abra | Assembly Based ReAligner | Genomics library

 by   mozack Java Version: v0.97c License: MIT

kandi X-RAY | abra Summary

kandi X-RAY | abra Summary

abra is a Java library typically used in Artificial Intelligence, Genomics applications. abra has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However abra has 53 bugs. You can download it from GitHub.

ABRA is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular). Here is an ABRA realigned region (original reads on top, ABRA realigned reads on bottom). The original set of reads have rather "noisy" alignments with several variations from the reference and a fair bit of high quality soft clipping. The ABRA realignments present a more parsimonious representation of the reads including a previously unobserved large deletion.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              abra has a low active ecosystem.
              It has 62 star(s) with 11 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 16 open issues and 25 have been closed. On average issues are closed in 67 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of abra is v0.97c

            kandi-Quality Quality

              OutlinedDot
              abra has 53 bugs (17 blocker, 1 critical, 22 major, 13 minor) and 1003 code smells.

            kandi-Security Security

              abra has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              abra code analysis shows 0 unresolved vulnerabilities.
              There are 23 security hotspots that need review.

            kandi-License License

              abra 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

              abra releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              abra saves you 5038 person hours of effort in developing the same functionality from scratch.
              It has 10600 lines of code, 831 functions and 95 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed abra and discovered the below as its top functions. This is intended to give you an instant insight into abra implemented functionality, and help decide if they suit your requirements.
            • Gets the trio
            • Parses a Freebayes line
            • Parses a sequence line
            • Parse a Gocus genotype line
            • Main method for testing
            • Runs the diagnostic
            • Run a shell command
            • Runs a shell command
            • Main method for testing
            • Converts a SAM file into a single pair of regions
            • Main method to compare to two reads
            • Eval region
            • The main entry point
            • Returns the next record from the cache
            • Run the test
            • Main method to test
            • Process a Process
            • Validates the configuration
            • Gets the alternate reference
            • Run the regions with the specified region
            • Simple test to stdout
            • Command - line tool for testing
            • Main entry point
            • Utility method for debugging
            • Returns the option parser
            • Run the test
            Get all kandi verified functions for this library.

            abra Key Features

            No Key Features are available at this moment for abra.

            abra Examples and Code Snippets

            ABRA - Assembly Based ReAligner,Running
            Javadot img1Lines of Code : 1dot img1License : Permissive (MIT)
            copy iconCopy
            java -Xmx4G -jar $JAR --in input.bam --out output.bam --ref hg19.fasta --targets targets.bed --threads 8 --working abra_temp_dir > abra.log 2>&1
              
            Somatic mode
            Javadot img2Lines of Code : 1dot img2License : Permissive (MIT)
            copy iconCopy
            java -Xmx4G -jar $JAR --in normal.bam,tumor.bam --out normal.abra.bam,tumor.abra.bam --ref hg19.fasta --targets targets.bed --threads 8 --working abra_temp_dir --sv abra.sv.txt > abra.log 2>&1
              
            Speeding things up
            Javadot img3Lines of Code : 1dot img3License : Permissive (MIT)
            copy iconCopy
            java -Xmx4G -cp abra.jar abra.KmerSizeEvaluator      
              
            r brute force - force backward search .
            pythondot img4Lines of Code : 24dot img4no licencesLicense : No License
            copy iconCopy
            def brute_force_backward_search(pattern, txt):
                '''
                >>> test_data = 'ABACADABRAC'
                >>> pattern = 'ABRA'
                >>> brute_force_backward_search(pattern, test_data)
                6
                >>> pattern2 = 'ACNOTEXIST'
                &g  

            Community Discussions

            QUESTION

            Webscraping Data : Which Pokemon Can Learn Which Attacks?
            Asked 2022-Apr-04 at 22:59

            I am trying to create a table (150 rows, 165 columns) in which :

            • Each row is the name of a Pokemon (original Pokemon, 150)
            • Each column is the name of an "attack" that any of these Pokemon can learn (first generation)
            • Each element is either "1" or "0", indicating if that Pokemon can learn that "attack" (e.g. 1 = yes, 0 = no)

            I was able to manually create this table in R:

            Here are all the names:

            ...

            ANSWER

            Answered 2022-Apr-04 at 22:59

            Here is the a solution taking the list of url to webpages of interest, collecting the moves from each table and creating a dataframe with the "1s".
            Then combining the individual tables into the final answer

            Source https://stackoverflow.com/questions/71731208

            QUESTION

            Webscraping Pokemon Data
            Asked 2022-Apr-03 at 18:58

            I am trying to find out the number of moves each Pokemon (first generation) could learn.

            I found the following website that contains this information: https://pokemondb.net/pokedex/game/red-blue-yellow

            There are 151 Pokemon listed here - and for each of them, their move set is listed on a template page like this: https://pokemondb.net/pokedex/bulbasaur/moves/1

            Since I am using R, I tried to get the website addresses for each of these 150 Pokemon (https://docs.google.com/document/d/1fH_n_BPbIk1bZCrK1hLAJrYPH2d5RTy9IgdR5Ck_lNw/edit#):

            ...

            ANSWER

            Answered 2022-Apr-03 at 18:32

            You can scrape all the tables for each of the pokemen using something like this:

            Source https://stackoverflow.com/questions/71728273

            QUESTION

            Null output dealing with file IO in C#
            Asked 2022-Mar-27 at 18:43
                    private async void btnClickThis_Click(object sender, EventArgs e)
                {
                    //using example code from: https://docs.microsoft.com/en-us/dotnet/api/system.windows.forms.filedialog?view=windowsdesktop-6.0
                    //to open a file dialog box and allow selection
            
                    //variable declaration by section
                    //file processing
                    var fileContent = string.Empty;
                    var filePath = string.Empty;
                    //counting vowels and storing the word
                    int vowelMax = 0;
                    int vowelCount = 0;
                    String maxVowels = "";
                    //finding length and storing longest word
                    int length = 0;
                    int lengthMax = 0;
                    String maxLength = "";
                    //for storing first and last words alphabetically
                    String first = "";
                    String last = "";
            
                    using (OpenFileDialog openFileDialog = new OpenFileDialog())
                    {
                        openFileDialog.InitialDirectory = "c:\\";
                        openFileDialog.Filter = "txt files (*.txt)|*.txt|All files (*.*)|*.*";
                        openFileDialog.FilterIndex = 2;
                        openFileDialog.RestoreDirectory = true;
            
                        if (openFileDialog.ShowDialog() == DialogResult.OK)
                        {
                            //Get the path of specified file
                            filePath = openFileDialog.FileName;
            
                            //Read the contents of the file into a stream
                            var fileStream = openFileDialog.OpenFile();
                            using StreamWriter file = new("Stats.txt", append: true);
                            using (StreamReader reader = new StreamReader(fileStream))
                            {
            
                                do
                                {
                                    //try catch in case file is null to begin with
                                    try
                                    {
                                        //read one line at a time, converting it to lower case to start
                                        fileContent = reader?.ReadLine()?.ToLower();
                                        //split line into words, removing empty entries and separating by spaces
                                        var words = fileContent?.Split(' ', StringSplitOptions.RemoveEmptyEntries);
                                        if (words != null)
                                        {
                                            foreach (var word in words)
                                            {
                                                //if the string is null, immediately store word
                                                //if word < first, store word as first
                                                if (first == null || String.Compare(word, first) < 0)
                                                {
                                                    first = word;
                                                }
                                                //if the string is null, immediately store word
                                                //if word > last, store word as last
                                                else if (last == null || String.Compare(word, last) > 0)
                                                {
                                                    last = word;
                                                }
            
                                                //find length of current word
                                                length = word.Length;
                                                //if len is greater than current max len, store new max len word
                                                if (length > lengthMax)
                                                {
                                                    maxLength = word;
                                                }
                                                //iterate over each letter to check for vowels and total them up
                                                for (int i = 0; i < length; i++)
                                                {
                                                    if (word[i] == 'a' || word[i] == 'e' || word[i] == 'i' || word[i] == 'o' || word[i] == 'u')
                                                    {
                                                        vowelCount++;
                                                    }
                                                }
                                                //if vowelCount is greater than max, store word as new max
                                                if (vowelCount > vowelMax)
                                                {
                                                    maxVowels = word;
                                                }
                                                await file.WriteLineAsync(word);
                                            }
                                        }
                                    } catch (IOException error)
                                    {
                                        Console.WriteLine("IOException source: {0}", error.Source);
                                    }
                                } while (fileContent != "");
                                //append file stats after processing is complete
                                await file.WriteLineAsync("First word(Alphabetically): " + first);
                                await file.WriteLineAsync("Last word(Alphabetically): " + last);
                                await file.WriteLineAsync("Longest word: " + maxLength);
                                await file.WriteLineAsync("Word with the most vowels: " + maxVowels);
                            }
                        }
                    }
                    MessageBox.Show(fileContent, "File Content at path: " + filePath, MessageBoxButtons.OK);
                }
            
            ...

            ANSWER

            Answered 2022-Mar-27 at 18:43

            here you try to find first (min ) word.

            Source https://stackoverflow.com/questions/71638459

            QUESTION

            ContentPresenter's "Content" not centrally aligned vertically in UWP Controls
            Asked 2022-Mar-09 at 03:03

            I am using a ToggleSwitch control to display 2 exclusive options in the application. Unfortunately, when FontSize increases the "Content" part seems to be not centrally aligned vertically. To verify the issue I tried with a simple ContentPresenter even though I have provided VerticalAlignment, VerticalContentAlignment, etc.

            Not sure if it's an open issue or I am missing something here?

            White line shows the center of the image here. This is just one case but as font size differs the alignment also changes. Thus we cannot provide a padding/margin as it is different for various FontSizes.

            ...

            ANSWER

            Answered 2022-Mar-04 at 19:01

            Probably not the ideal answer; but you could always use the RenderTransform to adjust it to your liking.

