BamM | Metagenomics-focused BAM file manipulation

 by   Ecogenomics C Version: 1.7.3 License: LGPL-3.0

kandi X-RAY | BamM Summary

kandi X-RAY | BamM Summary

BamM is a C library. BamM has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

BamM is a c library, wrapped in python, that parses BAM files. The code is intended to provide a faster, more stable interface to parsing BAM files than PySam, but doesn't implement all/any of PySam's features. Do you want all the links that join two contigs in a BAM? Do you need to get coverage? Would you like to just work out the insert size and orientation of some mapped reads?.
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              BamM has a low active ecosystem.
              It has 14 star(s) with 8 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 12 open issues and 21 have been closed. On average issues are closed in 22 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of BamM is 1.7.3

            kandi-Quality Quality

              BamM has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              BamM is licensed under the LGPL-3.0 License. This license is Weak Copyleft.
              Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

            kandi-Reuse Reuse

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

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            BamM Key Features

            No Key Features are available at this moment for BamM.

            BamM Examples and Code Snippets

            No Code Snippets are available at this moment for BamM.

            Community Discussions

            QUESTION

            How to target each page of the pagination for adding an event in Vuejs?
            Asked 2021-May-18 at 13:37

            ...

            ANSWER

            Answered 2021-May-18 at 13:37

            If i understand your problematic correctly, you want the pagination component to trigger an event each time the page is changed, right?

            To do that, you might want to listen for the "page-click" event returned by the pagination component each time a page is changed. It returns the page number and the according event. Whenever the event is triggered, you can call a method which handles what you want basically.

            If that doesn't work for you and you need more specific usage, you could create a wrapper component for the pagination to emit the events you want for you usage. Though bare in mind that this solution will be harder to maintain and that it is preferred to use the events of the library when you use one.

            Here is a very simple example on how to use the page-click event, like any other event emitted by a component in vue :

            Source https://stackoverflow.com/questions/67586722

            QUESTION

            Vue b-table change one column into link
            Asked 2021-Apr-11 at 21:07

            I am really new to vue and for this project I am using Vue, Bootstrap-vue to paginate my data teamList. Is there a way that I can change the teamList.first_name into the link so that I can use onSelect or onClick event once the user clicks on the first_name value.

            Code on JsFiddle = https://jsfiddle.net/ujjumaki/aLdgo7xq/8/

            VIEW

            ...

            ANSWER

            Answered 2021-Apr-11 at 21:07

            QUESTION

            How can I use a changing int value to call different functions on an Arduino?
            Asked 2021-Feb-15 at 16:14

            I am programming (kind of) a stopwatch with start buttons and a 4-digit seven-segment LED display on my Arduino Uno.

            With functions like this one I can put numbers on the SevSeg without problems:

            ...

            ANSWER

            Answered 2021-Feb-15 at 16:14

            The problem here is you're not calling any function. To call a function you do:

            Source https://stackoverflow.com/questions/66050455

            QUESTION

            Project Lombok AllArgsConstructor not working
            Asked 2020-Nov-22 at 11:28

            It seems like many people are having this problem, but none of the problems i have researched so far are that basic like my problem.

            I only got this object:

            and a basic call in my main method:

            Bamm... already not working. The compilataion fails with this error

            I am using IntelliJ and have installed the Lombok plugin.

            If it helps... here is my build.gradle:

            Any ideas ?

            ...

            ANSWER

            Answered 2020-Nov-22 at 11:28

            Lombok uses the annotation processor to do its magic so you have to add lombok annotationProcessor dependency in your build.gradle file. Add this line inside your dependencies block:

            Source https://stackoverflow.com/questions/64953427

            QUESTION

            Cannot Implicitly Convert FileStream to StreamWriter for Json File
            Asked 2020-Apr-16 at 19:54

            So, I'm reading a book about .NET Core 3 and I'm at a section where I'm learning how to serialize JSON files. I have run into a problem with types that I haven't been able to figure out a solution to. I have tried working around it, but then I run into other type issues. The problem I get with the code below is CS0029 in the last using statement of Main at File.Create(jsonPath):

            Cannot implicitly convert type 'System.IO.FileStream' to 'System.IO.StreamWriter'

            I have tried changing the using statement to use a FileStream type instead of a StreamWriter, as per the example I got from Microsoft documentation, but that produces an error at the jsonStream variable on the jsonSerializer.Serialize(jsonStream, people) line that says:

            Cannot convert from 'System.IO.FileStream' to 'System.IO.TextWriter

            Here is the code below:

            ...

