Merge branch 'develop'

Fixes for #228 and #229. Many thanks
to @knokknok for helping find and resolve
these bugs.

.travis.yml

@@ -1,52 +1,29 @@
-#whitelist
-sudo: required
-dist: precise
-
-branches:
-    only:
-        - master
-        - develop
-
+sudo: false
 language: cpp
 
-compiler: gcc
-
-addons:
-  apt:
-    sources:
-      - boost-latest
-      - kalakris-cmake
-      - ubuntu-toolchain-r-test
-      - george-edison55-precise-backports
-    packages:
-      - cmake
-      - cmake-data
-      - gcc-4.9
-      - g++-4.9
-
-before_install:
-#    - echo "yes" | sudo apt-add-repository ppa:boost-latest
-#    - echo "yes" | sudo apt-add-repository ppa:mapnik/boost-backports-1-54
-#    - echo "yes" | sudo apt-add-repository ppa:h-rayflood/gcc-upper
-#    - echo "yes" | sudo add-apt-repository ppa:george-edison55/precise-backports
-#    - sudo apt-get clean -qq
-#    - sudo apt-get update -qq
-#    - sudo apt-mark showhold -qq
-#    - sudo apt-get install -qq cmake
-#    - sudo apt-get install -qq gcc-4.9 g++-4.9 
-    - export CC="gcc-4.9"
-    - export CXX="gcc-4.9"
-    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50
-    - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50
+matrix:
+  include:
+    - os : linux
+      compiler : gcc-7
+      addons:
+        apt:
+          sources: ['ubuntu-toolchain-r-test']
+          packages: ['g++-7', 'gcc-7', 'cmake', 'cmake-data', 'zlib1g-dev', 'libbz2-dev']
 
 install:
-    - export CXX="g++-4.9"
-    - export CC="gcc-4.9"
+    - export CXX="g++-7"
+    - export CC="gcc-7"
+    - mkdir -p latest-gcc-symlinks
+    - ln -s /usr/bin/g++-7 latest-gcc-symlinks/g++
+    - ln -s /usr/bin/gcc-7 latest-gcc-symlinks/gcc
+    - export PATH=$PWD/latest-gcc-symlinks:$PATH
+    - export AR=gcc-ar-7
+    - export RANLIB=gcc-ranlib-7
 
 script: 
     - mkdir build 
     - cd build 
-    - cmake -DCONDA_BUILD=TRUE -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
+    - cmake -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
     - travis_wait 45 make 
     - travis_wait make install
     - travis_wait make test VERBOSE=1
@@ -57,3 +34,63 @@ after_success:
 
 after_failure:
     - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/LastTest.log
+
+#whitelist
+#sudo: required
+#dist: precise
+#
+#branches:
+#    only:
+#        - master
+#        - develop
+#
+#language: cpp
+#
+#compiler: gcc
+#
+#addons:
+#  apt:
+#    sources:
+#      - boost-latest
+#      - kalakris-cmake
+#      - ubuntu-toolchain-r-test
+#      - george-edison55-precise-backports
+#    packages:
+#      - cmake
+#      - cmake-data
+#      - gcc-4.9
+#      - g++-4.9
+#
+#before_install:
+##    - echo "yes" | sudo apt-add-repository ppa:boost-latest
+##    - echo "yes" | sudo apt-add-repository ppa:mapnik/boost-backports-1-54
+##    - echo "yes" | sudo apt-add-repository ppa:h-rayflood/gcc-upper
+##    - echo "yes" | sudo add-apt-repository ppa:george-edison55/precise-backports
+##    - sudo apt-get clean -qq
+##    - sudo apt-get update -qq
+##    - sudo apt-mark showhold -qq
+##    - sudo apt-get install -qq cmake
+##    - sudo apt-get install -qq gcc-4.9 g++-4.9 
+#    - export CC="gcc-4.9"
+#    - export CXX="gcc-4.9"
+#    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50
+#    - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50
+#
+#install:
+#    - export CXX="g++-4.9"
+#    - export CC="gcc-4.9"
+#
+#script: 
+#    - mkdir build 
+#    - cd build 
+#    - cmake -DCONDA_BUILD=TRUE -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
+#    - travis_wait 45 make 
+#    - travis_wait make install
+#    - travis_wait make test VERBOSE=1
+#
+#after_success: 
+#    - cd $TRAVIS_BUILD_DIR
+#    - ./scripts/push-binary.sh
+#      
+#after_failure:
+#    - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/LastTest.log

