cpsr | Cancer Predisposition Sequencing Reporter | Genomics library

 by   sigven R Version: v0.6.2 License: Non-SPDX

kandi X-RAY | cpsr Summary

kandi X-RAY | cpsr Summary

cpsr is a R library typically used in Artificial Intelligence, Genomics applications. cpsr has no bugs, it has no vulnerabilities and it has low support. However cpsr has a Non-SPDX License. You can download it from GitHub.

The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets and classifies germline DNA variants identified from next-generation sequencing in the context of cancer predisposition and inherited cancer syndromes. The workflow can also report incidental findings (ACMG v3.0) as well as the genotypes of common germline variants associated with cancer risk, as reported in the NHGRI-EBI GWAS catalog. The CPSR workflow is integrated with the framework that underlies the Personal Cancer Genome Reporter - PCGR. While PCGR is intended for reporting and analysis of somatic variants detected in a tumor,. CPSR accepts a query file from a single case/patient, containing raw germline variant calls encoded in the VCF format (i.e. SNVs/InDels). A comprehensive set of virtual cancer predisposition gene panels harvested from the Genomics England PanelApp allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report.
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            kandi-support Support

              cpsr has a low active ecosystem.
              It has 43 star(s) with 12 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 32 have been closed. On average issues are closed in 46 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of cpsr is v0.6.2

            kandi-Quality Quality

              cpsr has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              cpsr 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

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

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            cpsr Key Features

            No Key Features are available at this moment for cpsr.

            cpsr Examples and Code Snippets

            No Code Snippets are available at this moment for cpsr.

            Community Discussions

            QUESTION

            What is the Hypervisor mode in arm?
            Asked 2022-Mar-28 at 17:20

            The macro safe_svcmode_maskall in arch/arm/kernel/head.S is defined in arch/arm/include/assembler.h,which is

            ...

            ANSWER

            Answered 2022-Mar-28 at 17:20
            Last question

            But I can't find the definition of ':req' in gnu arm assembler manual.

            From the GNU assembler manual,

            You can qualify the macro argument to indicate whether all invocations must specify a non-blank value (through ‘:req’), or whether it takes all of the remaining arguments (through ‘:vararg’). You can supply a default value for any macro argument by following the name with ‘=deflt’.

            And the example,

            Source https://stackoverflow.com/questions/71650696

            QUESTION

            Firebase Test Lab result fails radomly
            Asked 2022-Feb-03 at 21:20

            I'm currently working on a Unity application, where the app started to crash randomly in the firebase test lab. Earlier, my SDK version was 29 and every time I make an internal test, it works well with no issues. And recently, Google made it mandatory to keep the SDK version to 30. And from there, I started to face errors and failures in the test lab. I tried many different solutions. So sometimes, the test lab returns success with no issues. And I retest the same build, but the second time, it shows that A native crash was detected.

            These are the logs

            ...

            ANSWER

            Answered 2021-Dec-08 at 16:08

            Update your Unity Editor to something above 2020.

            Source https://stackoverflow.com/questions/70248131

            QUESTION

            Expo app working on Expo Go and iOS Simulator but crashes on real device
            Asked 2022-Jan-28 at 19:56

            I have an iOS Expo based project using the managed workflow. My app runs perfectly fine on the simulator and on Expo Go but on my device (installed with TestFlight) it crashes immediately after seeing the splash screen fade away for a second. Can anyone detect the problem is based on the below logs?

            Expo Diagnostics:

            ...

            ANSWER

            Answered 2022-Jan-28 at 19:56

            To answer my own issue, the problem was I had a switch statement at the top level of my app that did not have a corresponding break a the end of the case.

            Editing for clarity...

            Here was the offending code:

            Source https://stackoverflow.com/questions/70844025

            QUESTION

            CarryFrom operation on arm processors
            Asked 2021-Oct-30 at 23:18

            The Arm Architecture manual says for the ADC instruction to set the C (carry) flag in the CPSR if the S-Flag is set and a carry "occured". From the book (page 155):

            ...

            ANSWER

            Answered 2021-Oct-30 at 23:18

            Simply binary addition, x is the carry in to the operation and y is the carry out. For a normal add carry in is a 0 and for a normal subtract carry in is a 1. (adders are used to do subtraction, one of the features of twos complement)

            Source https://stackoverflow.com/questions/69698426

            QUESTION

            Understanding segmentation fault in core dump on NULL pointer check
            Asked 2021-Sep-16 at 19:25

            I am having difficulty understanding how this segmentation fault is possible. The architecture of the machine is armv7l.

            The core dump:

            ...

            ANSWER

            Answered 2021-Sep-16 at 19:25

            The assembly code resolves the address of global variable gl_pClient using dll relocations, which are loaded using program-counter-relative addressing. Then the code loads from that address and crashes. It looks like the relocations got corrupted, so that the resolved address is invalid.

            There isn't much else can be said without a reproduction.

            You may like to run your program under valgrind which may report memory corruption.

            Source https://stackoverflow.com/questions/69213753

            QUESTION

            Static variable getting pre initialized with random values
            Asked 2021-Sep-08 at 09:05

            Can someone please explain why a member variable (char m_DBFileName[257]) of static variable (g_JournalDB) getting initialized with a random value? I expect it to be populated with '\0's.

            More info: g_JournalDB is part of a dynamic library loaded on app startup via

            ...

            ANSWER

            Answered 2021-Sep-06 at 12:07

            Did you try m_DBFileName as std::string instead of char * or array?

            And please try to share a minimal reproducible example for static variable initialization.

            Source https://stackoverflow.com/questions/69032640

            QUESTION

            ARM64 Buffer Overflow-Cannot overwrite $pc
            Asked 2021-Aug-13 at 23:19

            This is the source code.

            ...

            ANSWER

            Answered 2021-Aug-13 at 23:19

            As you can see from the code, the compiler has placed the return address below the buffer on the stack, so it is impossible for you to overwrite it, no matter how many bytes you write.

            Specifically, stp x29, x30, [sp, #-96]! is pre-decrement, so it stores x29 at the new address of [sp], and x30, which contains the return address, at [sp, 8]. The buffer, on the other hand, is at [sp, 32] (note the add x0, sp, 0x20). This is typical for ARM64; the pre-decrement addressing mode makes it convenient to store the return address at the bottom of the stack frame, below all the function's local variables.

            What you may be able to overwrite instead is the return address saved by whatever function called main (somewhere in the C startup code, e.g. glibc's __libc_start_main()). That would only happen when that other function returns to its own caller, so you have stopped the program too soon.

            Unfortunately for you, on many systems, that function does not return at all; it calls exit() instead. That's what glibc's __libc_start_main does.. As such, unless I am missing something, this kind of buffer overflow will not work on such a system when gets is called from within main. If you want to play with it, try writing a different program where it's called from some subroutine:

            Source https://stackoverflow.com/questions/68774522

            QUESTION

            Crash on a protocol witness related issue
            Asked 2021-Jun-15 at 13:26

            In my iOS app "Progression" there is rarely a crash (1 crash in ~1000+ Sessions) I am currently not able to fix. The message is

            Progression: protocol witness for TrainingSetSessionManager.update(object:weight:reps:) in conformance TrainingSetSessionDataManager + 40

            This crash points me to the following method:

            ...

            ANSWER

            Answered 2021-Jun-15 at 13:26

            While editing my initial question to add more context as Jay proposed I think it found the issue.

            What probably happens? The view where the crash is, contains a table view. Each cell will be configured before being presented. I use a flag which holds the information, if the amount of weight for this cell (it is a strength workout app) has been initially set or is a change. When prepareForReuse is being called, this flag has not been reset. And that now means scrolling through the table view triggers a DB write for each reused cell, that leads to unnecessary writes to the db. Unnecessary, because the exact same number is already saved in the db.

            My speculation: Scrolling fast could maybe lead to a race condition (I have read something about that issue with realm) and that maybe causes this weird crash, because there are multiple single writes initiated in a short time.

            Solution: I now reset the flag on prepareForReuse to its initial value to prevent this misbehaviour.

            The crash only happens when the cell is set up and the described behaviour happens. Therefor I'm quite confident I fixed the issue finally. Let's see. -- I was not able to reproduce the issue, but it also only happens pretty rare.

            Source https://stackoverflow.com/questions/67947819

            QUESTION

            GDB - $EBP does not exist in register
            Asked 2021-May-23 at 15:19

            I have been trying to debug an C application on aarch64 and I want to get the $ebp value. However, when I tried to use the following command, I get an error:

            ...

            ANSWER

            Answered 2021-May-23 at 15:19

            I have been trying to debug an C application on aarch64 and I want to get the $ebp value.

            There is no such register on the aarch64 processor, and your question makes no sense.

            In general, in order to debug at the machine instruction level, you must understand the CPU architecture your program is executing on: registers available, instructions, procedure calling conventions, etc.

            Without such understanding debugging at the instruction level is impossible.

            To understand aarch64 architecture, you could start here.

            Source https://stackoverflow.com/questions/67650517

            QUESTION

            android app doesnt install in version 9 and above
            Asked 2021-Feb-25 at 16:33

            Good day all, pls the app that i created doesnt work on android versions 9, 10 and 11..

            I tested the app on lower versions and it worked perfectly but when tested on version 9, 10 or 11, the app keeps crashing

            I really appreciate if my question is answered. Thanks

            Below is my build.gradle file

            ...

            ANSWER

            Answered 2021-Feb-15 at 01:16

            You have a permissions problem here, in low versions of Android, when you install the app, it guarantees all the permissions, but in the latest Android APIs, you have to request permission at runtime, if you don't and for example try read your app's storage information then your app will be crash

            Source https://stackoverflow.com/questions/66179057

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

            Vulnerabilities

            No vulnerabilities reported

            Install cpsr

            Installation instructions
            Run through an example
            Learn more about Details regarding the CPSR input file, and how it should be formatted The types and contents of CPSR output files ACMG variant classification procedure used in CPSR The list of virtual gene panels available in CPSR

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