paper | Python align paired-end reads

 by   qks1lver Python Version: Current License: No License

kandi X-RAY | paper Summary

kandi X-RAY | paper Summary

paper is a Python library. paper has no bugs, it has no vulnerabilities and it has low support. However paper build file is not available. You can download it from GitHub.

This is primarily for colleagues at Carnegie Institute for Science, Stanford.
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              paper has a low active ecosystem.
              It has 0 star(s) with 0 fork(s). There are 1 watchers for this library.
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              It had no major release in the last 6 months.
              paper has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of paper is current.

            kandi-Quality Quality

              paper has 0 bugs and 0 code smells.

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

            kandi-License License

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

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              paper releases are not available. You will need to build from source code and install.
              paper has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are available. Examples and code snippets are not available.
              It has 424 lines of code, 18 functions and 3 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed paper and discovered the below as its top functions. This is intended to give you an instant insight into paper implemented functionality, and help decide if they suit your requirements.
            • Write a slurm job file .
            • Generate bash script .
            • Parse local alignment file .
            • Initialize parameters .
            • Assign the relationship between two hits .
            • Submit bwa files
            • Submits the given bash script .
            • Get unmapped files .
            • Run local alignment .
            Get all kandi verified functions for this library.

            paper Key Features

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            paper Examples and Code Snippets

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            Community Discussions

            QUESTION

            Indexed Initial algebras for GADTs
            Asked 2022-Mar-31 at 09:23

            In his paper Generics for the Masses Hinze reviews encoding of data type.

            Starting from Nat

            ...

            ANSWER

            Answered 2022-Mar-14 at 18:05

            The difference is the category. Nat is an initial algebra in the category of types. Rep is an initial algebra in the category of indexed types. The category of indexed types has as objects type constructors of kind * -> *, and as morphisms from f ~> g, functions of type forall t. f t -> g t.

            Then Rep is the initial algebra for the functor RepF defined as follows:

            Source https://stackoverflow.com/questions/71469359

            QUESTION

            Why does the type signature of linear array change compared to normal array?
            Asked 2022-Feb-28 at 10:13

            I'm going through an example in A Taste of Linear Logic.

            It first introduces the standard array with the usual operations defined (page 24):

            Then suggests that a linear equivalent (using a linear logic for type signatures to restrict array copying) would have a slightly different type signature:

            This is designed with the idea that array contains values that are cheap to copy but that the array itself is expensive to copy and thus should be passed along from use to use as a handle.

            Question: The signatures for lookup and update correspond well to the standard signatures, but how do I interpret the signature for new?

            In particular:

            • The function new does not seem to return an array. How can I get an array to use if one is not provided?
            • I think I do understand that Arr –o Arr x X is not derivable using linear logic and therefore a function to extract individual values without consuming the array is needed, but I don't understand why new doesn't provide that function directly
            ...

            ANSWER

            Answered 2022-Feb-28 at 10:13

            In practical terms, this is about garbage collection.

            Linear logic avoids making copies as well as leaving unused values lying around. So when you create an array with new, you also need to make sure it's eventually cleaned up again.

            How can you make sure it is cleaned up? Well, in this example they do it by not giving back the array as the result, but instead “lending” it to the caller. The function ArrArrX must give an array back in the end, in addition to the result you're actually interested in. It's assumed that this will be a modified form of the array you started out with. Only the X is passed back to the caller, the Arr is deallocated.

            Source https://stackoverflow.com/questions/71292714

            QUESTION

            expo-barcode-scanner only works once with react-native version 0.64.2 and expo 43.0.0
            Asked 2022-Jan-12 at 17:35

            Because of Google Play, I had to update an old project of mine to the latest expo versions (version 43.0.0 to be exact). The idea is for the app to scan a QRCode and process the data, simply. However, expo-barcode-scanner only works once and after that I need to close and open the app again to work. Has anyone encountered this problem and (or) knows how to solve it? Below is my code:

            ...

            ANSWER

            Answered 2021-Nov-12 at 21:14

            Welcome @Backup Gov18,

            This is a documented issue.

            Note: Only one active BarCodeScanner preview is supported currently. When using navigation, the best practice is to unmount any previously rendered BarCodeScanner component so the following screens can use without issues.

