values at any of the covariates included.
If --step 2
is specified, then the covariate file should be the same
as that used in Step 1.
Phenotype file format
FID IID Y1 Y2
1 1 1.64818554321186 2.2765234736685
2 2 -2.67352013711554 -1.53680421614647
3 3 0.217542851471485 0.437289912695016
.
Line 1 : Header with FID, IID and phenotypes names.
Followed by lines of values. Space/tab separated.
Each line contains individual FID and IID followed by P phenotype values
(for binary traits, must be coded as 0=control, 1=case, NA=missing unless using --1
).
Samples listed in this file that are not in bgen/bed/pgen file are ignored. Genotyped samples that are not in this file are removed from the analysis.
Missing values must be coded as NA.
With QTs, missing values are mean-imputed in Step 1 and they are dropped when testing each phenotype in Step 2 (unless using --force-impute
).
With BTs, missing values are mean-imputed in Step 1 when fitting the level 0 linear ridge regression and they are dropped when fitting the level 1 logistic ridge regression for each trait . In Step 2, missing values are dropped when testing each trait.
To remove all samples that have missing values at any of the phenotypes, use option --strict
in Step 1 and 2.
If using the transposed phenotype file format with option --tpheno-file
,
the header line must contain subject IDs as "FID_IID",
otherwise use option --iid-only
and only include IIDs (so will assume FID=IID).
Predictions file format
Running --step 1 --out foo
will produce
- A set of files containing genomic predictions for each phenotype from Step 1 (see Output section below).
- A file called
foo_pred.list
listing the locations of the prediction files.
The file list is needed as an input file when using --step 2
via the --pred
option.
It has one line per phenotype (in any order) that specifies the name of the phenotype and its
corresponding prediction file name.
Each phenotype must have exactly one prediction file and phenotype names
must match with those in the phenotype file.
Phenotypes in this file not included in the analysis are ignored.
Each prediction file contains the genetic predictions for the phenotype (space separated).
Line 1 starts with 'FID_IID' followed by $N$ sample identifiers. It is followed by 23 lines containing the genetic predictions for each chromosome (sex chromosomes are collapsed into chromosome 23).
More specifically, each line has $N+1$ values which are the chromosome number followed by the $N$ leave-one chromosome out (LOCO) predictions for each individual.
Samples in this file not in the bed/pgen/bgen input file are ignored. Genotyped samples not present in this file will be ignored in the analysis of the corresponding trait.
Samples with missing LOCO predictions must have their corresponding phenotype value set to missing.
Options
| Option | Argument | Type | Description |
|---|---|---|---|
--step |
INT | Required | specify step for the regenie run (see Overview) [argument can be 1 or 2 ] |
--qt |
FLAG | Optional | specify that traits are quantitative (this is the default so can be ommitted) |
--bt |
FLAG | Optional | specify that traits are binary with 0=control,1=case,NA=missing |
-1,--cc12 |
FLAG | Optional | specify to use 1/2/NA encoding for binary traits (1=control,2=case,NA=missing) |
--bsize |
INT | Required | size of the genotype blocks |
--cv |
INT | Optional | number of cross validation (CV) folds [default is 5] |
--loocv |
FLAG | Optional | flag to use leave-one out cross validation |
--lowmem |
FLAG | Optional | flag to reduce memory usage by writing level 0 predictions to disk (details below). This is very useful if the number of traits is large (e.g. greater than 10) |
--lowmem-prefix |
FILE PREFIX | Optional | prefix where to temporarily write the level 0 predictions |
--split-l0 |
PREFIX,N | Optional | split level 0 across N jobs and set prefix of output files of level 0 predictions |
--run-l0 |
FILE,K | Optional | run level 0 for job K in {1..N} specifying the master file created from '--split-l0' |
--run-l1 |
FILE | Optional | run level 1 specifying the master file from '--split-l0' |
--l1-phenoList |
STRING | Optional | to specify a subset of phenotypes to analyze when using --run-l1 |
--keep-l0 |
FLAG | Optional | avoid deleting the level 0 predictions written on disk after fitting the level 1 models |
--print-prs |
FLAG | Optional | flag to print whole genome predictions (i.e. PRS) without using LOCO scheme |
--force-step1 |
FLAG | Optional | flag to run step 1 when >1M variants are used (not recommened) |
--minCaseCount |
INT | Optional | flag to ignore BTs with low case counts [default is 10] |
--apply-rint |
FLAG | Optional | to apply Rank Inverse Normal Transformation (RINT) to quantitative phenotypes (use in both Step 1 & 2) |
--nb |