CMakeLists.txt

@@ -4,10 +4,10 @@ enable_testing()
 
 project (Salmon)
 
-set(CPACK_PACKAGE_VERSION "0.10.0")
+set(CPACK_PACKAGE_VERSION "0.10.1")
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
 set(CPACK_PACKAGE_VERSION_MINOR "10")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
+set(CPACK_PACKAGE_VERSION_PATCH "1")
 set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
@@ -33,6 +33,7 @@ set (WARNING_IGNORE_FLAGS "")
 endif()
 
 if(CONDA_BUILD)
+  message("Building with CONDA_BUILD flag")
   set (CXXSTDFLAG "-std=c++11")
   set (GCCVERSION "4.8.5")
 else ()

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER [email protected]
 
 ENV PACKAGES git gcc make g++ cmake libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev curl unzip autoconf
-ENV SALMON_VERSION 0.10.0
+ENV SALMON_VERSION 0.10.1
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,2 +1,2 @@
 #! /bin/bash
-docker build -t combinelab/salmon:0.10.0 .
+docker build -t combinelab/salmon:0.10.1 .

include/SalmonConfig.hpp

@@ -27,8 +27,8 @@
 namespace salmon {
 constexpr char majorVersion[] = "0";
 constexpr char minorVersion[] = "10";
-constexpr char patchVersion[] = "0";
-constexpr char version[] = "0.10.0";
+constexpr char patchVersion[] = "1";
+constexpr char version[] = "0.10.1";
 constexpr uint32_t indexVersion = 2;
 constexpr char requiredQuasiIndexVersion[] = "q5";
 } // namespace salmon

scripts/fetchRapMap.sh

@@ -22,13 +22,11 @@ if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
     rm -fr ${INSTALL_DIR}/src/rapmap
 fi
 
-SVER=salmon-v0.10.0
+SVER=salmon-v0.10.1
 #SVER=develop-salmon
 
 mkdir -p ${EXTERNAL_DIR}
-#curl -k -L https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.8.2.zip -o ${EXTERNAL_DIR}/rapmap.zip
 curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-#curl -k -L https://github.com/COMBINE-lab/RapMap/archive/develop-salmon.zip -o ${EXTERNAL_DIR}/rapmap.zip
 
 hashcheck=""
 if exists sha256sum; then
@@ -42,7 +40,7 @@ fi
 if [ -z "${hashcheck-}" ]; then
     echo "Couldn't find shasum command; can't verify contents of downloaded RapMap";
 else
-    echo "c45140a8efc9258a1d52121c0f00e7ebb00c9165cf47bd52493540639d7a6d9b  ${EXTERNAL_DIR}/rapmap.zip" | ${hashcheck} -c - || { echo "rapmap.zip did not match expected SHA1! Exiting."; exit 1; }
+    echo "fca1323154b884a81bd61e3bdda06502fd3593f1622ad3b2dc98ef14dc4e6b6a  ${EXTERNAL_DIR}/rapmap.zip" | ${hashcheck} -c - || { echo "rapmap.zip did not match expected SHA1! Exiting."; exit 1; }
     #echo "not testing sha in develop branch"
 fi
 

src/CollapsedEMOptimizer.cpp

@@ -1,6 +1,7 @@
 #include <atomic>
 #include <unordered_map>
 #include <vector>
+#include <exception>
 
