Charles Dickens de Bruijn Graph

Standardized Velvet Assembly Report

http://code.google.com/p/standardized-velvet-assembly-report/

I finally got my Velvet Assembler report script up on google code. This "program" consists of some short scripts and a Sweave report designed to help Velvet users identify the optimal kmer and cvCut parameters.

GregorianCalendar foolishness

I wanted to add queries to my Grails application to find tasks that needed to be completed today, or were delinquent (due date < last midnight).
My application kept thinking things were delinquent the afternoon of the due date.

The problem was that I neglected to read how HOUR_OF_DAY differed from HOUR and absentmindedly mixed the two.
http://java.sun.com/j2se/1.4.2/docs/api/java/util/Calendar.html

You can try to set HOUR to 0 but it will default to 12. If it is the afternoon when you request the Calendar object then it will assume you mean 12 noon.

Calendar lastMidnight = Calendar.getInstance();
//DO NOT DO THIS!!
  lastMidnight.set( Calendar.HOUR, lastMidnight.getMinimum(Calendar.HOUR_OF_DAY ));
  ...snip...

  //this is ok
  lastMidnight.set( Calendar.HOUR_OF_DAY, lastMidnight.getMinimum(Calendar.HOUR_OF_DAY ));
  ...snip...

  //this is also ok
  lastMidnight.set( Calendar.AM_PM, Calendar.AM );
  lastMidnight.set( Calendar.HOUR, lastMidnight.getMinimum(Calendar.HOUR ));
  ...snip...

The other settings are pretty self-explanatory

  lastMidnight.set( Calendar.MINUTE, lastMidnight.getMinimum(Calendar.MINUTE));
  lastMidnight.set( Calendar.SECOND, lastMidnight.getMinimum(Calendar.SECOND));
  lastMidnight.set( Calendar.MILLISECOND,lastMidnight.getMinimum(Calendar.MILLISECOND));