INT | Optional | number of blocks (determined from block size if not provided) |
--strict |
FLAG | Optional | flag to removing samples with missing data at any of the phenotypes |
--ignore-pred |
FLAG | Optional | skip reading the file specified by --pred (corresponds to simple linear/logistic regression) |
--use-relative-path |
FLAG | Optional | to use relative paths instead of absolute ones for the step 1 output pred.list file |
--use-prs |
FLAG | Optional | flag to use whole genome PRS in --pred (this is output in step 1 when using --print-prs ) |
--gz |
FLAG | Optional | flag to output files in compressed gzip format (LOCO prediction files in step 1 and association results files in step 2) [this only works when compiling with Boost Iostream library (see Install tab)]. |
--force-impute |
FLAG | Optional | flag to keep and impute missing observations for QTs in step 2 |
--write-samples |
FLAG | Optional | flag to write sample IDs for those kept in the analysis for each trait in step 2 |
--print-pheno |
FLAG | Optional | flag to write phenotype name in the first line of the sample ID files when using --write-samples |
--firth |
FLAG | Optional | specify to use Firth likelihood ratio test (LRT) as fallback for p-values less than threshold |
--approx |
FLAG | Optional | flag to use approximate Firth LRT for computational speedup (only works when option --firth is used) |
--firth-se |
FLAG | Optional | flag to compute SE based on effect size and LRT p-value when using Firth correction (instead of based on Hessian of unpenalized log-likelihood) |
--write-null-firth |
FLAG | Optional | to write the null estimates for approximate Firth [can be used in step 1 or 2] |
--compute-all |
FLAG | Optional | to write the null Firth estimates for all chromosomes (regardless of the genotype file) |
--use-null-firth |
FILE | Optional | to use stored null estimates for approximate Firth in step 2 |
--spa |
FLAG | Optional | specify to use Saddlepoint approximation as fallback for p-values less than threshold |
--pThresh |
FLOAT | Optional | P-value threshold below which to apply Firth/SPA correction [default is 0.05] |
--test |
STRING | Optional | specify to carry out dominant or recessive test [default is additive; argument can be dominant or recessive ] |
--chr |
INT | Optional | specify which chromosomes to test in step 2 (use for each chromosome to include) |
--chrList |
STRING | Optional | Comma separated list of chromosomes to test in step 2 |
--range |
STRING | Optional | specify chromosome region for variants to test in step 2 [format=CHR:MINPOS-MAXPOS] |
--minMAC |
FLOAT | Optional | flag to specify the minimum minor allele count (MAC) when testing variants [default is 5]. Variants with lower MAC are ignored. |
--minINFO |
FLOAT | Optional | flag to specify the minimum imputation info score (IMPUTE/MACH R^2) when testing variants. Variants with lower info score are ignored. |
--sex-specific |
STRING | Optional | to perform sex-specific analyses [either 'male'/'female'] |
--af-cc |
FLAG | Optional | to output A1FREQ in case/controls separately in the step 2 result file |
--no-split |
FLAG | Optional | flag to have summary statistics for all traits output in the same file |
--starting-block |
INT | Optional | to start step 2 at a specific block/set number (useful if program crashes during a job) |
--nauto |
INT | Optional | number of autosomal chromosomes (for non-human studies) [default is 22] |
--maxCatLevels |
INT | Optional | maximum number of levels for categorical covariates (for non-human studies) [default is 10] |
--niter |
INT | Optional | maximum number of iterations for logistic regression [default is 30] |
--maxstep-null |
INT | Optional | maximum step size for logistic model with Firth penalty under the null [default is 25] |
--maxiter-null |
INT | Optional | maximum number of iterations for logistic model with Firth penalty under the null [default is 1000] |
--par-region |
STRING | Optional | specify build code to determine bounds for PAR1/PAR2 regions (can be 'b36/b37/b38/hg18/hg19/hg38' or 'start,end' bp bounds of non-PAR region) [default is hg38] |
--force-qt |
FLAG | Optional | force QT run for binary traits |
--threads |
INT | Optional | number of computational threads to use [default=all-1] |
--debug |
FLAG | Optional | debug flag (for use by developers) |
--verbose |
FLAG | Optional | verbose screen output |
--version |
FLAG | Optional | print version number and exit |
--help |
FLAG | Optional | Prints usage and options list to screen |
When step 1 of regenie is run in low memory mode (i.e. using --lowmem
),
temporary files are created on disk (using --lowmem-prefix tmp_prefix
determines
where the files are written [as in tmp_prefix_l0_Y1
,...,tmp_prefix_l0_YP
for P phenotypes]). If the prefix is not specified, the default is to use the
prefix specified by --out
(see below).
