opal | SIMD C/C library for massive optimal sequence alignment | Genomics library

 by   Martinsos C++ Version: Current License: MIT

kandi X-RAY | opal Summary

kandi X-RAY | opal Summary

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

Opal (ex Swimd) is SIMD C/C++ library for massive optimal sequence alignment. Opal is implemented mainly by Rognes's "Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation". Main difference is that Opal offers support for AVX2 and 4 alignment modes instead of just Smith-Waterman. SSE4.1 or higher. If AVX2 is available, Opal will consume two times more sequences and will therefore work two times faster. By compiling code with makefile and running ./test, you can see if you have SSE4.1 or AVX2 and also see if everything is working.
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              opal has a low active ecosystem.
              It has 20 star(s) with 8 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 18 open issues and 11 have been closed. On average issues are closed in 74 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of opal is current.

            kandi-Quality Quality

              opal has no bugs reported.

            kandi-Security Security

              opal has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              opal 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

              opal releases are not available. You will need to build from source code and install.
              Installation instructions are not available. Examples and code snippets are available.

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            opal Key Features

            No Key Features are available at this moment for opal.

            opal Examples and Code Snippets

            No Code Snippets are available at this moment for opal.

            Community Discussions

            QUESTION

            Why can't we replace the def of "many" with the code using <~> in Opal?
            Asked 2021-May-31 at 10:24

            I have an question about https://github.com/pyrocat101/opal/blob/master/opal.ml.

            At line 105, I replaced the definition of many with let rec many x = option [] (x <~> many x);;. Then, I got the following error message:

            Stack overflow during evaluation (looping recursion?).

            However, these two codes seem to be same. Why?

            I used OCaml version 4.12.0.

            ...

            ANSWER

            Answered 2021-May-31 at 10:24

            OCaml is an eager language. Thus in

            Source https://stackoverflow.com/questions/67765723

            QUESTION

            Sorting a 2D string array in c
            Asked 2021-May-28 at 04:45

            I am trying to sort this file that has this information below

            ...

            ANSWER

            Answered 2021-May-28 at 04:45

            Below part is problematic in some ways:

            Source https://stackoverflow.com/questions/67732772

            QUESTION

            MPI_alltoallw working and MPI_Ialltoallw failing
            Asked 2021-Apr-21 at 07:07

            I am trying to implement non-blocking communications in a large code. However, the code tends to fail for such cases. I have reproduced the error below. When running on one CPU, the code below works when switch is set to false but fails when switch is set to true.

            ...

            ANSWER

            Answered 2021-Apr-21 at 07:07

            The proposed program is currently broken when using Open MPI, see issue https://github.com/open-mpi/ompi/issues/8763. The current workaround is to use MPICH.

            Source https://stackoverflow.com/questions/66932156

            QUESTION

            Why is my for loop not pulling the correct data from my array of objects?
            Asked 2020-Dec-14 at 22:10

            I have successfully got my jQuery to load individual data from my array of objects but when I tried to add a jQuery click event to enable a toggle feature (that loads the image of the div into a bigger 'fullscreen' view) it only loads the very last array item's data.

            Sample of my array of objects I'm calling allPictures:

            ...

            ANSWER

            Answered 2020-Dec-14 at 07:52

            Try this one...I just your code copy and modify code..

            Source https://stackoverflow.com/questions/65284783

            QUESTION

            tidy select syntax for multiple variable
            Asked 2020-Dec-09 at 03:47

            I have been unable to find a good example of how to use across/c_across with tidy select syntax to select variables that contain multiple strings. I find str_detect works well, but it doesnt seem to work inside dplyr verbs? The first line of summarise works in the code, but am looking for correct syntax to find variables containing both substrings in second and third line:

            ...

            ANSWER

            Answered 2020-Dec-09 at 00:15

            You can use the matches tidyselect function. matches applies any arbitrary regular expression to select columns.

            Source https://stackoverflow.com/questions/65208818

            QUESTION

            Appending a key:value from one dictionary to another
            Asked 2020-Nov-21 at 06:55

            So i want to be able to make a multiple choice quiz program using dictionaries. I have one dictionary with all the questions as the key and the answer as a value and a second dictionary thats empty. I want to append all of the incorrect questions someone may have into the empty dictionary. i want to do this in order to allow users to retake the exam but only with the questions that they answered wrong. Yet i cannot find a way to append a key and value from one list to another without being specific.

