Seems to work.
Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
Making it write out '@' line again.
Adding smallOk option.
Seems to work.  Has run on about 1/3 of ENCODE2.
Adding new edwMakeContaminationQa program to build.
Making it so it only does work if it hasn't done it already.
Seems to work.  Sadly it does change line length.
Main ra parsing function is generate and passes visual inspection.  Haven't tried compiling it yet though.
Output now compiles.
Added basesInSample output.
Little fixer seems to work.
Improving comment.
Removing weak attempt at fix that Mark properly fixed.
Making raToStruct.c module compile.
Making it generate a new function.
Making it work ok with /dev/null as fastq output.  Fixing an integer overflow bug.
Adding edwFastqFile and edwQaRepeat tables.  Making a couple of edwValidFile indexes unique.
Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion.   Hmm,  it is a lot of code.  I'm glad I didn't clutter autoSql with it.