AGE | optimal alignment of sequences with structural variants
kandi X-RAY | AGE Summary
kandi X-RAY | AGE Summary
README file for AGE software distribution. ABOUT Software AGE implements optimal algorithms for aligning genomic sequences with structural variations (SVs). Precise alignment allows for correct breakpoint determination. The algorithms are described in the publication Bioinformatics. 2011 Mar 1;27(5):595-603. Epub 2011 Jan 13. Additional info on importance of breakpoints can be obtained from * Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27. * Nature. 2011 Feb 3;470(7332):59-65. The software runs on linux based systems.
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Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of AGE
AGE Key Features
AGE Examples and Code Snippets
Lines of Code : 9License : Permissive (MIT License)
Copypublic static List search(List people, String name, Integer age) {
// Null checks for people and name
final Integer ageFilter = age != null ? age : 0;
return people.stream()
.filter(p -> p.getName().equals( public static int compareByNameThenAge(final Human lhs, final Human rhs) {
if (lhs.name.equals(rhs.name)) {
return Integer.compare(lhs.age, rhs.age);
} else {
return lhs.name.compareTo(rhs.name);
}
Integer yearsToRetirement() {
Person p = null;
// ... p never gets set correctly...
return 65 - getAge(p);
} Community Discussions
Trending Discussions on AGE
QUESTION
Today i have got this email:
Last July, we announced Advertising policy changes to help bolster security and privacy. We added new restrictions on identifiers used by apps that target children. When users choose to delete their advertising ID in order to opt out of personalization advertising, developers will receive a string of zeros instead of the identifier if they attempt to access the identifier. This behavior will extend to phones, tablets, and Android TV starting April 1, 2022. We also announced that you need to declare an AD_ID permission when you update your app targeting API level to 31 (Android 12). Today, we are sharing that we will give developers more time to ease the transition. We will require this permission declaration when your apps are able to target Android 13 instead of starting with Android 12.
Action Items If you use an advertising ID, you must declare the AD_ID Permission when your app targets Android 13 or above. Apps that don’t declare the permission will get a string of zeros. Note: You’ll be able to target Android 13 later this year. If your app uses an SDK that has declared the Ad ID permission, it will acquire the permission declaration through manifest merge. If your app’s target audience includes children, you must not transmit Android Advertising ID (AAID) from children or users of unknown age.
My app is not using the Advertising ID. Should i declare the AD_ID Permission in Manifest or not?
ANSWER
Answered 2022-Mar-14 at 20:51Google describe here how to solve
https://support.google.com/googleplay/android-developer/answer/6048248?hl=en
Add in manifest
QUESTION
I am wondering how to solve this problem with basic Python (no libraries to be used): How to calculate when one's 10000 day after their birthday will be (/would be). For instance, given Monday 19/05/2008 the desired day is Friday 05/10/2035 (according to https://www.durrans.com/projects/calc/10000/index.html?dob=19%2F5%2F2008&e=mc2)
What I have done so far is the following script:
...ANSWER
Answered 2022-Mar-06 at 18:02Using base python packages only
On the basis that "no special packages" means you can only use base python packages, you can use datetime.timedelta for this type of problem:
QUESTION
[I ran into the issues that prompted this question and my previous question at the same time, but decided the two questions deserve to be separate.]
The docs describe using destructuring assignment with my and our variables, but don't mention whether it can be used with has variables. But Raku is consistent enough that I decided to try, and it appears to work:
ANSWER
Answered 2022-Feb-10 at 18:47This is currently a known bug in Rakudo. The intended behavior is for has to support list assignment, which would make syntax very much like that shown in the question work.
I am not sure if the supported syntax will be:
QUESTION
I am working with WSL a lot lately because I need some native UNIX tools (and emulators aren't good enough). I noticed that the speed difference when working with NPM/Yarn is incredible.
I conducted a simple test that confirmed my feelings. The test was running npx create-react-app my-test-app and the WSL result was Done in 287.56s. while GitBash finished with Done in 10.46s..
This is not the whole picture, because the perceived time was higher in both cases, but even based on that - there is a big issue somewhere. I just don't know where. The project I'm working on uses tens of libraries and changing even one of them takes minutes instead of seconds.
Is this something that I can fix? If so - where to look for clues?
Additional info:
my processor: Processor AMD Ryzen 7 5800H with Radeon Graphics, 3201 Mhz, 8 Core(s), 16 Logical Processors
I'm running Windows 11 with all the latest updates to both the system and the WSL. The chosen system is Ubuntu 20.04
I've seen some questions that are somewhat similar like 'npm install' extremely slow on Windows, but they don't touch WSL at all (and my pure Windows NPM works fast).
the issue is not limited to NPM, it's also for Yarn
another problem that I'm getting is that file watching is not happening (I need to restart the server with every change). In some applications I don't get any errors, sometimes I get the following:
...
ANSWER
Answered 2021-Aug-29 at 15:40Since you mention executing the same files (with proper performance) from within Git Bash, I'm going to make an assumption here. Correct me if I'm wrong on this, and I'll delete the answer and look for another possibility.