These are automatically deleted at the end of the program (unless the run
was not successful in which case the user would need to delete the files)
See the Wiki page for more details on how to run the level 0 models for Step 1 of regenie in parallel.
Output
| Option | Argument | Type | Description |
|---|---|---|---|
--out |
FILE PREFIX | Required | Output files that depends on --step |
A log file file.log
of the output is generated.
Using --step 1 --out file
For the phenotypes, files file_1.loco
,...,file_P.loco
are output with the
per-chromosome LOCO predictions as rows of the files
(following the order of the phenotypes in the phenotype file header).
If option --gz
was used, the files will be compressed in gzip format and have extension .loco.gz
.
Genotyped individuals specified using option --remove
are excluded from this file.
Individuals with missing phenotype values kept in the analysis
are included in the file and have their predictions set to missing.
The list of blup files needed for step 2 (association testing) is written to file_pred.list
.
If using --print-prs
, files file_1.prs
,...,file_P.prs
will be written with the
whole genome predictions (i.e. PRS) without using LOCO scheme (similar format as the .loco files).
The list of these files is written to file_prs.list
and can be used in step 2 with --pred
and
specifying flag --use-prs
. Note that as these are not obtained using a LOCO scheme,
association tests could suffer from proximal contamination.
If using option --write-null-firth
, the estimates for approximate Firth under the null will be written to files
file_1.firth,...,file_P.firth
and the list of these files is written to file_firth.list
. This can be
used in step 2 as --use-null-firth file_firth.list
. Note that it assumes the same set of covariates are
used in Step 1 and 2.
Using--step 2 --out file
By default, results are written in separate files for
each phenotype
file_<phenotype1_name>.regenie,...,file_<phenotypeP_name>.regenie
.
Each file has one line per
SNP along with a header line.
If option --gz
was used, the files will be compressed in gzip format and have extension .regenie.gz
.
The entries of each row specify chromosome, position, ID, reference allele (allele 0), alternative allele (allele 1), frequency of the alternative allele, sample size and the test performed (additive/dominant/recessive). With BGEN/PGEN files with dosages, the imputation INFO score is provided (IMPUTE info score for BGEN and Mach Rsq for PGEN). Allele frequency, sample size and INFO score, if applicable, are computed using only non-missing samples for each phenotype.
These are followed by the estimated effect sizes (for allele 1 on the original scale), standard errors, chi-square test statistics and p-value. An additional column is included to specify if Firth/SPA corrections failed.
With option --no-split
, the summary statistics for all traits are written to a single file file.regenie
,
with the same format as above. Additionaly, an accompanying file with the trait names corresponding to Y1,Y2,...
will be generated in ‘file.regenie.Ydict’. Note that allele frequency, sample size and INFO score are computed using
all analyzed samples.
If option --write-samples
was used, IDs of samples used for each trait will be written in files
file_<phenotype1_name>.regenie.ids,...,file_<phenotypeP_name>.regenie.ids
(tab separated, no header).
When using --par-region
, the default boundaries used for the chrX PAR regions are:
- b36/hg18: 2709520 and 154584238
- b37/hg19: 2699520 and 154931044
- b38/hg38: 2781479 and 155701383
Gene-based testing
Starting from version 3.0, Step 2 of regenie provides a complimentary set of gene-based test in addition to the burden testing functionality introduced in version 2.0. More specifically, for a given set of variants (eg within a gene) which can be defined using functional annotations, regenie can apply various set-based tests on the variants as well as collapse them into a single combined 'mask' genotype that can be tested for association just like a single variant.
Input
| Option | Argument | Type | Description |
|---|---|---|---|
--anno-file |
FILE | Required | File with variant annotations for each set |
--set-list |
FILE | Required | File listing variant sets |
--extract-sets |
FILE | Optional | Inclusion file that lists IDs of variant sets to keep |
--exclude-sets |
FILE | Optional | Exclusion file that lists IDs of variant sets to remove |
--extract-setlist |
STRING | Optional | Comma-separated list of variant sets to keep |
--exclude-setlist |
STRING | Optional | Comma-separated list of variant sets to remove |
--aaf-file |
FILE | Optional | File with variant AAF to use when building masks (instead of AAF estimated from sample) |
--mask-def |
FILE | Required | File with mask definitions using the annotations defined in --anno-file |
Note: multiple files can be specified for --extract-sets/--exclude-sets
by using a comma-separated list.