 #include "tbb/blocked_range.h"
 #include "tbb/parallel_for.h"
@@ -32,10 +33,11 @@
 
 using BlockedIndexRange = tbb::blocked_range<size_t>;
 
-// intelligently chosen value adopted from
+// intelligently chosen value originally adopted from
 // https://github.com/pachterlab/kallisto/blob/master/src/EMAlgorithm.h#L18
-constexpr double minEQClassWeight = std::numeric_limits<double>::denorm_min();
-constexpr double minWeight = std::numeric_limits<double>::denorm_min();
+// later modified since denorm_min seems to be too permissive.
+constexpr double minEQClassWeight = std::numeric_limits<double>::min();
+constexpr double minWeight = std::numeric_limits<double>::min();
 // A bit more conservative of a minimum as an argument to the digamma function.
 constexpr double digammaMin = 1e-10;
 
@@ -46,7 +48,7 @@ double normalize(std::vector<tbb::atomic<double>>& vec) {
   }
 
   // too small!
-  if (sum < minWeight) {
+  if (sum < ::minWeight) {
     return sum;
   }
 
@@ -121,7 +123,8 @@ void VBEMUpdate_(std::vector<std::vector<uint32_t>>& txpGroupLabels,
   for (size_t i = 0; i < M; ++i) {
     auto ap = alphaIn[i] + priorAlphas[i];
     if (ap > ::digammaMin) {
-      expTheta[i] = std::exp(boost::math::digamma(ap) - logNorm);
+        expTheta[i] =
+          std::exp(boost::math::digamma(ap) - logNorm);
     } else {
       expTheta[i] = 0.0;
     }
@@ -347,7 +350,7 @@ size_t markDegenerateClasses(
                   << ", aux = " << aux << "\n";
       }
     }
-    if (denom <= minEQClassWeight) {
+    if (denom <= ::minEQClassWeight) {
       fmt::MemoryWriter errstream;
 
       errstream << "\nDropping weighted eq class\n";
@@ -509,7 +512,7 @@ bool doBootstrap(
       alphaSum = truncateCountVector(alphas, cutoff);
     }
 
-    if (alphaSum < minWeight) {
+    if (alphaSum < ::minWeight) {
       jointLog->error("Total alpha weight was too small! "
                       "Make sure you ran salmon correclty.");
       return false;
@@ -784,8 +787,8 @@ bool CollapsedEMOptimizer::optimize(ExpT& readExp, SalmonOpts& sopt,
   // a linear combination of the online estimates
   // and the uniform distribution.
   double uniformPrior = totalWeight / static_cast<double>(numActive);
-  // double fracObserved = 1.0;
-  double fracObserved = std::min(1.0, totalWeight / sopt.numRequiredFragments);
+  double maxFrac = 0.999;
+  double fracObserved = std::min(maxFrac, totalWeight / sopt.numRequiredFragments);
   // Above, we placed the uniformative (uniform) initalization into the
   // alphasPrime variables.  If that's what the user requested, then copy those
   // over to the alphas
@@ -961,7 +964,7 @@ bool CollapsedEMOptimizer::optimize(ExpT& readExp, SalmonOpts& sopt,
   }
 
   /* -- v0.8.x
-  if (alphaSum < minWeight) {
+  if (alphaSum < ::minWeight) {
     jointLog->error("Total alpha weight was too small! "
                     "Make sure you ran salmon correclty.");
     return false;
@@ -986,7 +989,7 @@ bool CollapsedEMOptimizer::optimize(ExpT& readExp, SalmonOpts& sopt,
     alphaSum = truncateCountVector(alphas, cutoff);
   }
 
-  if (alphaSum < minWeight) {
+  if (alphaSum < ::minWeight) {
     jointLog->error("Total alpha weight was too small! "
                     "Make sure you ran salmon correclty.");
     return false;