STAR | Spliced Transcripts Alignment to a Reference © Alexander | Genomics library

 by   alexdobin C Version: STAR_2.7.10b_alpha_23-06-09 License: MIT

kandi X-RAY | STAR Summary

kandi X-RAY | STAR Summary

STAR is a C library typically used in Artificial Intelligence, Genomics applications. STAR has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

RNA-seq aligner

            kandi-support Support

              STAR has a medium active ecosystem.
              It has 1508 star(s) with 437 fork(s). There are 86 watchers for this library.
              There were 3 major release(s) in the last 12 months.
              There are 632 open issues and 1083 have been closed. On average issues are closed in 88 days. There are 6 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of STAR is STAR_2.7.10b_alpha_23-06-09

            kandi-Quality Quality

              STAR has 0 bugs and 0 code smells.

            kandi-Security Security

              STAR has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              STAR code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              STAR is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              STAR releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of STAR
            Get all kandi verified functions for this library.

            STAR Key Features

            No Key Features are available at this moment for STAR.

            STAR Examples and Code Snippets

            Perform a multi - star algorithm .
            pythondot img1Lines of Code : 74dot img1License : Permissive (MIT License)
            copy iconCopy
            def multi_a_star(start: TPos, goal: TPos, n_heuristic: int):
                g_function = {start: 0, goal: float("inf")}
                back_pointer = {start: -1, goal: -1}
                open_list = []
                visited = set()
                for i in range(n_heuristic):
            Add a star argument .
            pythondot img2Lines of Code : 8dot img2License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def add_stararg(self, a):
                            'tuple', ctx=gast.Load(), annotation=None, type_comment=None),
            Produces a star for the user .
            javascriptdot img3Lines of Code : 4dot img3no licencesLicense : No License
            copy iconCopy
            function starWarsFan() {
              const movie = 'Star Wars'; // {2}
              return movie;

            Community Discussions


            The unauthenticated git protocol on port 9418 is no longer supported
            Asked 2022-Mar-27 at 13:23

            I have been using github actions for quite sometime but today my deployments started failing. Below is the error from github action logs



            Answered 2022-Mar-16 at 07:01

            First, this error message is indeed expected on Jan. 11th, 2022.
            See "Improving Git protocol security on GitHub".

            January 11, 2022 Final brownout.

            This is the full brownout period where we’ll temporarily stop accepting the deprecated key and signature types, ciphers, and MACs, and the unencrypted Git protocol.
            This will help clients discover any lingering use of older keys or old URLs.

            Second, check your package.json dependencies for any git:// URL, as in this example, fixed in this PR.

            As noted by Jörg W Mittag:

            There was a 4-month warning.
            The entire Internet has been moving away from unauthenticated, unencrypted protocols for a decade, it's not like this is a huge surprise.

            Personally, I consider it less an "issue" and more "detecting unmaintained dependencies".

            Plus, this is still only the brownout period, so the protocol will only be disabled for a short period of time, allowing developers to discover the problem.

            The permanent shutdown is not until March 15th.

            For GitHub Actions:

            As in actions/checkout issue 14, you can add as a first step:



            Android Navigation Component : BottomNavigationView's selected tab icon is not updated
            Asked 2022-Mar-23 at 09:36

            I'm using BottomNavigationView with Navigation Component. When showing fragment is not root fragment, the tab icon is not updated (selected).

            When I switch between Tab Home with Fragment A (which is root fragment) and Tab Star with Fragment B (which is also root fragment) it is working fine.
            But when I navigate from Tab Home to another fragment, like fragment A2, and tap on Tab Star and again return to Tab Home, still Tab Star is selected in BottomNavigationView.

            It was working fine with version 2.4.0-alpha05, This is happening when I updated it to 2.5.0-alpha01.

            build.gradle (app)



            Answered 2022-Feb-12 at 06:00

            Given your navigation graph, there is no way to associate fragmentA2 with your menu item fragmentA, so fragmentA is not selected when you return to fragmentA2. As per this issue:

            NavigationUI has always used the current destination and what graph it is part of as the source of truth for what tab should be selected.

            This can be seen by calling navigate() to go to your SecondFragment - even though you haven't used the bottom nav button, the selected tab was changed because the current destination has changed to

            So when you navigate() to via your button in HomeFragment, NavigationUI receives a callback that the current destination has changed to It looks at that NavDestination and notes that there's no menu item that matches It then looks at the destination's parent graph - your element. There's no menu item that matches that ID either, so NavigationUI can't associated that destination with any menu item and therefore simply does nothing. That is true on all versions of Navigation.

            So what is different when you tap on a bottom navigation item? Well, nothing different from a NavigationUI perspective in fact: the exact same code runs and the current destination and what graph it is part of is the source of truth for what tab should be selected. In the Navigation 2.3.5, there was no state saved for each tab, so it only 'worked' because selecting a tab forced the ID of the current destination to match the destination of the menu item you just tapped.

            So what you're seeing in your sample app is that there's no link between and any menu item, which means NavigationUI does nothing. If you want to link to your Home tab, then that's exactly what a nested navigation graph can be used for.

            I.e., your navigation graph should instead look like:



            Counting all combinations of values in multiple columns
            Asked 2022-Feb-21 at 15:40

            The following is an example of items rated by 1,2 or 3 stars. I am trying to count all combinations of item ratings (stars) per month.

            In the following example, item 10 was rated in month 1 and has two ratings equal 1, one rating equal 2 and one rating equal 3.