            There is a workaround.

            Instead of conditionally rendering the component, you could render it inside another dedicated screen component.

            This way, after this new screen reads the barcode, you could navigate back to your first screen. Navigating back may unmount this new screen. You can force unmount if you need to.

            As you are using react-navigation, you had better use .pop() instead of goBack().

            Alternative

            You can also use expo-camera instead of expo-barcode-scanner. expo-camera does not have this issue. It also offers more options like flashlight/torch and switching cameras.

            Source https://stackoverflow.com/questions/69857156

            QUESTION

            Why is it allowed for the C++ compiler to opmimize out memory allocations with side effects?
            Asked 2022-Jan-09 at 20:34

            Another question discusses the legitimacy for the optimizer to remove calls to new: Is the compiler allowed to optimize out heap memory allocations?. I have read the question, the answers, and N3664.

            From my understanding, the compiler is allowed to remove or merge dynamic allocations under the "as-if" rule, i.e. if the resulting program behaves as if no change was made, with respect to the abstract machine defined in the standard.

            I tested compiling the following two-files program with both clang++ and g++, and -O1 optimizations, and I don't understand how it is allowed to to remove the allocations.

            ...

            ANSWER

            Answered 2022-Jan-09 at 20:34

            Allocation elision is an optimization that is outside of and in addition to the as-if rule. Another optimization with the same properties is copy elision (not to be confused with mandatory elision, since C++17): Is it legal to elide a non-trivial copy/move constructor in initialization?.

            Source https://stackoverflow.com/questions/70645211

            QUESTION

            What is the significance of 'strongly happens before' compared to '(simply) happens before'?
            Asked 2022-Jan-02 at 18:21

            The standard defines several 'happens before' relations that extend the good old 'sequenced before' over multiple threads:

            [intro.races]

            11 An evaluation A simply happens before an evaluation B if either

            (11.1) — A is sequenced before B, or
            (11.2) — A synchronizes with B, or
            (11.3) — A simply happens before X and X simply happens before B.

            [Note 10: In the absence of consume operations, the happens before and simply happens before relations are identical. — end note]

            12 An evaluation A strongly happens before an evaluation D if, either

            (12.1) — A is sequenced before D, or
            (12.2) — A synchronizes with D, and both A and D are sequentially consistent atomic operations ([atomics.order]), or
            (12.3) — there are evaluations B and C such that A is sequenced before B, B simply happens before C, and C is sequenced before D, or
            (12.4) — there is an evaluation B such that A strongly happens before B, and B strongly happens before D.

            [Note 11: Informally, if A strongly happens before B, then A appears to be evaluated before B in all contexts. Strongly happens before excludes consume operations. — end note]

            (bold mine)

            The difference between the two seems very subtle. 'Strongly happens before' is never true for matching pairs or release-acquire operations (unless both are seq-cst), but it still respects release-acquire syncronization in a way, since operations sequenced before a release 'strongly happen before' the operations sequenced after the matching acquire.

            Why does this difference matter?

            'Strongly happens before' was introduced in C++20, and pre-C++20, 'simply happens before' used to be called 'strongly happens before'. Why was it introduced?

            [atomics.order]/4 says that the total order of all seq-cst operations is consistent with 'strongly happens before'.

            Does it mean that it's not consistent with 'simply happens before'? If so, why not?

            I'm ignoring the plain 'happens before', because it differs from 'simply happens before' only in its handling of memory_order_consume, the use of which is temporarily discouraged, since apparently most (all?) major compilers treat it as memory_order_acquire.

            I've already seen this Q&A, but it doesn't explain why 'strongly happens before' exists, and doesn't fully address what it means (it just states that it doesn't respect release-acquire syncronization, which isn't completely the case).

            Found the proposal that introduced 'simply happens before'.

            I don't fully understand it, but it explains following:

            • 'Strongly happens before' is a weakened version of 'simply happens before'.
            • The difference is only observable when seq-cst is mixed with aqc-rel on the same variable (I think, it means when an acquire load reads a value from a seq-cst store, or when an seq-cst load reads a value from a release store). But the exact effects of mixing the two are still unclear to me.
            ...

