UNCALLED | Raw nanopore signal mapper | Genomics library
kandi X-RAY | UNCALLED Summary
kandi X-RAY | UNCALLED Summary
A Utility for Nanopore Current Alignment to Large Expanses of DNA. A read mapper which rapidly aligns raw nanopore signal to DNA references. Enables software-based targeted sequenceing on Oxford Nanopore (ONT) MinION or GridION via ReadUntil. Also includes a simulator which can be used to predict how much enrichment could be achieved on a given reference using raw signal data from previous nanopore runs.
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QUESTION
Moving from using Intel compiler & VC to Apple clang 12.0.
In my code there are functions that are never called for a certain project (but needed when included in other projects). Clang insists on compiling the uncalled functions and detects errors, where Intel and VC simply skipped compilation.
These are errors that are tricky to fix for that certain project.
Is there a Clang flag that means "Don't compile if not called"?
EDIT: example:
...ANSWER
Answered 2021-Jan-01 at 18:50Clang has a mode in which is tries to behave as if it's MSVC. This was introduced as part clang-cl, the driver for clang that accepts a lot of the same arguments as MSVC. You can find some information about it on the user manual and the MSVC compatibility pages.
Long story short, there is an option -fdelayed-template-parsing in clang that takes over the faulty behavior of the templates. As far as I'm aware, this ain't a 100% match, however, it is good enough.
If we add this to the example of Artyer, it compiles the code, see compiler-explorer.
From my experience of adding clang as 2nd compiler next to MSVC (it was still both on Windows using clang-cl, I didn't have to deal with the complexity of multiple OS and/or STL), I want to recommend to you to take this option as a temporary thing to get things working. Take your time removing this, as it will help making your code more maintainable.
EDIT: If you want to know more about why the compilation error is the right thing to do, you can lookup the term 2 phase lookup. You can find the announcement of it's introduction in the MSVC compiler here: https://devblogs.microsoft.com/cppblog/two-phase-name-lookup-support-comes-to-msvc/
From what I can see online, the intel compiler ain't doing 2 phase lookup either, or at least not the reporting of the errors.
QUESTION
I want to know if I for example wrote 100 function in a class or even without a class and only used one function in each time I call the class, Does these too many uncalled and unused functions influence the performance or count for something negative?
...ANSWER
Answered 2020-Jul-20 at 18:00The answer is practically no. Chunks of code that aren't executed don't influence the performance of the program. This is true for most / all programming languages - not just Python.
That being said, there are some scenarios where this is not accurate:
- If your program is very large, it may take a while to load. Once it loads, the execution time with or without the redundant code is the same, but there's a difference in load time.
- More code may impact memory organization, which in turn may impact the OS' ability to cache stuff in an effective manner. It's an indirect impact, and unless you know exactly what you're doing it's mostly theoretical.
- If you have a very large number of methods in a class, looking up a given method in a class' dictionary may take longer. The average cost of getting an item from a dict is O(1), but worst case can be O(N). You'll have to do a lot of optimization to (maybe) get to a point where you care about this.
- There might be some other obscure scenarios in which code size impacts performance - but again, it's more theory than practice.
QUESTION
I was wondering about this because I am planning to load my js file containing a lot of functions so I can efficiently call them whenever I needed them.
So I can efficiently not create a redundant function on the other page. Any answer is greatly appreciated.
And i am wondering if the uncalled functions will increase the page's loading time.
...ANSWER
Answered 2020-Jun-10 at 04:12They do add load time but it's not much if we're talking individual functions.
My question is why do you want to add functions you might use?
QUESTION
print(Exception is Exception())
print(Exception == Exception())
print(type(Exception))
print(type(Exception())
try:
raise Exception
except Exception:
print("Caught Exception with Exception")
try:
raise Exception()
except Exception:
print("Caught Exception() with Exception")
try:
raise Exception
except Exception():
print("Caught Exception with Exception()")
try:
raise Exception()
except Exception():
print("Caught Exception() with Exception()")
ANSWER
Answered 2020-Jun-08 at 06:34The difference is that Exception is a type and Exception() is an instance of that class.
Therefore, when you raise an exception you raise an instance of that class:
QUESTION
regular date index show fine, but once I add style it adds ugly midnight hours, how do I ged rid of these? here is an example:
...ANSWER
Answered 2020-Jun-07 at 11:10If possible you can convert values to dates:
QUESTION
I am trying to make a simple time-based script where the user inputs:
- Time after starting the script to call an object, called
dt_call- Generated by
time.perf_counter()(aka it's afloat)
- Generated by
- Object to call at that time
Is there a Python library that has a key-value store that meets the following conditions?
