cobs | Search Index for genomic data | Genomics library

I'm trying to find the best fitting curve through a given set of points. The fitted curve must also pass through these points. I found an answer on Cross Validated which suggested to use the cobs: Constrained B-Splines (Sparse Matrix Based) package. However, I got an error while testing it with my sample data:

In an Rcpp project I would like to be able to either call an R function (the cobs function from the cobs package to do a concave spline fit) or call the fortran code that it relies on (the cobs function uses quantreg's rq.fit.sfnc function to fit the constrained spline model, which in turn relies on the fortran coded srqfnc function in the quantreg package) within a pragma openmp parallel for loop (the rest of my code mainly requires some simple linear algebra, so that would be no problem, but sadly each inner loop iteration also requires me to do a concave spline fit). I was wondering if this would be allowed or possible though, as I presume such calls would not be thread safe? Would there be an easy fix for this, like to surround those calls by a #pragma omp critical ? Would anyone have any examples of this? Or would the only way in this case involve doing a full Rcpp port of the cobs & rq.fit.sfnc functions first using thread-safe Armadillo classes?

so im new in C# Programming. I have programmed a C# Forms Application in Visual Studio to communicate to/initialze a device over the Serial Port. The communication between the device is COBS coded, so there are no 0x00 bytes except on the end of each message. The messages sent and received have different length.

My problem is at the moment, that the Messages I receive are not complete or start at the middle of a message, so i cannot trigger sent messages on a specific value in the received messages. You can determine end of a message with received 0x00 (0x00 means end of message in COBS coded data)

So what i need is something to handle the complete message and put it in a byte array to analyze i.e. byte[11] for a specific value.

Here is what ive done so far:

I am working with a function that depends on quadratic B-spline interpolation estimated up front by the the cobs function in the same R package. The estimated knots and corresponding coefficients are given in code. Further on, I require the integral of this function from 0 to some value, for example 0.6 or 0.7. Since my function is strictly positive, the integral value should increase if the upper bound of the integral increases. However this is not the case for some values, as shown when using 0.6 and 0.7

I have a driver that builds on the new serdev bus in the linux kernel.

In my driver I receive messages from an external device, all messages ends with a null byte (0x00) and the protocol ensures that there are no null bytes in my data (COBS). Now I try to have the TTY layer hand me full messages by scanning for zeros in my input and if there are none I'll just return zero in the callback that is called from the tty layer when bytes are available.

This kind of works. Or rather it works for some messages. After a while though it locks up and the tty layer keeps sending the same size of received bytes indefinitely. My guess is that this happens when one half of the tty flip buffer is full and the rest of my message is in the other half.

I have two questions:

1. Am I correct in that the tty layer can "hang" until I read out all data in one half of the flip buffer?

2. If that is so, is there some way to prevent this from happening? I'd rather not implement my own buffering scheme on top of the tty buffer already available.

Thanks

I'm trying to run a cobweb code in Mathematica and I need the following script: