DSRC | DSRC - DNA Sequence Reads Compressor

 by   refresh-bio C++ Version: v2.0 License: No License

kandi X-RAY | DSRC Summary

kandi X-RAY | DSRC Summary

DSRC is a C++ library. DSRC has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

DSRC is a toolkit designed for efficient high-performance compression of sequencing reads stored in FASTQ format, where it's main features are:. For more information please check out the official website.
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              DSRC has a low active ecosystem.
              It has 48 star(s) with 20 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 13 open issues and 6 have been closed. On average issues are closed in 308 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of DSRC is v2.0

            kandi-Quality Quality

              DSRC has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              DSRC does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              DSRC releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            DSRC Key Features

            No Key Features are available at this moment for DSRC.

            DSRC Examples and Code Snippets

            Python library
            C++dot img1Lines of Code : 11dot img1no licencesLicense : No License
            copy iconCopy
            # To compile DSRC Python module please specify your boost installation directory below
            #
            use-project boost 
            	: /absolute/path/to/boost/directory/ ;
            
            name
            
            # Specify toolset according to your platform manually in case of compilation problems in form:   
            Usage,Usage examples
            C++dot img2Lines of Code : 7dot img2no licencesLicense : No License
            copy iconCopy
            dsrc c SRR001471.fastq SRR001471.dsrc
            
            dsrc c -m0 -c -t4 SRR001471.fastq SRR001471.dsrc
            
            dsrc c -d2 -q2 -b512 SRR001471.fastq SRR001471.dsrc
            
            dsrc c -m2 -l -f1,2,3,4 SRR001471.fastq SRR001471.dsrc
            
            cat SRR001471.fastq | dsrc c -m2 -s SRR001471.dsrc
            
              
            Building,Building on Linux,Binary
            C++dot img3Lines of Code : 2dot img3no licencesLicense : No License
            copy iconCopy
            make bin
            
            make -f Makefile.c++11 bin
              

            Community Discussions

            QUESTION

            Runtime errors on using veins and veins_inet content on same simulation
            Asked 2020-Aug-04 at 13:18

            Ubuntu - 20.04 , Omnetpp - 5.5.1 , veins - 5.0 , Sumo - 1.6.0 , Inet - 3.6.7

            I'm doing a project where I want to create a DSRC based and wifi based vehicular simulatons in the same simulate environment (same project).

            I tried to get RSU and the Car node from veins example to veins_inet example to simulate both there.

            ...

            ANSWER

            Answered 2020-Aug-04 at 13:18

            Please see the Veins FAQ at http://veins.car2x.org/documentation/faq/ for help on how to debug a simulation, specifically the entry What happened? My simulation crashed. and the entry How can I debug my OMNeT++ simulation models? How do I create a stack trace? (in brief: run the simulation in debug mode and set debug-on-errors = true)

            Source https://stackoverflow.com/questions/62787309

            QUESTION

            DSRC and WIFI (LTE/Cellular) in vehicular communication
            Asked 2020-Jul-26 at 16:58

            Can NS -2.35 simulate both DSRC and WIFI vehicular communication in the same environement?

            If not, is there any software simulation capable of ?

            ...

            ANSWER

            Answered 2020-Jul-26 at 16:58

            Veins 5.0 can be used to model wirelessly-networked road traffic (cars, trucks, bikes, trains, pedestrians). By default, Veins 5.0 includes models of DSRC, but it can be used together with projects like INET (for WiFi), SimuLTE (for 4G+ mobile broadband networking), or Veins VLC (for visible light communication). See http://veins.car2x.org/ for more information.

            Source https://stackoverflow.com/questions/62372602

            QUESTION

            Slow Azure Data Factory Pipeline
            Asked 2020-May-04 at 16:17

            I am using Azure Data Factory V2 to transfer some csv files from Azure Data Lake to Azure Synapse

            I have a loop to find all files in special folder on my DataLake.

            After i have a DataFlow to transfer data from staging to main table.

            In my for-each loop, at first i am cleaning my staging table by a SP then I am reading data from csv file (one by one). to transfer data from CVS to my staging table i am using Copy Data task. I am reading all columns as varchar and all columns in staging table are varchar(there is no casting here)

            Each file has about 20 columns and about 216 rows.

            I am wondering why for just three files my pipeline takes so much times?

            this is my task for cleaning staging table.

            This is my SQL server scale and usage.

            I ran my pipeline exactly after resuming my Synapse service. that is only pipeline and service that work with my synapse.

            This is my stored procedure :

            ...

            ANSWER

            Answered 2020-May-04 at 16:17

            I think the question is getting a bit muddled here, so I'm going to attempt an answer. Understand that there are a lot of potential factors and my response is not intended to be an exhaustive review of Data Flow performance techniques.