            ANSWER

            Answered 2022-Jan-02 at 18:21

            Here's my current understanding, which could be incomplete or incorrect. A verification would be appreciated.

            C++20 renamed strongly happens before to simply happens before, and introduced a new, more relaxed definition for strongly happens before, which imposes less ordering.

            Simply happens before is used to reason about the presence of data races in your code. (Actually that would be the plain 'happens before', but the two are equivalent in absence of consume operations, the use of which is discouraged by the standard, since most (all?) major compilers treat them as acquires.)

            The weaker strongly happens before is used to reason about the global order of seq-cst operations.

            This change was introduced in proposal P0668R5: Revising the C++ memory model, which is based on the paper Repairing Sequential Consistency in C/C++11 by Lahav et al (which I didn't fully read).

            The proposal explains why the change was made. Long story short, the way most compilers implement atomics on Power and ARM architectures turned out to be non-conformant in rare edge cases, and fixing the compilers had a performance cost, so they fixed the standard instead.

            The change only affects you if you mix seq-cst operations with acquire-release operations on the same atomic variable (i.e. if an acquire operation reads a value from a seq-cst store, or a seq-cst operation reads a value from a release store).

            If you don't mix operations in this manner, then you're not affected (i.e. can treat simply happens before and strongly happens before as equivalent).

            The gist of the change is that the synchronization between a seq-cst operation and the corresponding acquire/release operation no longer affects the position of this specific seq-cst operation in the global seq-cst order, but the synchronization itself is still there.

            This makes the seq-cst order for such seq-cst operations very moot, see below.

            The proposal presents following example, and I'll try to explain my understanding of it:

            Source https://stackoverflow.com/questions/70554277

            QUESTION

            Why does the C++23 ranges adaptor require a callable object to be copy_­constructible?
            Asked 2021-Dec-30 at 09:31

            Some ranges adaptors such as filter_­view, take_­while_­view and transform_view use std::optional's cousin copyable-box to store the callable object:

            ...

            ANSWER

            Answered 2021-Oct-09 at 14:20

            All the algorithms require copy-constructible function objects, and views are basically lazy algorithms.

            Historically, when these adaptors were added, views were required to be copyable, so we required the function objects to be copy_constructible (we couldn't require copyable without ruling out captureful lambdas). The change to make view only require movable came later.

            It is probably possible to relax the restriction, but it will need a paper and isn't really high priority.

            Source https://stackoverflow.com/questions/69507047

            QUESTION

            Detecting compile-time constantness of range size
            Asked 2021-Dec-30 at 08:54

            compiler explorer link

            Consider the following:

            ...

            ANSWER

            Answered 2021-Dec-30 at 08:54

            If you look closely at the specification of ranges​::​size in [range.prim.size], except when the type of R is the primitive array type, ranges​::​size obtains the size of r by calling the size() member function or passing it into a free function.

            And since the parameter type of transform() function is reference, ranges::size(r) cannot be used as a constant expression in the function body, this means we can only get the size of r through the type of R, not the object of R.

            However, there are not many standard range types that contain size information, such as primitive arrays, std::array, std::span, and some simple range adaptors. So we can define a function to detect whether R is of these types, and extract the size from its type in a corresponding way.

            Source https://stackoverflow.com/questions/70482497

            QUESTION

            Why is is_trivially_copyable_v different in GCC and MSVC?
            Asked 2021-Dec-08 at 16:06

            When running this simple program, different behaviour is observed depending on the compiler.

            It prints true when compiled by GCC 11.2, and false when compiled by MSVC 19.29.30137 with the (both are the latest release as of today).

            ...

            ANSWER

            Answered 2021-Dec-08 at 16:06

            GCC and Clang report that S is trivially copyable in C++11 through C++23 standard modes. MSVC reports that S is not trivially copyable in C++14 through C++20 standard modes.

            N3337 (~ C++11) and N4140 (~ C++14) say:

            A trivially copyable class is a class that:

            • has no non-trivial copy constructors,
            • has no non-trivial move constructors,
            • has no non-trivial copy assignment operators,
            • has no non-trivial move assignment operators, and
            • has a trivial destructor.

