@@ -1,5 +1,5 @@

 Package: CoGAPS

-Version: 3.3.8

+Version: 3.3.9

 Date: 2018-04-24

 Title: Coordinated Gene Activity in Pattern Sets

 Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,

@@ -1,4 +1,4 @@

-# CoGAPS Version: 3.3.8

+# CoGAPS Version: 3.3.9

 [![Bioc](https://bioconductor.org/images/logo_bioconductor.gif)](https://bioconductor.org/packages/CoGAPS)

 [![downloads](https://bioconductor.org/shields/downloads/CancerInSilico.svg)](https://bioconductor.org/packages/CoGAPS)

@@ -522,22 +522,19 @@ float m2, unsigned r1, unsigned c1, unsigned r2, unsigned c2)

 {

     if (r1 != r2 || c1 != c2) // automatically reject if change in same bin

     {

-        float pUpper = gaps::random::p_gamma(m1 + m2, 2.f, 1.f / mLambda);

-        float newMass = gaps::random::inverseGammaSample(0.f, pUpper, 2.f, 1.f / mLambda);

-

         if (impl()->canUseGibbs(r1, c1, r2, c2))

         {

             // swapping only effects alpha parameters - only effects gibbs

             // flips the sign of alpha parameters (only su)

             // flips sign in gibbs mass

             // can we swap after gibbsMass calculation?

-            if ((m1 > m2 && m1 > newMass) || (m2 > m1 && m2 < newMass))

+            /*if ((m1 > m2 && m1 > newMass) || (m2 > m1 && m2 < newMass))

             {

                 std::swap(r1, r2);

                 std::swap(c1, c2);

                 std::swap(p1, p2);

                 std::swap(m1, m2);

-            }

+            }*/

             AlphaParameters alpha = impl()->alphaParameters(r1, c1, r2, c2);

             std::pair<float, bool> gMass = gibbsMass(alpha, m1, m2);

@@ -549,6 +546,9 @@ float m2, unsigned r1, unsigned c1, unsigned r2, unsigned c2)

             }

         }

+        float pUpper = gaps::random::p_gamma(m1 + m2, 2.f, 1.f / mLambda);

+        float newMass = gaps::random::inverseGammaSample(0.f, pUpper, 2.f, 1.f / mLambda);

+

         float delta = m1 > m2 ? newMass - m1 : m2 - newMass; // change larger mass

         float pOldMass = 2.f * newMass > m1 + m2 ? gaps::max(m1, m2) : gaps::min(m1, m2);