This would be explained (and expected) if your files are stored on /mnt/c (a.k.a. C:, or /C under Git Bash) or any other Windows drive, as they would likely need to be to be accessed by Git Bash.
WSL2 uses the 9P protocol to access Windows drives, and it is currently known to be very slow when compared to:
- Native NTFS (obviously)
- The ext4 filesystem on the virtual disk used by WSL2
- And even the performance of WSL1 with Windows drives
I've seen a git clone of a large repo (the WSL2 Linux kernel Github) take 8 minutes on WSL2 on a Windows drive, but only seconds on the root filesystem.
Two possibilities:
If possible (and it is for most Node projects), convert your WSL to version 1 with
wsl --set-version 1. I always recommend making a backup withwsl --exportfirst.And since you are making a backup anyway, you may as well just create a copy of the instance by
wsl --importing your backup as--version 1(as the last argument). WSL1 and WSL2 both have their uses, and you may find it helpful to keep both around.See this answer for more details on the exact syntax..
Or just move the project over to somewhere under the WSL root, such as
/home/username/src/.
QUESTION
In light of recent malware in existing npm packages, I would like to have a mechanism that lets me do some basic checks before installing new packages or updating existing ones. My main issue are both the packages I install directly, and also the ones I install indirectly.
In general I want to get a list of package-version that npm would install before installing it. More specifically I want the age of the packages that would be installed, so I can generate a warning if any of them is less than a day old.
If I could do that directly with npm, that would be neat, but I'm afraid I need to do some scripting around it.
specific use case:
If I executed npm install react-native-gesture-handler on 2021-10-22 it would have executed the post-install hook of a malicious version of ua-parser and my computer would have been compromised, which is something I would like to avoid.
When I enter npm install react-native-gesture-handler --dry-run, it only tells me which version of react-native-gesture-handler it would have installed, but it would not tell me that it would install a version of ua-parser that was released on that day.
additional notes:
- I know that
npm i --dry-runexists, but it shows only the direct packages. - I know that
npm listexists, but it only shows packages after installing (and thus after install-hooks have already done their harm) - both only show packages version and not their age
- I do not know how I would get a list of packages that would come with a install-hook before installing them
- pointers to alternative ways to deal with malicious npm packages are welcome.
- so far my best solution would be to do "--ignore-scripts" but that would come with it's own set of problems
ANSWER
Answered 2021-Dec-07 at 07:26To find out the malicious package, you will need a script that will check your package for vulnerabilities against national vulnerabilities database
The National Vulnerability Database includes databases of security checklist references, security related software flaws, misconfigurations, product names, and impact metrics.
Mostly all software companies use application security tools like Veracode, Snyk or Checkmarx that does this usually in a stage before deployment in the CICD pipeline.
If you're looking to achieve this locally, you can try
QUESTION
I found that TypeScript produces never type at different levels when impossible intersections happen
ANSWER
Answered 2022-Jan-03 at 02:37Before TypeScript 3.9, both intersections would behave like your first example and be equivalent to {name: string, age: never}. TypeScript 3.9 introduced functionality to reduce intersections by discriminant properties. Discriminant properties are, roughly, those whose values are of single literal types (like string literal types, numeric literal types, boolean literal types, null, and undefined) or unions of such types. These are used in discriminated unions. If an intersection type causes a discriminant property to reduce to never, the compiler will reduce the whole intersection to never. See microsoft/TypeScript#36696 for details and motivation.
Anyway, the type boolean is represented as the union true | false of boolean literals, and therefore the age property in your second example is considered to be a discriminant property. On the other hand, number is a non-literal type and so the age property in your first example is not considered to be a discriminant property. This accounts for the difference in behavior you are seeing.
QUESTION
I need to write an algorithm where the user selects an option to filter a particular data and on every click it makes an api request returning the filtered data. As many times the user clicks it needs to continue to filter out the data. My question is, how can the algorithm save the most recent result and run a for/filter loop on the most recent results? Should I store the most recent results in localStorage in order to further filter the results? And when the user decides to unselect the data that they wanted to filter, it should show the user their previous results. The user should be able to continue to filter until they get the desired data. Please see example below.
...ANSWER
Answered 2021-Dec-28 at 18:47You can iterate the array and check if each object satisfies the passed filters. This works with filters having multiple elements and each element having multiple properties.
QUESTION
I have created a React hook:
...ANSWER
Answered 2021-Dec-18 at 21:55I bet that this is the result You want to achieve
QUESTION
When extending a class, I can easily add some new properties to it.
But what if, when I extend a base class, I want to add new properties to an object (a property which is a simple object) of the base class?
Here is an example with some code.
base class
...ANSWER
Answered 2021-Dec-07 at 15:50If you're just going to reuse a property from a superclass but treat it as a narrower type, you should probably use the declare property modifier in the subclass instead of re-declaring the field:
QUESTION
I'm looking for a way to have all keys / values pair of a nested object.
(For the autocomplete of MongoDB dot notation key / value type)
...ANSWER
Answered 2021-Dec-02 at 09:30In order to achieve this goal we need to create permutation of all allowed paths. For example:
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