chrisarg

• About: I like to use Perl for material other than text.

Recent Actions

• Posted Repository of examples using Perl and Assembly together to chrisarg

  Sometimes one needs an extra ounce of performance. Why not combine the high level semantics of Perl with the punch of assembly?

  This repo includes various examples of how this can be done.

• Commented on Caching & Memoization with state variables
  I am not sure I follow; are you saying that two different named subroutines can't have the same name for their state variables, i.e. it is not possible to have ? sub lucas () { state $statevar; ... } sub...
• Posted Caching & Memoization with state variables to chrisarg

  Chapter 3 of Higher Order Perl describes various approaches to memoization of an expensive function: private cache and the Memoize module. The book was written in 2005 (Perl was at version 5.8 back then) , so it does not include another way for function…

• Posted Parallel Perl/C applications without tears using OpenMP: Controlling the OpenMP environment to chrisarg

  Brett Estrade, did it again with yet another excellent talk at TPRC 2024 about the use of OpenMP for parallelizing Perl/C code. This is an area that is extremely interesting as OpenMP is a rather straightforward way to parallelize code…

• Commented on alienfile
  This post help me made sense of the manual :)...
• Posted Is Perl a write only language? to chrisarg

  I am sick and tired of hearing this, so let's put it this to the test. Assume you know little of Perl, or any programming language for that matter. Can you parse the code?

  https://chrisa…

• Posted Hash of Arrays Deathmatch : Native Perl vs. DBM::Deep vs. Redis to chrisarg
  Sometimes one has to make compromises between speed of execution and memory, other times one may not have to be. While working towards a fairly (at least in my mind) complete solution to map Nanopore Sequencing files, I ran against the need to create and access fairly large hash of arrays…
• Commented on Of Go, C, Perl and fastq file conversion Vol II : the Jedi regex
  Yes, it is intended to give emphasis :)...
• Posted Of Go, C, Perl and fastq file conversion Vol IV : gone in 60 seconds (or less) to chrisarg

  In the final part of this series, we will test the performance of the four parsers, in a scenario emulating the batch analysis of sequencing data. We will use the sample fastq file 3_OHara_S2_rbcLa_2019_minq7.fastq from https://zenodo.org/record/3736457. This is a 35MB file of 21791 long…

• Posted Of Go, C, Perl and fastq file conversion Vol III : pledging allegiance to the flag to chrisarg
  In the previous entry, we presented a regex based fastq parser. As the regex engine maps to a finite state automaton, we should be able to rewrite the parser without…
• Posted Of Go, C, Perl and fastq file conversion Vol II : the Jedi regex to chrisarg

  In the second part of this series about fast parsers for sequencing applications,  I will review the code for the regex based parser. This is shown below (I use v5.38, as…

• Posted Of Go, C, Perl and fastq file conversion Vol I : intro to chrisarg

  Next Generation Sequencing cost of experiments have dramatically declined. NGS decipher the identity (base composition, the sequence of letters in the alphabet of DN…

• Posted Using Perl to prepare sequencing files to submit to NCBI's GEO to chrisarg

  In the middle of a manuscript submission that requires sequencing data to be uploaded to NCBI's Gene Expression Omnibus.
  …

• Commented on open invitation to participate in Perl-OpenMP on Github
  This is absolutely so cool...

Comment Threads

• Brett Estrade commented on Caching & Memoization with state variables

  I love state variables, but oddly only use them when creating sub based state machine xD - which is typically just for show. But the idea of co-routines in Perl is nifty.
  
  I think E. Choroba means something like:

  sub foo {
    state $foo = 1;
    ...
    say $foo;
    ++$foo;
  }
  
  foreach my $i (1 .. 10) {
  
    foo();
  
  }
  
  

  versus,

  my $foo = 1;
  foreach my $i (1 .. 10) {
    my $sub = sub {
      my $myfoo = $foo;
      ...
      say $myfoo;
    };
    ++$foo;
    $sub->();
  }
  

• E. Choroba commented on Caching & Memoization with state variables

  No, I mean we only have one subroutine, but we want to use it to generate two different sequences.