            Here is my code below:

            ...

            ANSWER

            Answered 2020-Nov-21 at 06:55

            Interesting problem to solve. Look at this code and see if it provides you the repeatable process to keep continuing with your quiz. The only area that I have a bit of a problem is your big if statements that check for scores and print varying responses. When the user has fewer questions, I had to add the older answered questions to the tally to stay in the same range. Otherwise, this should work.

            Things I changed.

            #1: Questions is a list of tuples. Each tuple is a question and answer (q1,'c') as example.

            #2: Since we need to repeat the questions, I am iterating through incorrect question list each time. To start off, I set all questions as incorrect. So the incorrect questions list has values 0 thru 14.

            #3: Every time the user answers correctly, I am removing the question from the incorrect question list.

            #4: Since I am manipulating the list itself by removing the correctly answered question, I cannot use a for loop. Instead I am using a while loop and ensuring I am going through the list only till the max of list

            #5: I am looping the Quiz function until the user decides to stop playing. To start with, I am setting the flag as yes and checking for it before I call Quiz function. I am returning the user's decision back as a return statement. That is helping the loop to keep going.

            #6: Finally, I moved all the questions outside and made Questions a global variable. Since we are going to call Quiz a few times, I didn't want Questions to be defined every time. If you want to keep it inside, its your choice. It does not impact the overall solution. However, you need to make it a list of tuples. Additionally, inc_questions has to be global so you can manipulate it as many times as you need.

            Below is the code. Let me know if you find any errors.

            Source https://stackoverflow.com/questions/64938506

            QUESTION

            Mutate to remove all parenthesis (and contents) from string in R
            Asked 2020-Nov-12 at 10:09

            I'm trying to use mutate/str_replace to generate "Phenotype' from "Class" by removing parenthesis (including contents) but need some help with the Regex? I would also like to then reorder the text within "Phenotype" strings such that text is shown in order PanCK>PD-L1>CD8>FoxP3>PD-1>CD68. Apologies for the non-standard dataset! Many thanks!

            ...

            ANSWER

            Answered 2020-Nov-12 at 05:36

            QUESTION

            Dropdown value change style of pages dynamically
            Asked 2020-Oct-23 at 11:39

            I am building a muti-page website with Kendo UI for Jquery. I have a dropdown to select the style the user want. For now I can change the style, but it doesn't stick; as soon as I refresh the page it goes back to the default style. I want the style to also change for all the other pages.

            Here is my code:
            HTML

            ...

            ANSWER

            Answered 2020-Oct-23 at 11:39

            Set the session storage value inside the changeTheme function with the chosen theme name:

            Source https://stackoverflow.com/questions/64495300

            QUESTION

            Anchor image from top in CSS when resizing window
            Asked 2020-Aug-28 at 20:20

            Is there a way to anchor an image from the top when you resize a window?

            Take a look at this Imgur post. When I resize the window, it anchors from the center, which zooms in the image to the center. That is cool, but the end goal here is to have it zoom in from the top. I want to be able to see the "Luna Li" and "Opal Angel" text even if the screen is wide.

            I want the end goal to look like this screenshot, where you can still see the text even if the window isn't a square (this concept was made by changing top: 30%;, but this causes the issue of making the background look like this in a small window).

            ...

            ANSWER

            Answered 2020-Aug-28 at 20:20

            I believe what you are looking for is object-position:

            Source https://stackoverflow.com/questions/63640353

            QUESTION

            UDP bytes received with hex and ascii mixed; How to decode?
            Asked 2020-Jun-13 at 22:05

            I am running a UDP client in a real-time simulation (OPAL RT), it is basically sending two doubles (1 and 1) and I am receiving the values with some timestamps and header information (I guess). In total 24 bytes, 8 bytes for header info, 8 bytes for the double data. When I run the following code in Python 3 using UDP socket:

            '''

            ...

            ANSWER

            Answered 2020-Jun-13 at 22:03

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

            Vulnerabilities

            No vulnerabilities reported

            Install opal

            You can download it from GitHub.

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            gh repo clone Martinsos/opal

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