Annotation input files
The following files are used to define variant sets and functional annotations which will be used to generate masks.
Annotation file
1:55039839:T:C PCSK9 LoF
1:55039842:G:A PCSK9 missense
.
This file defines functional annotations for variants. It is designed to accommodate for variants with separate annotations for different sets/genes.
Each line contains the variant name, the set/gene name and a single annotation category (space/tab separated).
Variants not in this file will be assigned to a default "NULL" category. A maximum of 63 annotation categories (+NULL category) is allowed.
For gene sets, tools you can use to obtain variant annotations per transcripts are snpEFF or VEP. To obtain a single annotation per gene, you could choose the most deleterious functional annotation across the gene transcripts or alternatively use the canonical transcript (note that its definition can vary across software).
We have implemented an extended 4-column format of the annotation file which also categorizes sets into domains (e.g. for gene sets, these would correspond to gene domains).
1:55039839:T:C PCSK9 Prodomain LoF
1:55039842:G:A PCSK9 Prodomain missense
.
Masks will be generated for each domain (maximum of 8 per set/gene) in addition to a mask combining across all domains. Variants can only be assigned to a single domain for each set/gene.
Set list file
This file lists variants within each set/gene to use when building masks. Each line contains the set/gene name followed by a chromosome and physical position for the set/gene, then by a comma-separated list of variants included in the set/gene.
A1BG 19 58346922 19:58346922:C:A,19:58346924:G:A,...
A1CF 10 50806630 10:50806630:A:G,10:50806630:A:AT,...
.
Set inclusion/exclusion file format
The file must have a single column of set/gene names corresponding to those in the set list file.
PIGP
ZBTB38
.
AAF file (optional)
Both functional annotations and alternative allele frequency (AAF) cutoffs are used when building masks (e.g. only considering LoF sites where AAF is below 1%). By default, the AAF for each variant is computed from the sample but alternatively, the user can specify variant AAFs using this file.
Each line contains the variant name followed by its AAF (it should correspond to ALT allele used in the genetic data input).
7:6187101:C:T 1.53918207864341e-05
7:6190395:C:A 2.19920388819247e-06
.
Since singleton variants cannot be identified from this file, they are determined by default
based on the input genetic data. To enforce which sites should be included in the singleton masks
(see --set-singletons
), you can add a third column in the file with a binary indicator
(1=singleton; 0=not singleton). So only variants which are specified as singletons will be
considered for the singleton masks, regardless of whether they are singletons in the input genetic data.
Note that with this flag, singleton sites will be included in all masks (regardless of the AAF in file).
7:6187101:C:T 1.53918207864341e-05 0
7:6190395:C:A 2.19920388819247e-06 1
.
Mask definitions
Mask file
This file specifies which annotation categories should be combined into masks. Each line contains a mask name followed by a comma-seperated list of categories included in the mask (i.e. union is taken over categories).
For example below, Mask1 uses only LoF variants and Mask2 uses LoF and missense annotated variants.
Mask1 LoF
Mask2 LoF,missense
.
AAF cutoffs
Option --aaf-bins
specifies the AAF upper bounds used to generate burden masks
(AAF and not MAF [minor allele frequency] is used when deciding which variants go into a mask).
By default, a mask based on singleton sites are always included.
For example, --aaf-bins 0.01,0.05
will generate 3 burden masks for AAFs in
[0,0.01], [0,0.05] and singletons.
SKAT/ACAT tests
The option --vc-tests
is used to specify the gene-based tests to run.
By default, these tests use all variants in each mask category.
If you'd like to only include variants whose AAF is below a given threshold
,e.g. only including rare variants, you can use --vc-maxAAF
.
| Test | Name in regenie | Description |
|---|---|---|
| SKAT | skat | Variance component test |
| SKATO | skato | Omnibus test combining features of SKAT and Burden |
| SKATO-ACAT | skato-acat | Same as SKATO but using Cauchy combination method to maximize power across SKATO models |
| ACATV | acatv | Test using Cauchy combination method to combine single-variant p-values |
| ACATO | acato | Omnibus test combining features of ACATV, SKAT and Burden |
| ACATO-FULL | acato-full | Same as ACATO but using the larger set of SKATO models used in the SKATO test |
For example, --vc-tests skato,acato-full
will run SKATO and ACATO
(both using the default grid of 8 rho
values for the SKATO models) and
the p-values for SKAT, SKATO, ACATV and ACATO will be output.
