GenomicsDB | Highly performant data storage for importing , querying

 by   GenomicsDB C++ Version: 1.5.1 License: Non-SPDX

kandi X-RAY | GenomicsDB Summary

kandi X-RAY | GenomicsDB Summary

GenomicsDB is a C++ library typically used in Big Data, Spark applications. GenomicsDB has no bugs, it has no vulnerabilities and it has low support. However GenomicsDB has a Non-SPDX License. You can download it from GitHub.

GenomicsDB, originally from Intel Health and Lifesciences, is built on top of a fork of htslib and a tile-based array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data. GenomicsDB is a highly performant scalable data storage written in C++ for importing, querying and transforming genomic variant data. GenomicsDB is packaged into gatk4 and benefits qualitatively from a large user base. The GenomicsDB documentation for users is hosted as a Github wiki:
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              GenomicsDB has a low active ecosystem.
              It has 81 star(s) with 19 fork(s). There are 11 watchers for this library.
              There were 1 major release(s) in the last 12 months.
              There are 22 open issues and 16 have been closed. On average issues are closed in 194 days. There are 6 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of GenomicsDB is 1.5.1

            kandi-Quality Quality

              GenomicsDB has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              GenomicsDB 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

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

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of GenomicsDB
            Get all kandi verified functions for this library.

            GenomicsDB Key Features

            No Key Features are available at this moment for GenomicsDB.

            GenomicsDB Examples and Code Snippets

            External Contributions,Checklist before creating Pull Request
            C++dot img1Lines of Code : 13dot img1License : Non-SPDX (NOASSERTION)
            copy iconCopy
            Use spaces instead of tabs.
            Use 2 spaces for indenting.
            Add brackets even for one line blocks e.g. 
                    if (x>0)
                       do_foo();
             should ideally be 
                   if (x>0) {
                     do_foo();
                   }
            Pad header e.g.
                    if(x>0) shoul  

            Community Discussions

            QUESTION

            How to group unassociated content
            Asked 2022-Apr-15 at 12:43

            I have a hive table that records user behavior

            like this

            userid behavior timestamp url 1 view 1650022601 url1 1 click 1650022602 url2 1 click 1650022614 url3 1 view 1650022617 url4 1 click 1650022622 url5 1 view 1650022626 url7 2 view 1650022628 url8 2 view 1650022631 url9

            About 400GB is added to the table every day.

            I want to order by timestamp asc, then one 'view' is in a group between another 'view' like this table, the first 3 lines belong to a same group , then subtract the timestamps, like 1650022614 - 1650022601 as the view time.

            How to do this?

            i try lag and lead function, or scala like this

            ...

            ANSWER

            Answered 2022-Apr-15 at 12:43

            If you use dataframe, you can build partition by using window that sum a column whose value is 1 when you change partition and 0 if you don't change partition.

            You can transform a RDD to a dataframe with sparkSession.createDataframe() method as explained in this answer

            Back to your problem. In you case, you change partition every time column behavior is equal to "view". So we can start with this condition:

            Source https://stackoverflow.com/questions/71883786

            QUESTION

            Using Spark window with more than one partition when there is no obvious partitioning column
            Asked 2022-Apr-10 at 20:21

            Here is the scenario. Assuming I have the following table:

            identifier line 51169081604 2 00034886044 22 51168939455 52

            The challenge is to, for every single column line, select the next biggest column line, which I have accomplished by the following SQL:

            ...

            ANSWER

            Answered 2022-Apr-10 at 20:21

            Using your "next" approach AND assuming the data is generated in ascending line order, the following does work in parallel, but if actually faster you can tell me; I do not know your volume of data. In any event you cannot solve just with SQL (%sql).

            Here goes:

            Source https://stackoverflow.com/questions/71803991

            QUESTION

            What is the best way to store +3 millions records in Firestore?
            Asked 2022-Apr-09 at 13:18

            I want to store +3 millions records in my Firestore database and I would like to know what is the best way, practice, to do that.

            In fact, I want to store every prices of 30 cryptos every 15 minutes since 01/01/2020.

