Reflection to discover function keyword arguments in Julia

Posted on Thu 12 January 2017 in Julia

I needed to extract the named keyword arguments for a function in Julia. In Python we have the inspect.getargspec function but in Julia there doesn't seem to be any standard way to do so. Obviously it's possible because calling methods on a function lists them at the ...

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Avrum's Clock Domain Crossing Widsom

Posted on Mon 22 August 2016 in Hardware • Tagged with VHDL, Vivado

Avrum is an active fellow on the Xilinx forums whenever clock domain crossing (CDC) issues crop up. By default, and in contrast to ISE, Vivado assumes all clocks are related. Thus, even with a proper synchronization circuit, Vivado needs to be explicitly told not to try and time these paths ...

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Variant calls with GATK

Posted on Sun 29 May 2016 in Bioinformatics • Tagged with Julia

I had to replace a CLC Bio variant calling pipeline with an open-source equivalent. These notes are mainly an update of another blog post Variant calling with GATK.

Tools Setup

  1. Build and install (to ~/.local) bwa
  2. Build and install samtools
  3. Download and extract GATK under non-comercial license
  4. Download and extract ...
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Bitfield nicities in Python

Posted on Mon 08 February 2016 in Software • Tagged with Python

With code contributions from Graham Rowlands.

For low level device drivers or communications protocols it's handy to be able to bounce the individual bits in an integer around as several fields might be packed into a larger integer in a bitfield.

There are, of course, already several ways to ...

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