- Keys are
float - Values are
object - Keys are sorted
More Information
This will be part of a scheduler, where every so often the scheduler:
- Gets the current time since starting the script (sec), called
dt - Maybe call the object, depending on if it's call time has passed
- Looks to see
if dT >= dt_call - If yes: check if the associated object has been called. If uncalled, then call the object.
- If no: do nothing
- Looks to see
Current Best Idea
Currently, my best idea is based on this: Sort a list of tuples by 2nd item (integer value)
Before starting the script:
- Store
dt_call+ object pairs in atuple - Store all pairs in a list
- Sort using this: https://stackoverflow.com/a/44852626/11163122
ANSWER
Answered 2020-May-10 at 02:18Your mention needing a data structure which allows:
QUESTION
I'm working with an IAR project where there are ILINK Configuration Files (.icf) for both a bootloader and the main application. Each file defines the __ICFEDIT_intvec_start__ symbol and later places it referencing their respective .intvec sections (there are 2 cstartup.s files, each with their own .intvec section):
Bootloader .icf:
ANSWER
Answered 2020-Feb-06 at 15:35It seems that the answer is a lot more obvious than I thought. According to the section "Linking—an overview" in "IAR C/C++ Development Guide", IAR's linker software ILINK ignores duplicate sections. Thus, if a section is already referenced in one binary object or ILINK configuration file (ICF), all other references to it are ignored.
In this project, since the bootloader takes precedence (is loaded and flashed before the application [defined in the project's .board files; more info here]), the application code's .intvec is seen as a duplicate and is thus ignored/discarded.
QUESTION
I would like to extend an allocatable attribute of a structure and MOVE_ALLOC() seems the cleanest way to do it. So I created a routine using a Pointer, Intent(in) pointing to the structure as argument and tried to call:
ANSWER
Answered 2020-Jan-29 at 21:33For a pointer dummy argument the intent(in) attribute means that the pointer shall not appear in a so-called pointer association context. Loosely, this means that you aren't allowed to (potentially) change the pointer association of the dummy argument. You are allowed the change the value of the target of this pointer.
For a pointer dummy argument the intent(in) attribute does not "cascade" to the subojects of the argument (such as in this case the component arrayofint): the component arrayofint of the target of str1 does not have the intent(in) attribute.
In a reference like str1%arrayofint with str1 a pointer, this is a reference to the component arrayofint of the target of str1. Even if the intent(in) attribute did apply to subobjects of the pointer dummy argument the object referenced by str1%arrayofint is not a subobject of str1.
ifort is wrong to think that such an object has the intent(in) attribute. You have found a valid way to work around such shortcomings in ifort. You should consider reporting this flaw to Intel.
Finally, there may be better ways to solve your problem of resizing the component without using pointer dummy arguments, but I won't consider those in this answer.
QUESTION
I am running delta streaming queries and I keep getting zillions of updates and QueryProgressEvent intercepted by StreamingQueryListener while "Nothing" is really happening - or so it seems.
Why are those event fired if no rows were detected to be processed ? What is considered a "progress" ?
To me this is just log pollution that is uncalled for, and I had to find a way to mute it until something is "really" happening, but I still am curious on the why and how.
...ANSWER
Answered 2020-Jan-02 at 02:12Why are those event fired if no rows were detected to be processed ?
Structured Streaming is not event driven. A structured stream runs either continuously or through micro batching.
- Continuous: Your stream is running nonstop. As soon as one run ends, the next begins.
- Microbatching: Your stream runs on an interval based on your trigger rule (say 5 seconds). When one stream run ends, it waits 5 seconds until re-running.
In either case, the stream always checks to see if there any new files in its input location to process. If there are new files, it processes them as configured and writes the file names to its checkpoint so that those files are not re-processed as new. If there are no new files, it finishes the run as it sees that there is no work to. That is why these events are fired even if no rows are detected.
What is considered a "progress" ?
Progress is seen as the conclusion of a successful run, as shown by the logs you posted. The stream made "progress" by running.
QUESTION
I have 3 Tables:
Customers
- id
- name
Sales
- customer_id
- sale_date
Contacts
- customer_id
- contact_date
There aren't any update operations in the contacts table. Each process opens a new record in the contacts table. So, a user can have more than one records in the contacts table.
Here are my relations in models:
Customer
ANSWER
Answered 2019-Sep-03 at 14:09I'm not sure, but can you try to do the following:
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