ReformatReads readme by Brian Bushnell
Last updated February 26, 2014.
Please contact me at bbushnell@lbl.gov if you have any questions or encounter any errors.

This is currently a stub.

Change Log:

Moved processing phase from constructor into a new function.
Added pigz (parallel gzip) support, at suggestion of Rob Egan.
Added ftr/ftl (force trim to a certain base position), at request of Alicia Clum.
Added shellscript support for java -Xmx flag (Suggested by James Han).
Fixed stdout.fa.gz writing uncompressed via ReadStreamWriter.
Added scarf input support.
Major refactoring.
Output quality switch (qout) was being ignored and ASCII33 was always used; this has been fixed.
TrimRead.testOptimal() mode added, and made default when quality trimming is performed; old mode can be used with 'otf=f' flag.
Fixed bug in ByteBuilder for reads with no quality values.  Noted by Brian Foster.
All program message information now defaults to stderr.
Added 'tbs' (trim bad sequence) flag to fix broken files from NCBI (like NT).  Works in test cases, but causes problems with NT for unknown reasons. 
Added 'rbb' (requirebothbad) flag for tossing pairs shorter than minlen.  Default: false.