            ANSWER

            Answered 2020-Apr-16 at 03:41

            You can use this JSONHelpers.

            Source https://stackoverflow.com/questions/61241077

            QUESTION

            Run python script by PHP from another server
            Asked 2019-Feb-21 at 05:59

            I am making APIs. I'm using CentOS for web server, and another windows server 2016 for API server. I'm trying to make things work between web server and window server.

            My logic is like following flow.

            1) Fill the data form and click button from web server

            2) Send data to windows server

            3) Python script runs and makes more data

            4) More made data must send back to web server

            5) Web server gets more made datas

            6) BAMM! Datas append on browser!

            I had made python scripts. but I can't decide how to make datas go between two servers..

            Should I use ajax Curl in web server? I was planning to send a POST type request by Curl from web server to Windows server. But I don't know how to receipt those datas in windows server. Please help! Thank you in advance.

            ...

            ANSWER

            Answered 2019-Feb-21 at 05:59

            First option: (Recommended) You can create the python side as an API endpoint and from the PHP server, you need to call the python API.

            Second option: You can create the python side just like a normal webpage and whenever you call that page from PHP server you pass the params along with HTTP request, and after receiving data in python you print the data in JSON format.

            Source https://stackoverflow.com/questions/54799927

            QUESTION

            combining "LIKE", "NOT LIKE" & "OR"
            Asked 2018-Jun-07 at 12:37

            I am learning MySQL and I have tried to combine "NOT LIKE" with "OR" in my queries in vain.

            Assuming I have a table1 with one column called "word" as below :

            ...

            ANSWER

            Answered 2018-Jun-07 at 12:16

            If I understand correctly, you just need parentheses:

            Source https://stackoverflow.com/questions/50740981

            QUESTION

            Spring REST GET request produces hashes
            Asked 2018-Apr-17 at 09:45

            Here's my code to retrieve the JSON string from the specific API:

            ...

            ANSWER

            Answered 2018-Apr-17 at 09:45

            When querying your URL with firefox, I see that in response headers, I've got "Compression=deflate". That means returned stream is GZIP encoded. So, the returned string is in fact the compressed content, not the json. I find it strange that RestTemplate does not take care of it by default.

            To make your example work, I've followed this answer (tested locally, response look ok) :

            Source https://stackoverflow.com/questions/49873691

            QUESTION

            ngram representation and distance matrix in R
            Asked 2018-Mar-13 at 10:51

            Assume that we have this data:

            ...

            ANSWER

            Answered 2018-Mar-13 at 10:04

            You can do in this way :

            Source https://stackoverflow.com/questions/49252396

            QUESTION

            Combine results of multiple MySQL queries (w/ Group By) on 1 table
            Asked 2017-Jun-16 at 15:06

            What's the best way to do this?

            I'll describe below, but here is a setup at rextester.com data to play with- http://rextester.com/PXQOV60475

            I have a table called "cases" that contains info on repair jobs basically. There is a field for the Case Manager called "case_mgr", and also a field for "case_mgr_first" because the Case Manager can be changed so this contains the original. There is another similar field for "who_last_called" which would be the user that last contacted the customer. Those all contain usernames... though "case_mgr_first" and "who_last_called" could be null ("case_mgr_first" is a new field and there may have been nobody that called).

            To continue the repair job, the item to be repaired has to be received. Once it is received, the field "item_received_date" is set, otherwise it's null. There is also a date the record is created saved in the field "created_date".

            So, the goal is to find the receiving % for users multiple ways. I'd like to find this receiving rate for the users as the current Case Manager ("case_mgr"), as "case_mgr_first", and as "who_last_called"... for a certain time period by the "created_date".

            I already had a query for one of these, and it worked fine.

            ...

            ANSWER

            Answered 2017-Jun-15 at 22:38

            I guess you could cook up a solution, where you do a UNION sub select and group again over that sub select, but it's not gonna be pretty:

            Source https://stackoverflow.com/questions/44577774

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

            Vulnerabilities

            No vulnerabilities reported

            Install BamM

            There are 3 ways to install BamM:.
            Through GNU Guix with guix package --install bamm
            From source
            The BAM parsing is done using c and a few external libraries. This slightly complicates the BamM installation process but fortunately not too much.
            Samtools: http://sourceforge.net/projects/samtools (tested with version: 1.2)
            BWA: https://github.com/lh3/bwa (tested with version: 0.7.12)

            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:

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            CLONE
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            https://github.com/Ecogenomics/BamM.git

          • CLI

            gh repo clone Ecogenomics/BamM

          • sshUrl

            git@github.com:Ecogenomics/BamM.git

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