jmaguire 961dbbd4ef Now output bases and qhat and qstar into the GFF. ... Quals coming soon (four-base) QHAT : Most likely alt allele freq (unconstrained by number of chromosomes). QSTAR : Most likely alt allele freq (constrained by number of chromosomes). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-14 15:23:00 +00:00
..
fourbasecaller	Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller.	2009-04-13 00:49:41 +00:00
gatk	Now output bases and qhat and qstar into the GFF.	2009-04-14 15:23:00 +00:00
illumina	Make output type identical to the bustard parser so the values can be easily swapped for one another.	2009-04-09 20:49:34 +00:00
indels	there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2	2009-04-14 00:45:47 +00:00
samples	Added a sample xml marshaller / unmarshaller.	2009-04-07 22:28:16 +00:00
utils	Now output bases and qhat and qstar into the GFF.	2009-04-14 15:23:00 +00:00
ValidateSAM.java	generic declarations added here and there to eliminate a few annoying warnings; no consequential changes	2009-04-02 20:53:01 +00:00