From 59d3f64158e93c6a6aad05fc79152c1fa5c35901 Mon Sep 17 00:00:00 2001
From: Rob Patro <robp@ocean.compbio.cs.cmu.edu>
Date: Fri, 16 Jan 2015 02:21:00 -0500
Subject: [PATCH] Minor changes and version bump

---
 include/SalmonConfig.hpp         |  4 ++--
 include/Sampler.hpp              | 19 +++++++++----------
 src/SalmonQuantifyAlignments.cpp |  1 +
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/SalmonConfig.hpp b/include/SalmonConfig.hpp
index c7348b4..6df38d9 100644
--- a/include/SalmonConfig.hpp
+++ b/include/SalmonConfig.hpp
@@ -28,8 +28,8 @@
 namespace salmon {
 	constexpr char majorVersion[] = "0";
 	constexpr char minorVersion[] = "2";
-	constexpr char patchVersion[] = "3";
-	constexpr char version[] = "0.2.3";
+	constexpr char patchVersion[] = "5";
+	constexpr char version[] = "0.2.5";
 }
 
 #endif // SALMON_CONFIG_HPP
diff --git a/include/Sampler.hpp b/include/Sampler.hpp
index 1a4800b..a6894ae 100644
--- a/include/Sampler.hpp
+++ b/include/Sampler.hpp
@@ -158,16 +158,14 @@ namespace salmon {
                                     double logFragProb = sailfish::math::LOG_1;
 
                                     if (!salmonOpts.noFragLengthDist) {
-                                        switch (aln->fragType()) {
-                                            case ReadType::SINGLE_END:
-                                                if (aln->isLeft() and transcript.RefLength - aln->left() < fragLengthDist.maxVal()) {
-                                                    logFragProb = fragLengthDist.cmf(transcript.RefLength - aln->left());
-                                                } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) {
-                                                    logFragProb = fragLengthDist.cmf(aln->right());
-                                                }
-                                                break;
-                                            case ReadType::PAIRED_END:
-                                                logFragProb = fragLengthDist.pmf(static_cast<size_t>(aln->fragLen()));
+                                        if(aln->fragLen() == 0) {
+                                            if (aln->isLeft() and transcript.RefLength - aln->left() < fragLengthDist.maxVal()) {
+                                                logFragProb = fragLengthDist.cmf(transcript.RefLength - aln->left());
+                                            } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) {
+                                                logFragProb = fragLengthDist.cmf(aln->right());
+                                            }
+                                        } else {
+                                            logFragProb = fragLengthDist.pmf(static_cast<size_t>(aln->fragLen()));
                                         }
                                     }
 
@@ -214,6 +212,7 @@ namespace salmon {
                                     double massInc{0.0};
                                     bool choseAlignment{false};
                                     for (auto& aln : alnGroup->alignments()) {
+                                        if (aln->logProb == LOG_0) { continue; }
                                         aln->logProb -= sumOfAlignProbs;
 
                                         massInc = std::exp(aln->logProb);
diff --git a/src/SalmonQuantifyAlignments.cpp b/src/SalmonQuantifyAlignments.cpp
index e8b6ed8..94ea9cf 100644
--- a/src/SalmonQuantifyAlignments.cpp
+++ b/src/SalmonQuantifyAlignments.cpp
@@ -236,6 +236,7 @@ void processMiniBatch(AlignmentLibrary<FragT>& alnLib,
 
                     // Normalize the scores
                     for (auto& aln : alnGroup->alignments()) {
+                        if (aln->logProb == LOG_0) { continue; }
                         aln->logProb -= sumOfAlignProbs;
 
                         double r = uni(eng);