chisel | CHISEL -- Copy-number Haplotype Inference | Genomics library

by raphael-group Python Version: v1.1.4 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | chisel Summary

chisel is a Python library typically used in Artificial Intelligence, Genomics applications. chisel has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub.

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

Support

Quality

Security

License

Reuse

Support

chisel has a highly active ecosystem.

It has 34 star(s) with 10 fork(s). There are 10 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 22 have been closed. On average issues are closed in 79 days. There are 1 open pull requests and 0 closed requests.

It has a positive sentiment in the developer community.

The latest version of chisel is v1.1.4

Quality

chisel has 0 bugs and 0 code smells.

Security

chisel has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

chisel code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

chisel is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

chisel releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

chisel saves you 1166 person hours of effort in developing the same functionality from scratch.

It has 2631 lines of code, 124 functions and 17 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed chisel and discovered the below as its top functions. This is intended to give you an instant insight into chisel implemented functionality, and help decide if they suit your requirements.

K - clustering
Generate a new shared share matrix
K clustering
Calculate the ordinal value of a grid
Parse command line arguments
Log a message to stderr
Return the full path to a program
Run k clustering
Generate a random indoice from weights
Match fastq files
Make fastqinfo output files
Run alignment
Align BAM files
Generate rbplot plot
Compute the total cns
Make fastqinfo from input files
Run a shell command
Run BAM
Reads the cells from the file
Setup the folder
Perform alignment of markers
Read a TSV file
Make the rdr plot
Make the cbaf plot
Calculate alleles
Create marker for a barcode job
Simulate sequencing stats

Get all kandi verified functions for this library.

chisel Key Features

No Key Features are available at this moment for chisel.

chisel Examples and Code Snippets

No Code Snippets are available at this moment for chisel.

Community Discussions

Trending Discussions on chisel

Can chisel print time like verilog

how to set generated directory of emitVerilog?

Scala/Chisel Data to be connected must be hardware, not a bare Chisel type

Scala Chisel Ripple Carry Adder Syntax

Using existing Scala Class in new Class [Scala Chisel]

Retrieve values from deep array PHP

Chisel: How to wait for signal assertion in ChiselScalatestTester?

Creating string debug Vec for state machine

Can I compute constants in software before Chisel begins designing hardware?

Returning multiple elements for apply method

QUESTION

Can chisel print time like verilog

Asked 2021-May-26 at 17:58

In digital circuit simulation verification, time is a very important parameter. Verilog can use the $time function to obtain simulation time. I want to know if chisel has the same function.

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ANSWER

Answered 2021-May-26 at 17:58

I do not believe that Chisel has this functionality. However if there is something you need to use this for inside of a design, you can always create a Chisel BlackBox and include the $time print in that.

Chisel generally only prints synthesizable Verilog. That being said, it's possible someone has a library that includes this and can extend the print through a FIRRTL transform.

Source https://stackoverflow.com/questions/67656174

QUESTION

how to set generated directory of emitVerilog?

Asked 2021-May-25 at 16:17

I just started with chisel-template.

I added below statement in DecoupledGCD.scala per a stackoverflow post.

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ANSWER

Answered 2021-May-23 at 19:26

Set the arguments as a call to the ChiselStage. Below is an example. This will put the Verilog and FIRRTL in the output dir. The output dir will be created if it doesn't exists.

Source https://stackoverflow.com/questions/67657956

QUESTION

Scala/Chisel Data to be connected must be hardware, not a bare Chisel type

Asked 2021-May-15 at 21:52

im trying to design the following Ripple Carry Adder made of Fulladers. I tried a lot so far, but I'm struggling with Chisel Syntax. Could someone help me out and point out what I'm doing wrong? This is my Code below:

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ANSWER

Answered 2021-May-15 at 21:52

| Stevo | is right about the Wire wrapper being necessary but there are a couple of other errors.

Add Wire wrapper to summ and carry
Your for statement should use until and not to
Should be io.cout := carry(n) not n+1

The following code should work.

Source https://stackoverflow.com/questions/67536239

QUESTION

Scala Chisel Ripple Carry Adder Syntax

Asked 2021-May-14 at 17:21

...

ANSWER

Answered 2021-May-14 at 17:21

You are very close to getting it working. One problem you are having is that you cannot assign to a bit subset on the left hand side of :=. One way of getting around this is to create a Vec of UInt(1.W) and then use that as the RHS as a single as a single assignment. I think you have a problem with your ifs, I'd recommend using foldLeft instead of for because it provides a mechanism of accessing the previous elements. Put that all together and I think what you want is something like this.

Source https://stackoverflow.com/questions/67534935

QUESTION

Using existing Scala Class in new Class [Scala Chisel]

Asked 2021-May-14 at 14:19

This is probably a very basic question, but for the life of me I could not find an answer.

I have this existing logical AND class:

...

ANSWER

Answered 2021-May-13 at 23:59

val a_and_b = Module(new DelayedAND(2))
a_and_b.io.a  := io.a
a_and_b.io.b  := io.b
io.cout       := a_and_b.io.out

Source https://stackoverflow.com/questions/67519994

QUESTION

Retrieve values from deep array PHP

Asked 2021-Apr-24 at 06:24

I have a 3 deep array. Currently, the code will isolate a record based on one field ($profcode) and show the heading. Eventually, I am going to build a table showing the information from all the other fields. The code so far is using in_array and a function that accepts $profcode. I am unsure if (and how) I need to use array_keys() to do the next part when I retrieve the "Skills" field. I tried:

...

