shrimp | software package for aligning genomic reads | Script Programming library

 by   compbio-UofT C Version: Current License: Non-SPDX

kandi X-RAY | shrimp Summary

kandi X-RAY | shrimp Summary

shrimp is a C library typically used in Programming Style, Script Programming applications. shrimp has no bugs, it has no vulnerabilities and it has low support. However shrimp has a Non-SPDX License. You can download it from GitHub.

Assume we downloaded the linux binary package in ./SHRiMP_2_1_1.lx26.x86_64.tar.gz. $ tar xvzf SHRiMP_2_1_1.lx26.x86_64.tar.gz $ cd SHRiMP_2_1_1 $ file bin/gmapper bin/gmapper: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, statically linked, for GNU/Linux 2.6.9, not stripped $ export SHRIMP_FOLDER=$PWD. Done! At this point the binaries are in bin/, and the various scripts are in utils/.
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            kandi-support Support

              shrimp has a low active ecosystem.
              It has 6 star(s) with 5 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 0 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of shrimp is current.

            kandi-Quality Quality

              shrimp has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              shrimp has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              shrimp 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.
              It has 1218 lines of code, 25 functions and 19 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            shrimp Key Features

            No Key Features are available at this moment for shrimp.

            shrimp Examples and Code Snippets

            No Code Snippets are available at this moment for shrimp.

            Community Discussions

            QUESTION

            Find top 3 most ordered product per supplier in mysql 8.x
            Asked 2022-Apr-08 at 11:06

            I'd like to find the top 3 most ordered products per supplier in mySql. Here's my simplified model and its tables (primary keys are in italics):

            Product : product_id, name, supplier_id

            Supplier : supplier_id, name

            Order_item : order_item_id, product_id

            So 1 supplier can have N products, 1 order_item has 1 product.

            So far this is what i was able to get :

            ...

            ANSWER

            Answered 2022-Apr-08 at 11:06

            In MySQL 8 you should be able to:

            Source https://stackoverflow.com/questions/71794523

            QUESTION

            Print Multi-dimensional array using loop in PHP
            Asked 2022-Feb-21 at 15:15

            I don't understand how to use nested loops(for, foreach,while,dowhile) for printing this multi-dimensional array values in separate lines. I am new in this sector.

            Here is the code:

            ...

            ANSWER

            Answered 2022-Feb-21 at 15:15

            you have associative array inside associative array You have to loop the first associative array and inside it loop the associative array like this

            Source https://stackoverflow.com/questions/71208363

            QUESTION

            Connect to mongodb URL fails after creating admin user
            Asked 2022-Feb-16 at 11:40

            I have a web application that connects to MongoDB. Everything works fine before I create the admin user in mongodb:

            ...

            ANSWER

            Answered 2022-Feb-15 at 09:40

            What library or driver are you using? Regardless, you could try adding ?authenticationDatabase=admin to end of the url.

            Source https://stackoverflow.com/questions/71124075

            QUESTION

            Issue in decoding string in python
            Asked 2022-Jan-30 at 15:03

            I have a set of strings that need to be decoded. The strings format varies with products on the site. So its pretty unpredictable. Few examples of the format are given below:

            ...

            ANSWER

            Answered 2022-Jan-30 at 15:03

            This is fixed in python3 now. Used below code to convert :

            temp['Key_Features']=longDescription.encode().decode('unicode-escape').encode('latin1').decode('utf8').replace('&','&').replace(' ','').replace('"','"')

            This happened because data was in different encoding formats and couldn't be handled by a single encoding/decoding. The above logic works for all.

            Source https://stackoverflow.com/questions/69712680

            QUESTION

            ReactJS: Images are sometimes not appearing on button click
            Asked 2022-Jan-24 at 02:29

            I am a React noob. I am using Material UI and Material UI icons and React to create a title with a forward and back button, so the user can scroll through the pictures on display. When I press the forward button, the picture in "index 2" shows nothing. When I press the back button, the picture in "index 0" is blank (weird, right?). This seems like a super weird bug in my mind. Is there something I am missing here? It is making no sense to me.

            Here is my code (as you can see I'm still editing things, so I still have the default text from when I grabbed this from Material UI).

            ...

            ANSWER

            Answered 2022-Jan-24 at 02:29

            In your handler functions, the array index may go out of bound. So you should modify your handler functions like below:

            Source https://stackoverflow.com/questions/70828103

            QUESTION

            Create an element if it doesn't exist then move up on an other element
            Asked 2022-Jan-10 at 09:57

            This is the current XML:

            ...

            ANSWER

            Answered 2022-Jan-10 at 09:57

            I would let the minprice element trigger the insertion e.g.

            Source https://stackoverflow.com/questions/70634656

            QUESTION

            Decrement function in Reactjs doesn't work
            Asked 2021-Dec-30 at 11:22

            I am using ReactJs and React-dom in 17.02 version.

            I had the same problem described in this question: a value to increment and decrement using button. I used the solution proposed, changed my previous code.

            From this one:

            ...

            ANSWER

            Answered 2021-Dec-29 at 20:33

            You didn't show where the reference to card comes from in handleDecrement, but somewhere the reference is changed so it won't work in indexOf. Instead, create a new list and avoid using mutation.

            Source https://stackoverflow.com/questions/70524004

            QUESTION

            How to make converter with var and api
            Asked 2021-Nov-18 at 13:54

            I want to make a converter between crypto coins. I found unit converter sample from Codepen. converter works fine. My coingecko api work fine. But ı can't combine them. I can convert coin price but ı want to use APİ for current coin price. I searched on internet to use APİ in js 'var' but ı don't know maybe it's not possible to use api in input.

            This is converters: https://codepen.io/devere-here/pen/OzbpKY

            (I changed value to coins prices.(meters: usd, kilometers: ethereum, centimeters: bitcoin)

            This is converter JS

            ...

            ANSWER

            Answered 2021-Nov-18 at 13:54

            You need to rewrite de conversion code, for the help i make an basic code.

            Source https://stackoverflow.com/questions/70020400

            QUESTION

            Create a new column in pandas df with the result of .diff() function based on a condition in another column
            Asked 2021-Nov-09 at 01:25

            I need to apply function .diff() to a column. if the row value in another column is equal to the previous row of the same column.

            Example:

            ...

            ANSWER

            Answered 2021-Nov-09 at 01:25

            Is this what you want?

            Source https://stackoverflow.com/questions/69891548

            QUESTION

            Boxing large objects in image containing both large and small objects of similar color and in high density from a picture
            Asked 2021-Oct-12 at 10:58

            For my research project I'm trying to distinguish between hydra plant (the larger amoeba looking oranges things) and their brine shrimp feed (the smaller orange specks) so that we can automate the cleaning of petri dishes using a pipetting machine. An example of a snap image from the machine of the petri dish looks like so:

            I have so far applied a circle mask and an orange color space mask to create a cleaned up image so that it's mostly just the shrimp and hydra.

            There is some residual light artifacts left in the filtered image, but I have to bite the cost or else I lose the resolution of the very thin hydra such as in the top left of the original image.

            I was hoping to box and label the larger hydra plants but couldn't find much applicable literature for differentiating between large and small objects of similar attributes in an image, to achieve my goal.

            I don't want to approach this using ML because I don't have the manpower or a large enough dataset to make a good training set, so I would truly appreciate some easier vision processing tools. I can afford to lose out on the skinny hydra, just if I can know of a simpler way to identify the more turgid, healthy hydra from the already cleaned up image that would be great.

            I have seen some content about using openCV findCountours? Am I on the right track?

            Attached is the code I have so you know what datatypes I'm working with.

            ...

            ANSWER

            Answered 2021-Oct-12 at 10:58

            You are on the right track, but I have to be honest. Without DeepLearning you will get good results but not perfect.

            That's what I managed to get using contours:

            Code:

            Source https://stackoverflow.com/questions/69503515

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

            Vulnerabilities

            No vulnerabilities reported

            Install shrimp

            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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            CLONE
          • HTTPS

            https://github.com/compbio-UofT/shrimp.git

          • CLI

            gh repo clone compbio-UofT/shrimp

          • sshUrl

            git@github.com:compbio-UofT/shrimp.git

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