            For example:

            • ETH price at 01/01/2020 at 00h00 = xxx
            • ETH price at 01/01/2020 at 00h15 = xxx
            • ETH price at 01/01/2020 at 00h30 = xxx
            • ...
            • ETH price at 09/04/2022 at 14h15 = xxx

            and this, for 30 cryptos (or more).

            So, 120 prices per day multiplied by 829 days multiplied by 30 cryptos ~= 3M records

            I thought of saving this like this:

            [Collection of Crypto] [Document of crypto] [Collection of dates] [Document of hour] [Price]

            I don't know if this is the right way, that's why I come here :)

            Of course, the goal of this database will be to retrieve ALL the historical prices of a currency that I would have selected. This will allow me to make statistics etc later.

            Thanks for your help

            ...

            ANSWER

            Answered 2022-Apr-09 at 13:18

            For the current structure, instead of creating a document every 15 minutes you can just create a "prices" document and store an array of format { time: "00:00", price: 100 } which will cost only 1 read to fetch prices of a given currency on a day instead of 96.

            Alternatively, you can create a single collection "prices" and create a document everyday for each currency. A document in this collection can look like this:

            Source https://stackoverflow.com/questions/71808107

            QUESTION

            spark-shell throws java.lang.reflect.InvocationTargetException on running
            Asked 2022-Apr-01 at 19:53

            When I execute run-example SparkPi, for example, it works perfectly, but when I run spark-shell, it throws these exceptions:

            ...

            ANSWER

            Answered 2022-Jan-07 at 15:11

            i face the same problem, i think Spark 3.2 is the problem itself

            switched to Spark 3.1.2, it works fine

            Source https://stackoverflow.com/questions/70317481

            QUESTION

            For function over multiple rows (i+1)?
            Asked 2022-Mar-30 at 08:31

            New to R, my apologies if there is an easy answer that I don't know of.

            I have a dataframe with 127.124 observations and 5 variables

            Head(SortedDF)

            ...

            ANSWER

            Answered 2022-Mar-30 at 08:31
            library(tidyverse)
            
            data <- tibble(x = c(1, 1, 2), y = "a")
            data
            #> # A tibble: 3 × 2
            #>       x y    
            #>    
            #> 1     1 a    
            #> 2     1 a    
            #> 3     2 a
            
            same_rows <-
              data %>%
              # consider all columns
              unite(col = "all") %>%
              transmute(same_as_next_row = all == lead(all))
            
            data %>%
              bind_cols(same_rows)
            #> # A tibble: 3 × 3
            #>       x y     same_as_next_row
            #>                
            #> 1     1 a     TRUE            
            #> 2     1 a     FALSE           
            #> 3     2 a     NA
            

            Source https://stackoverflow.com/questions/71673259

            QUESTION

            Filling up shuffle buffer (this may take a while)
            Asked 2022-Mar-28 at 20:44

            I have a dataset that includes video frames partially 1000 real videos and 1000 deep fake videos. each video after preprocessing phase converted to the 300 frames in other worlds I have a dataset with 300000 images with Real(0) label and 300000 images with Fake(1) label. I want to train MesoNet with this data. I used costum DataGenerator class to handle train, validation, test data with 0.8,0.1,0.1 ratios but when I run the project show this message:

            ...

            ANSWER

            Answered 2021-Nov-10 at 14:23

            QUESTION

            Designing Twitter Search - How to sort large datasets?
            Asked 2022-Mar-24 at 17:25

            I'm reading an article about how to design a Twitter Search. The basic idea is to map tweets based on their ids to servers where each server has the mapping

            English word -> A set of tweetIds having this word

            Now if we want to find all the tweets that have some word all we need is to query all servers and aggregate the results. The article casually suggests that we can also sort the results by some parameter like "popularity" but isn't that a heavy task, especially if the word is an hot word?

            What is done in practice in such search systems?

            Maybe some tradeoff are being used?

            Thanks!

            ...

            ANSWER

            Answered 2022-Mar-24 at 17:25

            First of all, there are two types of indexes: local and global.

            A local index is stored on the same computer as tweet data. For example, you may have 10 shards and each of these shards will have its own index; like word "car" -> sorted list of tweet ids.