Ultra-rare variants (defined by default as MAC$\le$10, see --vc-MACthr
) are collapsed into
a burden mask which is then included in the tests instead of the individual variants.
For additional details on the tests, see here.
Joint test for burden masks
The following tests can be used to combine different burden masks generated using different annotation classes as well as AAF thresholds.
| Test | Name in regenie | QT | BT | Robust to LD | Assumes same effect direction |
|---|---|---|---|---|---|
| Minimum P-value | minp | $\checkmark$ | $\checkmark$ | $\times$ | $\times$ |
| ACAT | acat | $\checkmark$ | $\checkmark$ | $\checkmark$ | $\times$ |
| SBAT | sbat | $\checkmark$ | $\times$ | $\checkmark$ | $\checkmark$ |
The ACAT test combines the p-values of the individual burden masks using the Cauchy combination method (see ref. 14 here). The SBAT test is described into more detail here.
If you only want to output the results for the joint tests (ignore the marginal tests), use --joint-only
.
LOVO/LODO schemes
The leave-one-variant-out (LOVO) scheme takes all sites going into a mask, and builds LOVO masks by leaving out one variant at a time from the full set of sites. The mask including all sites will also be computed.
The argument for --mask-lovo
is a comma-separated list which
consists of
the set/gene name,
the mask name,
and the AAF cutoff (either 'singleton' or a double in (0,1)).
If using a 4-column annotation file, then --mask-lovo
should have
the gene name,
the domain name,
the mask name,
and the AAF cutoff.
So the LOVO masks will be generated for a specific gene domain.
The leave-one-domain-out (LODO) scheme (specified by --mask-lodo
)
takes all sites going into a mask and builds a LODO mask for each domain specified for the gene
by excluding all variants in the domain.
The full mask including all sites will also be computed.
The argument for --mask-lodo
should have the gene name, the mask name and the AAF cutoff.
Writing mask files
Burden masks built in regenie can be written to PLINK bed format. If the input genetic data contains dosages, the masks dosages will be converted to hard-calls prior to being written to file and these hard-calls will be used for the association testing.
The PLINK bed file is written using 'ref-last' encoding (i.e. REF allele is listed last in the bim file).
Note that this cannot be used with the LOVO/LODO schemes.
Options
| Option | Argument | Type | Description |
|---|---|---|---|
--aaf-bins |
FLOAT,...,FLOAT | Optional | comma-separated list of AAF upper bounds to use when building masks [default is a single cutoff of 1%] |
--build-mask |
STRING | Optional | build masks using the maximum number of ALT alleles across sites ('max' ; the default), or the sum of ALT alleles ('sum' ), or thresholding the sum to 2 ('comphet' ) |
--singleton-carrier |
FLAG | Optional | to define singletons as variants with a single carrier in the sample (rather than alternative allele count=1) |
--set-singletons |
FLAG | Optional | to use 3rd column in AAF file to specify variants included in singleton masks |
--write-mask |
FLAG | Optional | write mask to PLINK bed format (does not work when building masks with 'sum') |
--vc-tests |
STRING | Optional | comma-separated list of SKAT/ACAT-type tests to run |
--vc-maxAAF |
FLOAT | Optional | AAF upper bound to use for SKAT/ACAT-type tests [default is 100%] |
--skat-params |
FLOAT,FLAT | Optional | a1,a2 values for the single variant weights computed from Beta(MAF,a1,a2) used in SKAT/ACAT-type tests [default is (1,25)] |
--skato-rho |
FLOAT,...,FLOAT | Optional | comma-separated list of $\rho$ values used for SKATO models |
--vc-MACthr |
FLOAT | Optional | MAC threshold below which to collapse variants in SKAT/ACAT-type tests [default is 10] |
--joint |
STRING | Optional | comma-separated list of joint tests to apply on the generated burden masks |
--skip-test |
FLAG | Optional | to skip computing association tests after building masks and writing them to file |
--mask-lovo |
STRING | Optional | to perform LOVO scheme |
--lovo-snplist |
FILE | Optional | File with list of variants for which to compute LOVO masks |
--mask-lodo |
FLAG | Optional | to perform LODO scheme |
--write-mask-snplist |
FLAG | Optional | to write list of variants that went into each mask to file |
--check-burden-files |
FLAG | Optional | to check the concordance between annotation, set list and mask files [see below] |
--strict-check-burden |
FLAG | Optional | to exit early if the annotation, set list and mask definition files dont agree [see below] |
Three rules can be used to build masks with --build-mask
as shown in diagram below,
where the last rule comphet
applies a threshold of 2 to the mask from the sum
rule.
Output
With --out file
Results are written in separate files for each phenotype
file_<phenotype1_name>.regenie,...,file_<phenotypeP_name>.regenie
with the same output format mentioned above.
Additionally, a header line is included (starting with ##
)
which contains mask definition information.
Masks will have name <set_name>.<mask_name>.<AAF_cutoff>
with the
chromosome and physical position having been defined in the set list file,
and the reference allele being ref
, and the alternate allele corresponding to
<mask_name>.<AAF_cutoff>
.
When using --mask-lovo
, the mask name will be the same as above but have suffix
_<variant_name>
to specify the variant which was excluded when building the mask.
With --build-mask sum
, the reported mask AAF corresponds to the average
AAF across sites included in the mask.
If using --write-mask
, the masks will be saved to
file_masks.{bed,bim,fam}
and if using --write-mask-snplist
,
the list of variants included in each mask will be saved to file_masks.snplist
.
Example run
Using Step 1 results from the Step 1 command above, we use the following command to build and test masks in Step 2
./regenie \
--step 2 \
--bed example/example_3chr \
--covarFile example/covariates.txt \
--phenoFile example/phenotype_bin.txt \
--bt \
--remove example/fid_iid_to_remove.txt \
--firth --approx \
--pred fit_bin_out_pred.list \
--anno-file example/example_3chr.annotations \
--set-list example/example_3chr.setlist \
--mask-def example/example_3chr.masks \
--aaf-bins 0.1,0.05 \
--write-mask \
--bsize 200 \
--out test_bin_out_firth
For each set, this will produce masks using 3 AAF cutoffs (singletons, 5% and 10% AAF).
The masks are written to PLINK bed file (in test_bin_out_firth_masks.{bed,bim,fam}
)
and tested for association with each binary trait using Firth approximate test
(summary stats in test_bin_out_firth_<phenotype_name>.regenie
).
Note that the test uses the whole genome regression LOCO PRS from Step 1 of regenie (specified by --pred
).
Checking input files
To assess the concordance between the input files for building masks, you can use --check-burden-files
which will generate a report in file_masks_report.txt
containing:
-
for each set, the list the variants in the set-list file which are unrecognized (not genotyped or not present in annotation file for the set)
-
for each mask, the list of annotations in the mask definition file which are not in the annotation file
Additionally, you can use --strict-check-burden
to
enforce full agreement between the three files
(if not, program will terminate) :
-
all genotyped variants in the set list file must be in the annotation file (for the corresponding set)
-
all annotations in the mask definition file must be present in the annotation file
Interaction testing
Starting from regenie v3.0, you can perform scans for interactions (either GxE or GxG).
For GxE tests, the interacting variable should be part of the covariate file
(if it is categorical, specify it in --catCovarList
).
For GxG tests, the interacting variant can be part of the input genetic file
or it can be present in an external file (see --interaction-snp-file
)
Options
| Option | Argument | Type | Description |
|---|---|---|---|
--interaction |
STRING | Optional | to run GxE test specifying the interacting covariate (see below) |
--interaction-snp |
STRING | Optional | to run GxG test specifying the interacting variant (see below) |
--interaction-file |
FORMAT,FILE | Optional | external genotype file containing the interacting variant [FORMAT can be bed/bgen/pgen and FILE is the file name (bgen) or file prefix (bed/pgen)] |
--interaction-file-sample |
FILE | Optional | accompagnying sample file for BGEN format |
--interaction-file-reffirst |
FLAG | Optional | use the first allele as the reference for BGEN or PLINK BED formats |
--no-condtl |
FLAG | Optional | to print out all the main effects from the interaction model (see Output section below) |
--force-condtl |
FLAG | Optional | to include the interacting SNP as a covariate in the marginal test (see Output section below) |
--rare-mac |
FLOAT | Optional | minor allele count (MAC) threshold below which to use HLM method for QTs [default is 1000] |
For GxE tests where the interacting variable is categorical, you can specify the baseline level using --interaction VARNAME[BASE_LEVEL]
(e.g. --interaction BMI[<25]
). Otherwise, the first value found in the covariate file will be used as the baseline level.
