MBG | Minimizer based sparse de Bruijn Graph constructor | Genomics library

 by   maickrau C++ Version: version1.0.13 License: MIT

kandi X-RAY | MBG Summary

kandi X-RAY | MBG Summary

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

Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify and homopolymer decompress. Suggested input is PacBio HiFi/CCS reads. May or may not work with Illumina reads. Algorithmic details and citation: Bioconda: conda install -c bioconda mbg. eg MBG -i reads.fa -o graph.gfa -k 1501 -w 1450 -a 1 -u 3. Multiple read files can be inputted with "-i file1.fa -i file2.fa" etc. Input read type can be .fa / .fq / .fa.gz / .fq.gz. k and w can be arbitrarily large but at some point the error rate and limited read length will cause the graph to be fragmented. Runtime stays approximately the same if the ratio k/w is kept constant. All repeats shorter than k are separated, all repeats longer than k+w are collapsed, and repeats in between may be separated or collapsed depending on if a k-mer was selected from within the repeat. When using --blunt, you should clean the graph afterwards with vg. --blunt uses an extension of an algorithm invented by Hassan Nikaein (personal communication).
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            kandi-support Support

              MBG has a low active ecosystem.
              It has 44 star(s) with 0 fork(s). There are 4 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 3 open issues and 13 have been closed. On average issues are closed in 43 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of MBG is version1.0.13

            kandi-Quality Quality

              MBG has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              MBG 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

              MBG releases are available to install and integrate.

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            MBG Key Features

            No Key Features are available at this moment for MBG.

            MBG Examples and Code Snippets

            No Code Snippets are available at this moment for MBG.

            Community Discussions

            QUESTION

            JpaRepository.save() generates hql inserting null values into the tables
            Asked 2020-Sep-30 at 03:11

            In my Spring boot+ hibernates+mysql application I have my own UserRepository :

            ...

            ANSWER

            Answered 2020-Sep-30 at 03:11

            The (?, ?, ?, ...) is normal in hibernate logs, the actual parameter values are not logged, that doesn't mean that the inserted values are null.

            Note that the query is inserting the field "create_ime" and the error says the column that does not accept nulls is "create_time", so it seems you have both columns in the table, probably caused by a typo correction or rename.

            Source https://stackoverflow.com/questions/64130074

            QUESTION

            Is there a function in R that will let me create a new data frame that contains the duplicated values from the first data frame?
            Asked 2020-Apr-10 at 23:44

            This is my example. From this data frame I want to create a new data frame that contains the rows that based on matches in column, mgb and column, tsg thereby omitting the other rows.

            ...

            ANSWER

            Answered 2020-Apr-10 at 14:42

            If you would simply like to remove NA's and write to a new dataframe:

            Source https://stackoverflow.com/questions/61142406

            QUESTION

            How to set custom name, suffix for mapper files and interfaces in mybatis generator?
            Asked 2019-May-15 at 20:04

            Can you set custom suffix and naming rule mapper xml and interfaces in MyBatis Generator (MBG)?

            For example, When generating mapper files for class Book. MBG generates mapper file BookMapper.xml and interface PartnerDao.java. However, I wish to change the suffix to something else, like BookMapperBase.xml or BookDaoBase.xml, and PartnerMapperBase.java or PartnerDaoBase.java.

            The reason is, former colleagues were using BookMapper.xml for their hand-written sql statements and using the same name would cause confusion. Moreover, I do not wish to use generated mappers directly, but use custom mapper files that extend BookMapperBase.xml.

            I have searched online and found some github projects and hot rod ORM, but is it really not supported by official Mybatis Generator? If not, what is your recommended alternative?

            ...

            ANSWER

            Answered 2019-May-15 at 20:04

            There are a couple of options.