            By this definition, S is trivially copyable.

            N4659 (~ C++17) says:

            A trivially copyable class is a class:

            • where each copy constructor, move constructor, copy assignment operator, and move assignment operator is either deleted or trivial,
            • that has at least one non-deleted copy constructor, move constructor, copy assignment operator, or move assignment operator, and
            • that has a trivial, non-deleted destructor

            By this definition, S is not trivially copyable.

            N4860 (~ C++20) says:

            A trivially copyable class is a class:

            • that has at least one eligible copy constructor, move constructor, copy assignment operator, or move assignment operator,
            • where each eligible copy constructor, move constructor, copy assignment operator, and move assignment operator is trivial, and
            • that has a trivial, non-deleted destructor.

            By this definition, S is not trivially copyable.

            Thus, as published, S was trivally copyable in C++11 and C++14, but not in C++17 and C++20.

            The change was adopted from DR 1734 in February 2016. Implementors generally treat DRs as though they apply to all prior language standards by convention. Thus, by the published standard for C++11 and C++14, S was trivially copyable, and by convention, newer compiler versions might choose to treat S as not trivially copyable in C++11 and C++14 modes. Thus, all compilers could be said to be correct for C++11 and C++14.

            For C++17 and beyond, S is unambiguously not trivially copyable so GCC and Clang are incorrect. This is GCC bug #96288 and LLVM bug #39050

            Source https://stackoverflow.com/questions/70267387

            QUESTION

            Is std::decay_t decay_copy(T&&) equivalent to auto decay_copy(auto&&)?
            Asked 2021-Nov-19 at 06:47

            ANSWER

            Answered 2021-Oct-26 at 20:04

            It wasn't in 2011, because:

            • We didn't have auto return type deduction for functions (that's a C++14 feature), and
            • We didn't have auto&& parameters for functions (that's a C++20 feature), and
            • Rvalue references were not implicitly moved from in return statements (that's also a C++20 feature)

            But in C++20, yes, that is now a valid way to implement decay_copy. auto deduction does decay, return v; implicitly forwards, and everything else is the same.

            I guess technically there's an edge case like:

            Source https://stackoverflow.com/questions/69729033

            QUESTION

            How to calculate correlation coefficients using sklearn CCA module?
            Asked 2021-Nov-16 at 18:53

            I need to measure similarity between feature vectors using CCA module. I saw sklearn has a good CCA module available: https://scikit-learn.org/stable/modules/generated/sklearn.cross_decomposition.CCA.html

            In different papers I reviewed, I saw that the way to measure similarity using CCA is to calculate the mean of the correlation coefficients, for example as done in this following notebook example: https://github.com/google/svcca/blob/1f3fbf19bd31bd9b76e728ef75842aa1d9a4cd2b/tutorials/001_Introduction.ipynb

            How to calculate the correlation coefficients (as shown in the notebook) using sklearn CCA module?

            ...

            ANSWER

            Answered 2021-Nov-16 at 10:07

            In reference to the notebook you provided which is a supporting artefact to and implements ideas from the following two papers

            1. "SVCCA: Singular Vector Canonical Correlation Analysis for Deep Learning Dynamics and Interpretability". Neural Information Processing Systems (NeurIPS) 2017
            2. "Insights on Representational Similarity in Deep Neural Networks with Canonical Correlation". Neural Information Processing Systems (NeurIPS) 2018

            The authors there calculate 50 = min(A_fake neurons, B_fake neurons) components and plot the correlations between the transformed vectors of each component (i.e. 50).

            With the help of the below code, using sklearn CCA, I am trying to reproduce their Toy Example. As we'll see the correlation plots match. The sanity check they used in the notebook came very handy - it passed seamlessly with this code as well.

            Source https://stackoverflow.com/questions/69800500

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            Vulnerabilities

            No vulnerabilities reported

            Install paper

            Currently no wheel, sorry! So just clone the repository and navigate to src/ folder and run. Essentially follow these steps:.
            Open a terminal and log into a server (i.e. Memex)
            navigate to a directory that you are willing to store this tool in
            Clone repo by typing this in terminal: git clone https://github.com/qks1lver/paper.git This creates a folder called paper/ with all the codes inside

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