For GxG tests, the default coding for the interacting variant is additive. If you would like to use dominant/recessive/categorical coding, use --interaction-snp SNP_NAME[dom/rec/cat]
(for example with dominant coding, --interaction-snp SNPNAME[dom]
will allow for separate effects between carriers vs non-carriers of the interacting variant). The allowed values in the brackets are add/dom/rec/cat
.
Output
The result files will contain multiple lines for the same variant corresponding to the different null hypotheses being tested in the interaction model
The suffix in the "TEST" column indicates which hypothesis is being tested:
- "ADD": marginal test where the interacting variable has not been added as a covariate $-$ this corresponds to $H_0: \beta = 0$ given $\alpha=\gamma = 0$
- this is only printed for GxG tests by default, or GxE using
--no-condtl
- this is only printed for GxG tests by default, or GxE using
- "ADD-CONDTL": marginal test where the interacting variable has been added as a covariate (default for GxE tests) $-$ this corresponds to $H_0: \beta = 0$ given $\gamma = 0$
- this is only printed for GxE tests by default, or GxG using
--force-condtl
- this is only printed for GxE tests by default, or GxG using
- "ADD-INT_VAR": test for the main effect of the interaction variable ("VAR" will be replaced by the name of the interacting variable) $-$ this corresponds to $H_0: \alpha = 0$
- this is only printed for GxG tests by default, or GxE using
--no-condtl
- If the interacting variable is categorical, you will have separate lines for each level aside from the baseline level (e.g. "ADD-INT_BMI=25-30" and "ADD-INT_BMI=30+" where baseline level is "$<$25")
- will also output the effect of $E^2$ in "ADD-INT_VAR^2" if the trait is binary (see here)
- this is only printed for GxG tests by default, or GxE using
- "ADD-INT_SNP": test for main effect of tested SNP in the interaction model $-$ this corresponds to $H_0: \beta = 0$
- "ADD-INT_SNPxVAR": test for interaction effect ("VAR" will be replaced by the name of the interacting variable) $-$ this corresponds to $H_0: \gamma = 0$
- If the interacting variable is categorical, you will have separate lines for each level aside from the baseline level (e.g. "ADD-INT_SNPxBMI=25-30" and "ADD-INT_SNPxBMI=30+" where baseline level is "$<$25")
- With Firth correction, only the effect sizes for the interaction effect at each level will be reported and the LRT p-value will only be computed for the joint test on the interaction effects
- If the interacting variable is categorical, you will have separate lines for each level aside from the baseline level (e.g. "ADD-INT_SNPxBMI=25-30" and "ADD-INT_SNPxBMI=30+" where baseline level is "$<$25")
- "ADD-INT_$k$DF": joint test for main and interaction effect of tested variant ($k\ge2$ for categorical interacting variables) $-$ this corresponds to $H_0: \beta = \gamma = 0$
Conditional analyses
Starting from regenie v3.0, you can specify genetic variants to add to the set of covariates when performing association testing. This works in both step 1 and 2, and can be used in conjunction with the gene-based tests or the interactiong testing feature. The conditioning variants will automatically be ignored from the analysis.
| Option | Argument | Type | Description |
|---|---|---|---|
--condition-list |
FILE | Required | file with list of variants to condition on |
--condition-file |
FORMAT,FILE | Optional | get conditioning variants from external file (same argument format as --interaction-file ) |
--condition-file-sample |
FILE | Optional | accompagnying sample file for BGEN format |
--max-condition-vars |
INT | Optional | maximum number of conditioning variants [default is 10,000] |


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Stops
You can set and query stops using the foreign conjunctions dbss (13!:3) and dbsq (13!:2), and using the utilities dbstop and dbstopme.
You can also set and view stops with Debug:
-
The stop name button in the Debug toolbar sets stops on all lines in the selected name.
-
The Debug Stop Manager lets you set stops on any active definition.
For names whose definition has more than one line, Debug distinguishes between stops set on specific lines (marked with *) and stops set on all lines (marked with |). For one-line definitions, only the "all lines" marker is used.
The namelist in the Stop Manager defaults to the selected definition (if any), and the names on the stack. Select the In Locale checkbox to view names by locale. Place the cursor on a name, and run the Stop Manager toolbar button to view that name.
Notes
Comment lines are ignored when setting stops.
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Consider a unit square surface, \(D\), surrounded by a closed loop \(C\).
The circulation \((\Gamma)\) of a vector field is defined as the line integral of the
vector field \((\vec{A})\) around a closed loop C, orientated here anti-clockwise.