            Answered 2022-Feb-20 at 22:37


            Rasterize polygons based on maximum overlap (using R packages terra or stars)
            Asked 2022-Feb-13 at 07:20

            I have a question concerning rasterization of polygons by maximum overlap, i.e assign the value of the polygon that has the highst area overlap with the raster cell.

            The real world exercise is to rasterize polygons of soil-IDs in R, in order to produce relatively low resolution maps of soil properties as model inputs.

            The problem is that the rasterize() function of the terra package (and similar stars' st_rasterize()) assigns the cell value from the polygon that contains the cell midpoint. If a raster cell contains multiple polygons, I would rather like to select the value of the polygon (soil-ID), which has the highest aerea cover in a raster cell.

            Here is a small self-contained example that visualizes my problem, using terra.



            Answered 2022-Feb-10 at 14:38

            Please find one possible solution using terra and sf libraries.

            The idea is to convert the SpatRaster r into a SpatVector and then into an sf object in order to take advantage of the sf::st_join() function using the largest = TRUE argument. The rest of the code then consists of simply converting the sf object back into a SpatVector and then a SpatRaster using the terra::rasterize() function.

            So, please find below a reprex that details the procedure.


            • Code



            .NET 6 failing at Decompress large gzip text
            Asked 2022-Feb-01 at 10:43

            I have to decompress some gzip text in .NET 6 app, however, on a string that is 20,627 characters long, it only decompresses about 1/3 of it. The code I am using code works for this string in .NET 5 or .NETCore 3.1 As well as smaller compressed strings.



            Answered 2022-Feb-01 at 10:43

            Just confirmed that the article linked in the comments below the question contains a valid clue on the issue.

            Corrected code would be:



            Determine if a polygon is star-shaped
            Asked 2022-Jan-26 at 09:34

            I need some hints on this one:

            A polygon P is star-shaped if there exists a point p in the interior of P such that any other point (vertex) on the boundary is visible to p.

            Given a polygon P, how can i determine if P is a star shaped polygon?

            Time complexity should be o(n) on average.

            Ive been sitting on this for a while now, Any help will be appericiated.



            Answered 2022-Jan-26 at 09:34

            very weird definition of star according to that circle and pie are also stars ...

            First simple and O(n) possibility I can think of is to render visibility map:

            1. compute BBOX of the shape

            2. create 2D map of the BBOX and clear it with zero

              so map 2D array (texture) to the BBOX of some resolution xs*ys

            3. for each convex vertex increment visibility map

              simply by rendering "infinite" triangle/quad onto the map

              You can use winding rule to chose if vertex is convex or concave by simply checking the sign of z coordinate of the adjacent edges cross product against the winding rule of your shape.

            4. scan the 2D map for cells containing number of convex vertexes

              all the cells/pixels containing number of convex vertexes are your possible Z so if any found your shape is a "star".

            This is O(n*xs*ys) where n is number of (convex) vertexes and xs*ys is resolution of the visibility map. Note if your resolution is too low due to inaccuracies you might produce false negatives/positives ... if (max) resolution of the map is constant then the complexity will turn to O(n).

            The rendering can be done simply for example with OpenGL and STENCIL buffer which directly has operation to increment STENCIL pixel however that one will limit the n to 255 as STENCIL is only 8 bit these days (after changes in OpenGL)... However you can workaround this by seting the BBOX to 1 and clear the exterior of the triangle/quad instead of incrementing its interrior. then the pixels holding 1 are your Z this might be used with any rendering engine no need for STENCIL



            Static initialization block differences between Java 13 and Java 8; with different IDE versions (netbeans 8.2 vs outdated apache netbeans 12)
            Asked 2022-Jan-25 at 14:50

            The only discernable difference between these two programs is the Java version.

            The question is: what on earth is going on?

            This image is proof that both programs contain exactly the same code, while producing different results.

            here is the code:



            Answered 2022-Jan-25 at 14:49

            ANSWER: Underlying problem determined to exist in IDE's compilation/build/execution routine.

            Reinstall and update IDE, adoption of non-EOL JDK.

            Also, I did not import existing IDE settings.



            printf() and fork() produce less output than expected
            Asked 2022-Jan-13 at 09:45

            I'm learning about forking processes and memory management and I have come across this piece of code:



            Answered 2022-Jan-13 at 09:36

            When running this code from a terminal you will notice that your missing * on some runs is not missing at all but printed after your program is finished.

            For better understanding you might print the PID's instead of stars and an additional line when the process is about to finish:



            Can not use theme color with text or bg
            Asked 2022-Jan-05 at 14:58

            I overwrite bootstrap's theme-colors in my scss file, as following



            Answered 2022-Jan-05 at 14:58

            I recently answered a similar question, but there does seem to be a new issue introduced in 5.1.0 because of this change mentioned on the Bootstrap blog...

            "Updated .bg- and .text- utilities Our new RGB values are built to help us make better use of CSS variables across the entire project. To start, our background-color and color utilities have been updated to use these new RGB values for real-time customization without recompiling Sass and on-the-fly transparency for any background or text color."

            Currently in 5.1.0 you'd need to rebuild all the bg-* and text-* classes like this...



            How to draw circles around polygon/spider chart, without plotting libraries
            Asked 2021-Dec-17 at 07:04

            Without using ggplot2 or other plotting libraries, I would need to draw circles around a polygon/star chart vertices, i.e. each circle with a radius equal to the respective polygon radius. You can see an example here:



            Answered 2021-Dec-16 at 21:12

            I don't know of any functions in base R that do circles for you, but you can concoct them manually.


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

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            You can download it from GitHub.


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