            First, let me sum up the project as I understand it. For each file in an ADLS folder, it appears you have the following:

            1. Stored Procedure to truncate a Synapse staging table.
            2. Copy activity to copy data from ADLS to Synapse staging table
            3. DataFlow to read the data from the Synapse staging table, process it, and Write it back to a different Synapse table
            4. Execute another pipeline to Archive the file.

            From what I gather, it seems that this process is working. The question is in regards to the execution time of the Data Flow.

            GENERAL performance guidelines to consider:

            • Since you are running multiple DFs in succession, use a Custom Integration Runtime with ComputeOptimized type, 4 Cores, and Time To Live (TTL) greater than 0. [Not too long though, as you will pay for the environment to be active during the TTL time.] NOTE: last I was aware, DF requires the Region to be "Auto Resolve".

            • Any time you WRITE to Synapse, make sure to define a Polybase Staging Storage Account:

            • Be aware of cross-region operations: network Latency can be a real killer AND costs you money. For fastest performance, the Storage, Data Factory, and Synapse resources should all be in the same data center.

            • Source and Sink partitioning CAN help with very large data sets and complex scenarios, but is a fairly tricky topic and (most likely) would not help in your scenario.

            SPECIFIC to your posted scenario, I would consider redesigning the workflow. From a high level, you are doing the following for every (small) file:

            1. Clearing a Synapse table
            2. Writing from blob to Synapse
            3. Reading the data you just wrote from Synapse
            4. Writing the data back to Synapse [after some minimal processing].

            My personal rule of thumb is to not use Data Flow to cross the Synapse boundary: if the operation is from Synapse to the same Synpase, then run the logic in Synapse. In other words, since the Source and Sink are both in Synapse, I would replace the Data Flow with a Stored Procedure.

            Even better, I would consolidate the COPY activity and the Data Flow to a single Data Flow. The Data Flow can read the ADLS as a source, transform the data, and INSERT it to Synapse. This would remove the Staging table from the process. DF can even Archive the files after the operation:

            Finally, I would seek to limit the number of Data Flow executions. Is there a reason you have to process this file by file? The Data Flow source could easily process the entire folder, even capturing the file name as a column if you have logic based on that value [see image above]. This would remove the need to run the Data Flow many times and could dramatically improve overall performance.

            Source https://stackoverflow.com/questions/61532258

            QUESTION

            On hover swap images
            Asked 2018-Apr-05 at 14:14

            I have 2 dropdowns namely NEW & SHOP

            when I hover over the New Menu 1, it should show the related image and same when I hover over New Menu 2 it should show the related image in a div which has a class ".menu-viewer".

            Right now this works, but it changes the image of the shop menu also.

            Also, the default image for the shop is not shown by default.

            Please refer the Fiddle I have created and tell me what am I doing wrong.

            I hope I have explained my problem clearly. As it sounds a little confusing, please feel free to ask me.

            https://jsfiddle.net/cancerian73/qwtono6c/

            ...

            ANSWER

            Answered 2018-Apr-05 at 14:14

            You need to change the image within the current block. In the following I have used jQuery closest to get the closest ancestor megamenu and changed the image based on that:

            Source https://stackoverflow.com/questions/49671461

            QUESTION

            Image resampling on 3-channel thats not padded to 4 bytes?
            Asked 2018-Jan-15 at 00:39

            I found an image resampling algorithm that produces an extremely nice image when down-sizing. It works on a 3-channel image that's padded to 4 bytes per pixel. What do i change to make this work for a image that's not padded to 4 bytes per channel? Like a jpeg image. The destination image is 4-byte padded. Also, what name would you give this algorithm?

            Originally found here: http://www.geisswerks.com/ryan/FAQS/resize.html

            Code simplified:

            ...

            ANSWER

            Answered 2018-Jan-15 at 00:39

            The original code uses 3 bytes for color, and one byte for alpha or padding, for 4 bytes per pixel. It reads 32-bit integers, and masks the colors out. You don't have that 4th byte, so you need to change things to read from unsigned chars.

            Change dsrc and ddest to be an unsigned char *. The declaration for dsrc2 then becomes

            Source https://stackoverflow.com/questions/48255096

            QUESTION

            Trouble with quotes and optional wildcard in R, regex
            Asked 2017-Aug-08 at 01:19

            Given this character vector

            ...

            ANSWER

            Answered 2017-Aug-08 at 01:19

            I'm guessing you're just looking for entries that contain at least one space in between words. You can give this a try: "([\w%]+ [\w%]+(?: [\w%]+)*?)"