In 2D, we let \(\vec{A}=(P,\,Q,\,0) =P(x,\,y)\mathbf{\hat{i}}+Q(x,\,y)\mathbf{\hat{j}}\) then:
$$
\Gamma = \oint_C \vec{A} \cdot \, d\vec{r} = \oint_C P(x,\,y(x))\,dx+Q(x(y),\,y)\,dy
$$ where \(d\vec{r}=dx\mathbf{\hat{i}} + dy\mathbf{\hat{j}}\).
N.B. When integrating \(P\) and \(Q\), remember to convert \(P\) as a function of \(x\) only
and \(Q\) as a function of \(y\) only.
Circulation is a measure of how much the vector
field is "spinning" overall, it is sometimes called the macroscopic circulation
.
Recall the definition of the curl of a vector field \(\vec{A}\) is:
$$ \text{curl}\,\vec{A} = \nabla \times \vec{A} $$
We can think of the curl as a measure of "spinning per unit area". If we only consider
vector fields in 2D (i.e. \(\vec{A} = (P,Q,0) \)) and we "add up" all of these little rotating regions
by integrating the curl flux through our surface (here in the \(x-y\) plane) like:
$$ \iint_D (\nabla \times \vec{A}) \cdot \mathbf{\hat{k}} \, dS = \iint_D \Big( \frac{\partial Q}{\partial x}
(x,\,y)-\frac{\partial P}{\partial y}(x,\,y) \Big) \, dxdy
$$ We can think of the curl flux integral as being all the infinitesimally small regions of rotations "added up".
This is sometimes called microscopic circulation.
N.B. The curl of a 2D vector field \(\vec{A}=(P,Q,0)\) has only one component in the \(\pm\mathbf{\hat{k}}\)
-direction. Try calculating it yourself.
Now, we make the link between these 2 integrals. Consider breaking down our region
\(D\) into an \(n\times n\) grid.
Inside each small box, we have tiny rotating regions of the curl of our vector field. However, if we
look inside our grid, every arrow has a corresponding opposite arrow.
These arrows, coloured green, "cancel"
out and the only ones left are the ones coloured
magenta. Increase \(n\) using the slider
and you will see this is always the case.
We notice that after all the green arrows "cancel", the magenta arrows make
up the same contour as in the line integral we saw earlier.
This is the link between macroscopic and microscopic circulation
which gives us Green's Theorem:
∳\(\!_C\)\(\,P(x,y(x))\,dx+Q(x,x(y))\,dy = \iint_D \frac{\partial Q}{\partial x}(x,\,y)-
\frac{\partial P}{\partial y}(x,\,y)\,dx\,dy\)
↺   on the integral means that both sides of Green's Theorem have to be orientated in a self-consistent manner following the right-hand rule. The orientation of \(C\) needs to be consistent with the orientation of \(d\vec{S}\,\!\). For the 2D case (Green's Theorem):


Tracking a Heisenleak in our kitchen--the leaks stops when we're watching for it, then makes a lake of the countertop when we're away.
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Tracking a Heisenleak in our kitchen--the leaks stops when we're watching for it, then makes a lake of the countertop when we're away.
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idiom is a coffee-script library with idiomatic implementations of commonly needed behavior.
idiom
It's BSD-licensed for open usage, well-documented, and thoroughly tested.
npm install idiom
require('idiom').export(global)
idiom
idiom
is a coffee-script library with idiomatic implementations of commonly needed behavior.It's BSD-licensed for open usage, well-documented, and thoroughly tested.
Installation
Recommended usage


blockquote + cite
element
The people recognize themselves in their commodities; they find their
soul in their automobile, hi-fi set, split-level home, kitchen equipment.
— Herbert Marcuse
Code

The people recognize themselves in their commodities; they find their soul in their automobile,
hi-fi set, split-level home, kitchen equipment.

— Herbert Marcuse
blockquote
element with cite
attribute
For 50 years, WWF has been protecting the future of nature. The world's leading conservation organization, WWF works in 100 countries and is supported
by 1.2 million members in the United States and close to 5 million globally.
code

For 50 years, WWF has been protecting the future of nature. The world's leading conservation organization, WWF works in 100 countries and is supported
by 1.2 million members in the United States and close to 5 million globally.

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HTML5 blockquote element
HTML5 cite element


Located on the northern shore of the Marmara Sea about 25nm west of Istanbul.
Position 40° 00' N, 28° 30.3' E.
The marina can arrange clearance both n and out.
Last updated February 2014.
There is no other docking except at the marina, which provides good shelter except in SE winds.
Last updated February 2014.