pav | Phased assembly variant caller | Genomics library
kandi X-RAY | pav Summary
kandi X-RAY | pav Summary
PAV is a tool for discovering variation using assembled genomes aligned to a reference. It is designed explicitly for phased assemblies, however, it can be used for squashed assemblies by providing an empty FASTA for the second haplotype. PAV was developed for the Human Genome Structural Variation Consortium (HGSVC). Peter Ebert et al., “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation,” Science, February 25, 2021, eabf7117,
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Top functions reviewed by kandi - BETA
- Scan for events for events
- Finds the left homology between two sequences
- Count the number of bases in a record
- Convert CIGAR string to tuples
- Remove overlapping contigs in a contig space
- Trim an alignment record
- Finds the cut - sites for the alignment
- Translate a cigar sequence to zero
- Calculate the smoothed density of a tigmer
- Plot the kmer density diagram
- Plot the kmer density plot
- Extract stats from a fasta file
- Calculate n_stat
- Filter dataframe by reference tree
- Filters a DataFrame with only the values in the given tree
- Get configuration overrides for assembly
- Get configuration overrides
- Return a copy of the config with the given override configuration
- Write a table to a file
- Convert a boolean value to a boolean
- Get list of filenames
- Get assembly configuration
- Get a list of assembly files
- Expand a FASTA file into a FASTA object
- Check the record error string for the record
- Count the number of reference k -mers in a region
pav Key Features
pav Examples and Code Snippets
Community Discussions
Trending Discussions on pav
QUESTION
I have an object like this:
...ANSWER
Answered 2021-Mar-20 at 11:05You can spread the the array obtained by Object.keys method and pass that to push method of the array like
QUESTION
I am practing to Scrape the websites so I choosed a website https://www.dunzo.com/bangalore/nilgiris-supermarket-koramangala-ejipura
Here is the code that I am using
...ANSWER
Answered 2021-Jan-02 at 17:06Try this:
QUESTION
I am modifying a current query which returns n amount of rows. I would need to return the same amount of rows but with one more column of data.
I have two sql tables shown below. Products and Product Attribute Values. When i run this query
...ANSWER
Answered 2020-Nov-18 at 15:08I think this is what you want
SELECT * FROM Product p inner JOIN ProductAttributeValues pav ON pav.SerialNo = p.SerialNo WHERE (p.DealerRowId = '10') AND pav.SerialNo IS NOT NULL
Does this solves your problem. Also, why are you using pav.Name = 'sequence' in where. You can try it in the ON clause if you want to join your columns based on names.
QUESTION
Hello and sorry if question is strange and sorry for bad english. My code:
...ANSWER
Answered 2020-Oct-29 at 10:30Try following :
QUESTION
I'm trying to get email addresses from another file onto the active workbook that is being used, however I only need certain email addresses based on a region that is in the file that we get every morning. I'm currently wondering if there is a way to grab these email addresses without having to open the email list as that dictates whether the vlookup works?
The code is as follows:
...ANSWER
Answered 2020-Oct-06 at 01:04If you are familiar with SQL queries I would recommend using ADODB connection. It is very fast. It doesn't flicker Excel and you dont need to open the file.
QUESTION
My first task every morning is to grab two files that are generated by another department. I then essentially "move" information around within the file to prepare for emails. One of the things that must be done is to have the addition of new sheets in which I was able to write a macro for and add it to the personal macro workbook. The issue that I'm running into however is that whenever new sheets are added, the macro will add them to the personal macro workbook instead of the file that I open every morning and need the sheets added to.
I believe this is in part to the section of the code (Below) that adds the sheets, however i am not sure what to use in place of this. Can someone please assist? Thanks
...ANSWER
Answered 2020-Sep-16 at 02:54The problem is that ThisWorkbook refers to the workbook where the code is actually running from, in your case, your personal macro workbook.
Change the code to refer to ActiveWorkbook, which addresses the workbook that is currently in the active window.
Best would be to create a proper workbook variable and use that to reference workbooks and sheets within workbooks without any doubt.
QUESTION
I am trying to build a bot to send requests in linkedin. But after running this code, it works till 42 line, then stop. how I can find out the error? There is a config.txt file containing user and password. For security purpose, I am not giving this file. Can anyone help me in this regard?
...ANSWER
Answered 2020-Jul-20 at 16:05debugging the practice on software development where you can find out what's happening to you code.
If you're using vs code here is how you debug.
Vs code is a nice code editor with plenty of plugins that turns it into an IDE
But there're another options, like PyCharm
QUESTION
In an existing Android App project (MVVM is used as pattern) I have found a PagerAdapter to swipe several information within this adapter:
...ANSWER
Answered 2020-Jul-03 at 10:46Question 1: databinding or synthetics could be used use instead of findViewById. This could be legacy code or given the id of the view, it is possible that there are more views with same id and the developer wanted to avoid ambiguity by searching in a specific layout.
Question 2: Injecting or passing context (in most cases) is an antipattern. If the context is needed it can be retrieved from the container. the difference between
QUESTION
ANSWER
Answered 2020-Jun-19 at 13:09The non-confident region(ie., algorithm not sure what this the correct disparity) is marked as black pixels in the disparity map. This is much expected behaviour.
You have to do some post processing to fill the map. Use Guided filter to complete map. If matlab provides any guided filter you can try once. In OpenCV "WLS" is the most common guided filter to get a filled map.
QUESTION
I have a video file with 2 dot laser and I want to calculate the distance in pixels between them, I tried this code with OpenCV, but it is not working :
...ANSWER
Answered 2020-Jun-10 at 03:56You can do this:
- The function cv2.InRange() to find two red dots.
- The function cv2.connectedComponentsWithStats() to find the centroids of these red points.
- Calculate the Euclidean distance between centroids.
Also, you can select points by brightness only, without even using their color.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install pav
You can use pav like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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