            It looks like you're only trying to match letters and %, so using \w might be a bit dangerous (it also matches 0-9 and _). You can be more specific with "([A-Za-z%]+ [A-Za-z%]+(?: [A-Za-z%]+)*?)"

            Also, note that \s doesn't just mean a space (). It's the set of all whitespace characters so it will also match newlines, carriage returns, and tabs. If you want to match a space, just use a literal space.

            Source https://stackoverflow.com/questions/45557740

            QUESTION

            CMake: how to break a PRE_LINK infinite loop?
            Asked 2017-Apr-28 at 05:48

            I'm trying to automatically label my application sign-on line with a build number. This application is a plain vanilla C one without graphic UI; it is intended for command line, therefore it is a "simple" one.

            The sign-on id is located in a "template" source file which is customized by CMake with a configure_file() command. Recently, I fancied to include a build number in this sign-on id. Consequently, the customization can no longer be statically done at CMake time, but everytime make is invoked.

            To achieve that, there are two possibilities in CMake:

            1. add_custom_target(), but it is triggered even when nothing else changes in the source tree which does not reflect the state of the tree;
            2. add_custom_command(), which can be triggered only when the application (target) needs to be linked again.

            I opted for the second solution and did not succeed.

            Here is an extract of my CMakeLists.txt, the sign-on id being in file ErrAux.c (template in PROJECT_SOURCE_DIR, configured in PROJECT_BINARY_DIR):

            ...

            ANSWER

            Answered 2017-Apr-28 at 05:48

            The key to the solution is to put the generated module where make expects to find it. CMake organizes the build tree in a non-trivial way.

            The shortcomming in my added compilation in add_custom_command() was to believe that by default the binary will be stored in the "usual" CMake locations. Since I forge manually my compiler command, this is not the case.

            I found the module in the source directory, which is a consequence of the WORKING_DIRECTORY option, with name ErrAux.o and not ErrAux.c.o.

            To obtain the correct behavior, I force an output location with:

            Source https://stackoverflow.com/questions/43643306

            QUESTION

            Redirecting stderr to file and stdout to console
            Asked 2017-Jan-11 at 13:03
            dcc  -tPPCE200Z4VEN:simple -Xdialect-ansi -XO -g3 -Xsize-opt -Xsmall-data=0 -Xno-common -Xnested-interrupts -Xdebug-dwarf2 -Xdebug-local-all -Xdebug-local-cie -Xdebug-struct-all -Xforce-declarations -ee1481 -Xmacro-undefined-warn -Xlink-time-lint -W:as:,-l -Wa,-Xisa-vle -Xsmall-const=0 -Xforce-prototypes -Xpass-source -Xkeep-assembly-file -c -Xlint -Xenum-is-best -Xinline=0 -Xaddr-sconst=0x11 -Xaddr-sdata=0x11  -DDISABLE_MCAL_INTERMODULE_ASR_CHECK -DOSDIABPPC -DSC667349 -DFLASH_START -DV_SUPPRESS_EXTENDED_VERSION_CHECK -DV_USE_DUMMY_STATEMENT=STD_OFF -DEU_DISABLE_ANSILIB_CALLS -DMCAL_CER_VALIDATION -DOsAppMode=OSAPPMODEDEFAULT -DSKIP_MAGIC_NUMBER -DRTE_MICROSAR_PIM_EXPORT -DMEMIF_FAST_NVM_ACTIVATED=STD_ON -DESCLmgr_IsENABLED -DESCLmgr_CANrouting_RESvalidity=1 -DFEE_SWITCH_NOT_CONFIG_BLOCKS=STD_OFF -DFILL_NOINIT_WITH_ZERO -Dsrc -ID:\project\src -ID:\project\obj -E D:\project\src\hello.c 1> D:\project\obj\hello.i 2>&1
            
            ...

            ANSWER

            Answered 2017-Jan-11 at 13:03

            2>&1 doesn't mean "redirect stderr to console", it means "redirect stderr to the same place as stdout currently goes". If you do the redirections in the other order -- 2>&1 1>hello.i instead of 1>hello.i 2>&1 -- then you will get the effect I believe you are looking for.

            You need to think of the redirections happening one at a time. If you say 1>hello.i 2>&1 then this happens:

            • First, stdout is redirected to hello.i.
            • Then stderr is redirected to the current destination of stdout, namely hello.i.

            But if you say 2>&1 1>hello.i then this happens:

            • First, stderr is redirected to the current destination of stdout, namely the console.
            • Then stdout is redirected to hello.i.

            Source https://stackoverflow.com/questions/41591493

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

            Vulnerabilities

            No vulnerabilities reported

            Install DSRC

            Pre-built binaries and libraries for Linux, Mac OSX and Windows platforms can be downloaded from the official website.

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            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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