            Source https://stackoverflow.com/questions/71352886

            QUESTION

            Background reveal javascript not working properly
            Asked 2022-Jan-31 at 22:41

            By following this tutorial :https://codepen.io/xaviDDB/pen/ExaKeeN I made a section in my website with this background reveal. here is the link:http://example.com/abra/ The code works fine if I do not have any other section in this page. But if I do, then it gets very strange. The reveal circle move away from the Mouse. See the page, I have added a horse image & the code gets messy. How do I solve this?

            This is my current code:

            ...

            ANSWER

            Answered 2022-Jan-31 at 21:59

            You need to add the height of the previous element of your div.container

            html

            Source https://stackoverflow.com/questions/70932997

            QUESTION

            My Python Selenium code doesn't work with options
            Asked 2021-Oct-25 at 16:12

            i'm using a selenium code in spyder 3.8 with anaconda. The issue is that it works perfectly when i don't add any option to the driver, it goes to the url and click the thins it has to, but for some reason when i add options it just opens the browser, but doesn't go to the url and can't continue with the code. This is weird because i tried running this code on 2 other pc's with spyder 3.7 and an older version and it runs perfectly with the options.

            I would really appreciate if someone could help me with this, thanks for your attention!

            ...

            ANSWER

            Answered 2021-Oct-25 at 16:12

            The problematic entry in your options is:

            Source https://stackoverflow.com/questions/69647801

            QUESTION

            Why is it not accepting data in a function
            Asked 2021-Sep-06 at 09:09

            I was making a security application when I got stuck at this. The application catches scammers by scanning their data and reports it to the nearest police station. Currently it is on the login page and almost done for the first part. But The issue is that it is not inputting the values into the sheet .On Individual run, It works fine but when I import qwerty and use it, it doesn't ake values. Please help here too

            ...

            ANSWER

            Answered 2021-Sep-05 at 06:56

            on line 5 qwerty() expecting a positional argument, pass an argument to it.

            Source https://stackoverflow.com/questions/69061043

            QUESTION

            Is there a way to correct content "expanding" behavior caused by fr sizing when zooming out in browser?
            Asked 2021-May-18 at 00:33

            I created the following form layout with CSS grids, and as the gif shows, zooming out in the browser causes the content seem to expand while shrinking, instead of just shrinking the content towards the center as a whole just like with zoomed out stackoverflow.

            I've tried to use pixels instead of fr to size my containers and it solves my issue, but using fr for sizing grid columns gives much more precision and convenience.

            Is there a solution for this or is it to just stop using fr for css grids?

            ...

            ANSWER

            Answered 2021-May-18 at 00:33

            Wrap the the form elements in an additional div use that as your grid container and set a max width to the form, centering the grid container.

            Source https://stackoverflow.com/questions/67578418

            QUESTION

            can JTextField resizable in a gridlayout?
            Asked 2021-May-09 at 15:25

            Below is my code for testing BorderLayout and GridLayout, but I found that the JTextField in the JPanel using GridLayout is not resizable, no matter how many time I change the JTextField.setPreferredSize, it still remain the same. Hope somebody can help me, hahahah, I got stuck in this for two days....TQ

            (I will upload the solution when I solve the problem)

            ...

            ANSWER

            Answered 2021-May-09 at 06:04

            Refer to How to Use GridLayout.
            Here is a quote from that Web page:

            A GridLayout object places components in a grid of cells. Each component takes all the available space within its cell, and each cell is exactly the same size.

            In other words, GridLayout does not consider the preferred size of the components it contains.

            A layout manager that does consider its contained components' preferred size is GridBagLayout.

            BorderLayout only respects part of its contained components' preferred size. For the EAST component, BorderLayout uses its preferred width but not its preferred height. BorderLayout will initially use its CENTER component's preferred width and height.

            This is the window I get when I run your code.

            Here is your modified code using GridBagLayout instead of GridLayout.

            Source https://stackoverflow.com/questions/67454452

            QUESTION

            How to ignore a color or alpha when using clusters
            Asked 2021-Mar-16 at 17:07

            I am trying to find the dominant color of an image using Pil and cluster. My problem is that my images has a transparent background because these are .png and so i always get black as the dominant color. I'd like to ignore the first dominant color and pick the second most dominant color.

            Is there a way to ignore alpha color or just remove it from the result? I am afraid that by just removing the first most dominant color, i would sometimes remove the actual dominant color in case of the background being a really small part of the image.

            Here is my code :

            ...

            ANSWER

            Answered 2021-Mar-16 at 17:07

            You could avoid passing transparent pixels into the classifier like this, if that's what you mean:

            Source https://stackoverflow.com/questions/66657077

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

            Vulnerabilities

            No vulnerabilities reported

            Install abra

            You can download it from GitHub.
            You can use abra like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the abra component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/mozack/abra.git

          • CLI

            gh repo clone mozack/abra

          • sshUrl

            git@github.com:mozack/abra.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link