            When search is run we will have to send the query to every server. As we don't know where the most popular tweets are. That query will ask every server to return their top results. All of these results will be collected on the same box - the one executing the user request - and that process will pick top 10 of of entire population.

            Since all results are already sorted in the index itself, it is a O(1) operation to pick top 10 results from all lists - as we will be doing simple heap/watermarking on set number of tweets.

            Second nice property, we can do pagination - the next query will be also sent to every box with additional data - give me top 10, with popularity below X, where X is the popularity of last tweet returned to customer.

            Global index is a different beast - it does not live on the same boxes as data (it could, but does not have to). In that case, when we search for a keyword, we know exactly where to look for. And the index itself is also sorted, hence it is fast to get top 10 most popular results (or get pagination).

            Since the global index returns only tweet Ids and not tweet itself, we will have to lookup tweets for every id - this is called N+1 problem - 1 query to get a list of ids and then one query for every id. There are several ways to solve this - caching and data duplication are by far most common approaches.

            Source https://stackoverflow.com/questions/71588238

            QUESTION

            Unnest Query optimisation for singular record
            Asked 2022-Mar-24 at 11:45

            I'm trying to optimise my query for when an internal customer only want to return one result *(and it's associated nested dataset). My aim is to reduce the query process size.

            However, it appears to be the exact same value regardless of whether I'm querying for 1 record (with unnested 48,000 length array) or the whole dataset (10,000 records with unnest total 514,048,748 in total length of arrays)!

            So my table results for one record query:

            ...

            ANSWER

            Answered 2022-Mar-24 at 11:45

            This is happening because there is still need for a full table scan to find all the test IDs that are equal to the specified one.

            It is not clear from your example which columns are part of the timeseries record. In case test_id is not one of them, I would suggest to cluster the table on the test_id column. By clustering, the data will be automatically organized according to the contents of the test_id column.

            So, when you query with a filter on that column a full scan won't be needed to find all values.

            Read more about clustered tables here.

            Source https://stackoverflow.com/questions/71599650

            QUESTION

            handling million of rows for lookup operation using python
            Asked 2022-Mar-19 at 11:27

            I am new to data handling . I need to create python program to search a record from a samplefile1 in samplefile2. i am able to achieve it but for each record out of 200 rows in samplefile1 is looped over 200 rows in samplefile2 , it took 180 seconds complete execution time.

            I am looking for something to be more time efficient so that i can do this task in minimum time .

            My actual Dataset size is : 9million -> samplefile1 and 9million --> samplefile2.

            Here is my code using Pandas.

            sample1file1 rows:

            ...

            ANSWER

            Answered 2022-Mar-19 at 11:27

            I don't think using Pandas is helping here as you are just comparing whole lines. An alternative approach would be to load the first file as a set of lines. Then enumerate over the lines in the second file testing if it is in the set. This will be much faster:

            Source https://stackoverflow.com/questions/71526523

            QUESTION

            split function does not return any observations with large dataset
            Asked 2022-Mar-12 at 22:29

            I have a dataframe like this:

            ...

            ANSWER

            Answered 2022-Mar-12 at 22:29

            It is just that there are many unused levels as the column 'seqnames' is a factor. With split, there is an option to drop (drop = TRUE - by default it is FALSE) to remove those list elements. Otherwise, they will return as data.frame with 0 rows. If we want those elements to be replaced by NULL, then find those elements where the number of rows (nrow) are 0 and assign it to NULL

            Source https://stackoverflow.com/questions/71453084

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

            Vulnerabilities

            No vulnerabilities reported

            Install GenomicsDB

            You can download it from GitHub.

            Support

            GenomicsDB is open source and all participation is welcome. GenomicsDB is released under the MIT License and all external contributors are expected to grant an MIT License for their contributions.
            Find more information at:

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

            Find more libraries
            Install
            Maven
            Gradle
            CLONE
          • HTTPS

            https://github.com/GenomicsDB/GenomicsDB.git

          • CLI

            gh repo clone GenomicsDB/GenomicsDB

          • sshUrl

            git@github.com:GenomicsDB/GenomicsDB.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