ANSWER

Answered 2021-Apr-23 at 21:05

I picked from your code and ended up with this...The find function is fine as is...just replace this section

Source https://stackoverflow.com/questions/67195657

QUESTION

Chisel: How to wait for signal assertion in ChiselScalatestTester?

Asked 2021-Mar-30 at 16:43

I want to create a testbench for my Chisel-based module. So I'm using ChiselScalatestTester to create the testbench. My module use a custom protocol to communicate with the outside world. So inside the test class I have to wait for some signals to be asserted from DUT. Here is an example from my test class:

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ANSWER

Answered 2021-Mar-30 at 16:43

Looks like you almost have it. Try

Source https://stackoverflow.com/questions/66867399

QUESTION

Creating string debug Vec for state machine

Asked 2021-Mar-17 at 05:38

When designing a state machine in Verilog I will normally use localparam to define state names. Most simulators will be able to deduce this and during debugging you can view the state signal by name and not by a number. For simulators that don't figure this out automatically (Icarus), I will generally do something like the following:

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ANSWER

Answered 2021-Mar-17 at 05:38

An alternative method would be to automatically generate translation files for the waveform viewer.

Here's a FIRRTL transform targeting gtkwave. It creates translation filter files for all ChiselEnums definitions and a "gtkw" savefile populated with all ports and submodules.

https://gist.github.com/kammoh/b3c85db9f2646a664f8dc84825f1bd1d

You can use it with chiseltest (chisel-testers2) like this:

Source https://stackoverflow.com/questions/66615234

QUESTION

Can I compute constants in software before Chisel begins designing hardware?

Asked 2021-Mar-16 at 00:28

I'm new to Chisel, and I was wondering if it's possible to calculate constants in software before Chisel begins designing any circuitry. For instance, I have a module which takes one parameter, myParameter, but from this parameter I'd like to derive more variables (constant1 and constant2) that would be later used to initialize registers.

...

ANSWER

Answered 2021-Mar-16 at 00:28

I was wondering if it's possible to calculate constants in software before Chisel begins designing any circuitry

Unless I'm misunderstanding your question, this is, in fact, how Chisel works.

Fundamentally, Chisel is a Scala library where the execution of your compiled Scala code creates hardware. This means that any pure-Scala code in your Chisel only exists at elaboration time, that is, during execution of this Scala program (which we call a generator).

Now, values in your program are created in sequential order as defined by Scala (and more-or-less the same as any general purpose programming language). For example, io is defined before constant1 and constant2 so the Chisel object for io will be created before either constants are calculated, but this shouldn't really matter for the purposes of your question.

A common practice in Chisel is to create custom classes to hold parameters when you have a lot of them. In this case, you could do something similar like this:

Source https://stackoverflow.com/questions/66647412

QUESTION

Returning multiple elements for apply method

Asked 2021-Mar-10 at 19:02

I am working with a DSL (Chisel) in which one particular part of the library requires me to define a Seq of items. I have several companion objects to create some intermediate logic and return one of these items. I have a situation where I want to actually return two of these items, but I'm having a hard time figuring out how to do that.

Let's say the "items" here are Person. (What Person is here is not important)

The DSL wants you to describe all your Persons through a Seq.

...

ANSWER

Answered 2021-Mar-10 at 00:56

Return a Seq and concatenate?

Source https://stackoverflow.com/questions/66556738

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

Vulnerabilities

No vulnerabilities reported

Install chisel

To get started quickly, you can install CHISEL and test the complete CHISEL pipeline on example data using the 4 following commands.
CHISEL is distributed as a bioconda package, and can be installed either from conda or directly from source. Depending on your interest in using conda, there are three possible installation approaches for CHISEL. Additional notes and comments are reported at the end of this section.
Full automatic installation: creates a new conda installation with Miniconda and installs CHISEL on it;
Standard installation: uses an existing conda installation and installs CHISEL on it;
Custom installation: installs CHISEL from source without conda.
An automatic BASH script that fully installs conda through Miniconda and installs chisel on it is provided in install_full.sh. Simply run the following command from the CHISEL's home ${CHISEL_HOME}.
CHISEL can be installed using an existing installation of conda (e.g. either the compact Miniconda or the complete Anaconda) in two steps. First, bioconda requires to set the following channels in this exact order:.
CHISEL is written in python2.7 and requires few standard python packages and two additional standard tools. Once all the requirements have been successfully installed, chisel can be manually installed from ${CHISEL_HOME} as. CHISEL depends on the following standard python packages, which must be available in the python environment where the user runs CHISEL. CHISEL also requires few standard additional tools, which must be included in PATH (e.g. by executing export PATH=${SAMTOOLS_HOME}/bin/:${PATH}).

Support

CHISEL's repository is actively maintained by Simone Zaccaria, previously a Postdoctoral Research Associate at Princeton University in the research group of prof. Ben Raphael and currently group leader of the Computational Cancer Genomics lab at the UCL Cancer Institute.

Find more information at: