BamQC | Mapped QC analysis program | Genomics library

 by   s-andrews Java Version: Current License: Non-SPDX

kandi X-RAY | BamQC Summary

kandi X-RAY | BamQC Summary

BamQC is a Java library typically used in Artificial Intelligence, Genomics applications. BamQC has no bugs, it has no vulnerabilities and it has low support. However BamQC build file is not available and it has a Non-SPDX License. You can download it from GitHub.

BamQC is an application which takes a BAM file containing mapped data and runs a series of tests on it to generate a comprehensive QC report. This will help you to understand your data and will tell you if there is anything unusual the files you have analysed. Each test is flagged as a pass, warning or fail depending on how far it departs from what you'd expect from a normal large data set with no significant biases. It's important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.

            kandi-support Support

              BamQC has a low active ecosystem.
              It has 29 star(s) with 5 fork(s). There are 8 watchers for this library.
              It had no major release in the last 6 months.
              There are 4 open issues and 13 have been closed. On average issues are closed in 121 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of BamQC is current.

            kandi-Quality Quality

              BamQC has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              BamQC 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

              BamQC releases are not available. You will need to build from source code and install.
              BamQC has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions, examples and code snippets are available.
              BamQC saves you 7115 person hours of effort in developing the same functionality from scratch.
              It has 14726 lines of code, 990 functions and 146 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed BamQC and discovered the below as its top functions. This is intended to give you an instant insight into BamQC implemented functionality, and help decide if they suit your requirements.
            • Run the analysis
            • Process an embl file
            • Parses the given genome and extracts its features
            • Parse an annotation set
            • Start the HTML document
            • Loads the image from the classpath
            • Parse the annotation set
            • Extract the transcript_id from the attributes
            • Paint the foreground color
            • Compute the position of the first non - zero decimal digit
            • Create a JPanel that contains the statistics for the variant call analysis
            • Create a panel containing the statistics for the variant call detection
            • Paint the background
            • Create a panel containing the statistics for the variant call detector
            • Prints out informational messages
            • Run the set of mapped files
            • Load the preferences from the saved file
            • Read parameters from the annotation set
            • Paint the background color
            • Draws the background color
            • Reset the initial state
            • Process an annotation set
            • Draw the background color
            • Runs the application
            • Draw the background
            • Processes the specified SAMRecord
            Get all kandi verified functions for this library.

            BamQC Key Features

            No Key Features are available at this moment for BamQC.

            BamQC Examples and Code Snippets

            No Code Snippets are available at this moment for BamQC.

            Community Discussions


            "JAVA Parse Exception" error in Qualimap after MacOSX upgrade
            Asked 2019-Nov-06 at 15:48

            I recently upgraded my MacOSX system to Catalina and several files were placed automatically into "Relocated items" folder on my Desktop. I recently tried to run the following code which had previously worked:



            Answered 2019-Nov-06 at 15:48

            It seems what qualimap is a java application someone else wrote. I would raise a ticket with whomever wrote this app.


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


            No vulnerabilities reported

            Install BamQC

            Further instructions for installing and running the program can be found in the installation instructions file in the BamQC distribution.


            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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            gh repo clone s-andrews/BamQC

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