            1. You could use a domain object renaming rule as documented here: http://www.mybatis.org/generator/configreference/domainObjectRenamingRule.html

            2. If that doesn't work the way you want it to, you could write a MyBatis Generator plugin to change the names of the generated artifacts. There is an example here: https://github.com/mybatis/generator/blob/master/core/mybatis-generator-core/src/main/java/org/mybatis/generator/plugins/RenameExampleClassPlugin.java

            Source https://stackoverflow.com/questions/56150566

            QUESTION

            How to pass parameters to Google Maps initmap in XSLT?
            Asked 2018-Sep-26 at 21:19

            I'm trying to get the position by getting the latitude and longitude from an xml document, through an xslt stylesheet. I made xslt variables which return the correct latitude and longitude when I call them (for example with xsl:value-of). But I can't seem to access the same variables in the javascript snipet. From what I read it's possible to call an xslt variable inside javascript. So I don't know what I'm doing wrong.

            Here is my code:

            ...

            ANSWER

            Answered 2018-Sep-26 at 21:19

            I think you need to change your Javascript code to have a function you can call to create the appropriate map and marker, so outside of any grouping you put

            Source https://stackoverflow.com/questions/52521343

            QUESTION

            XSLT current-group select first and last element
            Asked 2018-Sep-23 at 19:01

            I have this xml:

            ...

            ANSWER

            Answered 2018-Sep-23 at 19:01

            Add the required braces to the second expression like below. In your sample code the first and the last values are output twice due to the xsl:for-each (don't know what it's good for).

            Source https://stackoverflow.com/questions/52468538

            QUESTION

            Conditional statement and inline styles - JQuery
            Asked 2018-Apr-20 at 08:01

            im trying to switch a background image out based upon the window size...

            https://codepen.io/anon/pen/qYdZox

            ...

            ANSWER

            Answered 2018-Apr-20 at 08:01

            You need to do something like this, where you use url(...) with the image source path

            Source https://stackoverflow.com/questions/49936760

            QUESTION

            How can I check if a particular class exists (html/css)?
            Asked 2018-Jan-25 at 20:00

            I use the following code which get applied on two different pages because both pages are using the same element:

            ...

            ANSWER

            Answered 2018-Jan-25 at 01:42

            I'm a little confused as to what your'e asking, but assuming you're asking how you can hide elements that have both the classes .SocialBar and .PersonalHome-interests, but show elements that only have the class .SocialBar, all you need to do is combine the class selectors into one as .SocialBar.PersonalHome-interests.u-mbg, and hide that.

            Because you're specifically targetting elements that have both classes, the element that only has one of the two classes will not have the display: none rule apply to it (and so it will remain visible).

            This can be seen in the following:

            Source https://stackoverflow.com/questions/48434323

            QUESTION

            Malware Infected PHP code (I need some help to decode)
            Asked 2017-Nov-28 at 23:03

            Today I saw the following PHP code snippets in the code of some files of my project. The code was single line. I have used PHP Formatter (http://beta.phpformatter.com/), but I still have not figured it out.

            Do you have any idea what it is?

            ...

            ANSWER

            Answered 2017-Nov-28 at 23:03

            I'm not gona writing a full tutorial about reverse engineering such code, but because I was curious, what your snippet really does, I did some work.

            If you follow all encoding layers, you will end with this code:

            Source https://stackoverflow.com/questions/47537186

            QUESTION

            BLE Services never discovered
            Asked 2017-Sep-05 at 12:53

            I want to send a message to a BLE device. In my understanding one first has to discover the devices services and then send the message to a service characteristic. So here is what I did:

            ...

            ANSWER

            Answered 2017-Sep-05 at 12:45

            You need to call discoverServices from within the onConnectionStateChange method of your GATT callback. Documentation of the discoverServices method:

            Discovers services offered by a remote device as well as their characteristics and descriptors.

            This is an asynchronous operation. Once service discovery is completed, the onServicesDiscovered(BluetoothGatt, int) callback is triggered. If the discovery was successful, the remote services can be retrieved using the getServices() function.

            In your case, updating your code as follows should do the trick:

            Source https://stackoverflow.com/questions/46055213

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

            Vulnerabilities

            No vulnerabilities reported

            Install MBG

            You can download it from GitHub.

            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 .
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