codoc | open file format and API for the lossless and lossy | Genomics library
kandi X-RAY | codoc Summary
kandi X-RAY | codoc Summary
CODOC is an open file format and API for the lossless and lossy compression of depth-of-coverage (DOC) signals stemming from high-throughput sequencing (HTS) experiments. DOC data is a one-dimensional signal representing the number of reads covering each reference nucleotide in a HTS data set. DOC is highly-valuable information for interpreting (e.g., RNA-seq), filtering (e.g., SNP analysis) or detecting novel features (e.g., structural variants) in sequencing data sets. CODOC exploits several characteristics of DOC data stemming from HTS data and uses a non-uniform quantization model that preserves DOC signals in low-coverage regions nearly perfectly while allowing more divergence in highly covered regions. CODOC reduces required file sizes for DOC data up to 3500X when compared to raw representations and about 4-32X when compared to the other methods. The CODOC API supports efficient sequential and random access to compressed data sets.
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Top functions reviewed by kandi - BETA
- Compresses the block data
- Gzip a file
- Copy a file to a output file
- Creates a temporary file with the given prefix
- Processes a single entity
- Emit a string
- Close the stream
- Push a data object
- Runs the version information
- Main launcher for testing
- Load the coverage data from the coverage file
- Main entry point for testing
- Main method for testing
- Gets the values of all properties
- Parses a compressed header from a string
- Returns the next object from the stream
- Closes this stream
- Calculate the mupos from the WigFile
- Determines the number of bytes used in the given file
- Decompress the block data
- Push data to the rle
- Calculates and returns the mean difference between 0 and maxPos
- Dump the header
- Pushes data to the stream
- Calculate the mupos difference between 0 and maxPos
- Queries the coverage data in the specified range of coverage
codoc Key Features
codoc Examples and Code Snippets
Lines of Code : 12
License : No License
Copy$ java -jar bin/codoc-0.0.1.jar
$ java -jar bin/codoc-0.0.1.jar compress
$ java -jar bin/codoc-0.0.1.jar decompress
$ java -jar bin/codoc-0.0.1.jar tools
$ java -jar bin/codoc-0.0.1.jar compress -bam -qmethod GRID -qparam 5 -filter "FLAGS^^1024" -f _________ ___ ____ _____
/ ___/ __ \/ _ \/ __ \/ ___/
/ /__/ /_/ / // / /_/ / /__
\___/\____/____/\____/\___/
Welcome to the CODOC project
----------------------------
MAPQ the mapping quality
FLAGS the read flags
STRAND the read strand (+/-)
FOPSTRAND the first-of-pair read strand (+/-)
-filter 'MAPQ>20' -filter 'H0=1'
Community Discussions
Trending Discussions on codoc
QUESTION
I have followed this example and tried to put a FlatList in one of the Tabs, but I can't get it to display.
So, this is my modification on the code :
...ANSWER
Answered 2021-Mar-24 at 16:22You need to do item.item.codoc in the renderItem.
More information in this post
Edit
I use this code.
QUESTION
I have a form with 1 input (file type) and I want to send zip file to serve, in server i cannot get any update in my database nor any file in my storage.
CodeForm
...ANSWER
Answered 2019-Nov-18 at 02:48Thanks for all down votes with no solution providing! here is how i solved my issue hope it help those in need:
View
QUESTION
I created a some custom fields for Woocommerce in the check-out page. I was able to display them in WP admin area, email and invoices but not in the Front-End for User's Dashboard.
This is the code I used to create the field "CODICE SNEP" in my CHILD-THEM on function.php file:
ANSWER
Answered 2018-Jun-29 at 09:08The code you are using is a bit outdated and/or some hooks are deprecated (even if they come from Woocommerce documentation).
The code below uses different hooks. It allows to display this field and the related data (when it exist), in checkout and in My account > Adresses > Billing fields, without any need of additional validation code.
Also when order is placed, the data is saved with one hook in the order and in the user meta data at the same time. So the code is more compact and uses the right hooks with the new CRUD methods introduced in Woocommerce 3.
Your revisited code:
QUESTION
I am using firebase. I have 2 collections - User Docs and Docs. I am iterating through the User Docs to get the Docs which will then return an array of docs under a User. As the parent key (as shown in code below) lies in the first loop, how can I access it in my child loop? ( I need the parent key because it contains the unique values which I require for my FlatList component). Thanks a lot for your guidance in advance :)
...ANSWER
Answered 2018-Jul-12 at 06:50There are 2 ways you can use it
1) Store it in variable
QUESTION
I have been asked to update my package Bolstad so that the definition of my S3 median method agrees with the new median generic in R 3.4.0. This means is needs to be able to deal with ... - That is fine, but I also need it to work with roxygen2. Here is my function definition etc.:
ANSWER
Answered 2017-Mar-30 at 22:29The solution that has gone up on CRAN is given below (based on something Kurt Hornik sent me). However, it too has a downside in that roxygen2 does not generate a help file for the median function.
QUESTION
how to remove empty line in between two firm.
...ANSWER
Answered 2017-Mar-22 at 21:32You have three different lines that say row = row + 1, within three nested loops. If you trace the logic for your first case, you encounter one of these for each of the three surveying assistants (sadoc), one for the land surveyor (lsdoc), and then one for the firm. That's five times that you execute row = row + 1 but you only generated three lines of data because the lsdoc information and firm information are on the same line as the first sadoc information.
If there is always at least one sadoc for each lsdoc, and always only one land surveyor for each firm, then the answer is easy: just get rid of the two extra row = row + 1 lines. Unfortunately, I see that you have a case where there is more than one lsdoc for one firm, and in that same case there is no sadoc for the second lsdoc for the firm so it's not going to be that simple.
You're going to have to keep track and only execute row = row + 1 when it is really necessary. I.e., change this
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install codoc
You can use codoc like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the codoc component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .
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