jmaguire af6788fa3d Misc: ... 1. Added logGamma function to utils 2. Required asserts to be enabled in the allele caller (run with java -ea) 3. put checks and asserts of NaN and Infinity in AlleleFrequencyEstimate 4. Added option FRACTIONAL_COUNTS to the pooled caller (not working right yet) AlleleFrequencyWalker: 5. Made FORCE_1BASE_PROBS not static in AlleleFrequencyWalker (an argument should never be static! Jeez.) 6. changed quality_precision to be 1e-4 (Q40) 7. don't adjust by quality_precision unless the qual is actually zero. 8. added more asserts for NaN and Infinity 9. put in a correction for zero probs in P_D_q 10. changed pG to be hardy-weinberg in the presence of an allele frequency prior (duh) 11. rewrote binomialProb() to not overflow on deep coverage 12. rewrote nchoosek() to behave right on deep coverage 13. put in some binomailProb() tests in the main() routine (they come out right when compared with R) Hunt for loci where 4bp should change things: 14. added FindNonrandomSecondBestBasePiles walker. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@471 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-19 15:35:07 +00:00
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src/org/broadinstitute/sting	Misc:	2009-04-19 15:35:07 +00:00
test/org/broadinstitute/sting	Changed interface from contig,pos,length to more common contig,start,stop interface.	2009-04-16 00:04:41 +00:00