Merge branch 'develop'

.travis.yml

@@ -1,49 +1,50 @@
+dist: trusty
 sudo: false
-language: cpp
-
+git:
+  depth: 1
+language: generic
 matrix:
   include:
-    - os : linux
-      compiler : gcc-7
-      addons:
-        apt:
-          update: true
-          sources:
-              - sourceline: 'ppa:mhier/libboost-latest'
-              - ubuntu-toolchain-r-test
-          packages: ['g++-7', 'gcc-7', 'zlib1g-dev', 'libbz2-dev']
+    - env: CC=gcc-7 CXX=g++-7 AR=gcc-ar-7 NM=gcc-nm-7 RANLIB=gcc-ranlib-7
+    - env: CC=gcc-5 CXX=g++-5 AR=gcc-ar-5 NM=gcc-nm-5 RANLIB=gcc-ranlib-5
 
 install:
-    - 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
-    - DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
-    - mkdir ${DEPS_DIR} && cd ${DEPS_DIR}
-    - travis_retry wget --no-check-certificate https://cmake.org/files/v3.12/cmake-3.12.0-Linux-x86_64.tar.gz
-    - tar -xzvf cmake-3.12.0-Linux-x86_64.tar.gz > /dev/null
-    - mv cmake-3.12.0-Linux-x86_64 cmake-install
-    - PATH=${DEPS_DIR}/cmake-install:${DEPS_DIR}/cmake-install/bin:$PATH
-    - cd ${TRAVIS_BUILD_DIR}
-
-script: 
-    - mkdir build 
-    - cd build 
-    - cmake -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
-    - travis_wait 45 make 
-    - travis_wait make install
+    # https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
+    - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+    - sudo apt-get update -qq
+    - sudo apt-get install -qq zlib1g-dev libbz2-dev cmake
+    - |
+      if [[ "${CC}" =~ gcc- ]]; then
+        echo "Installing ${CC}."
+        sudo apt-get install -qq "${CC}"
+      fi
+    - |
+      if [[ "${CXX}" =~ g\+\+- ]]; then
+        echo "Installing ${CXX}."
+        sudo apt-get install -qq "${CXX}"
+      fi
+
+script:
     - LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/lib:$LD_LIBRARY_PATH
-    - ./src/salmon -h
-    - travis_wait make test VERBOSE=1
+    - mkdir build
+    - pushd build
+    # Set make -j N considering Travis providing 2 cores.
+    # VERBOSE=1 to show the input commands in generatd Makefile for debug.
+    - |
+      cmake \
+        -DFETCH_BOOST=TRUE \
+        -DNO_RTM=TRUE \
+        .. && \
+      make -j 4 VERBOSE=1 && \
+      make install && \
+      ./src/salmon -h 
+    - |
+      make CTEST_OUTPUT_ON_FAILURE=1 VERBOSE=1 test 
+    - popd
 
-after_success: 
-    - cd $TRAVIS_BUILD_DIR
+after_success:
     - ./scripts/push-binary.sh
-      
+
 after_failure:
     - echo "Failure"
     - ls -laR $TRAVIS_BUILD_DIR/build/Testing/

CMakeLists.txt

@@ -1,5 +1,18 @@
 cmake_minimum_required (VERSION 3.9)
 
+if(DEFINED ENV{CC})
+  set(CC $ENV{CC})
+else()
+  set(CC gcc)
+endif()
+message("CC: ${CC}")
+
+set(CC_VERSION "")
+if(${CC} MATCHES ^gcc-)
+  string(REGEX REPLACE "gcc-" "" CC_VERSION ${CC})
+endif()
+message("CC version: ${CC_VERSION}")
+
 enable_testing()
 
 project (Salmon)
@@ -54,41 +67,59 @@ set (REMOVE_WARNING_FLAGS "-Wno-unused-function;-Wno-unused-local-typedefs")
 set (TGT_COMPILE_FLAGS "-ftree-vectorize;-funroll-loops;-fPIC;-fomit-frame-pointer;-O3;-DNDEBUG")
 set (TGT_WARN_FLAGS "-Wall;-Wno-unknown-pragmas;-Wno-reorder;-Wno-unused-variable;-Wreturn-type;-Werror=return-type;${REMOVE_WARNING_FLAGS}")
 
+
+###
+# Sanitizers BEGIN
+###
+#list(APPEND TGT_COMPILE_FLAGS "-fsanitize=address")
+#set(CMAKE_LINK_FLAGS "-fsanitize=address")
+###
+# Sanitizers END 
+###
+
 if (APPLE)
 set(WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
 list(APPEND TGT_WARN_FLAGS -Wno-deprecated-register)
 else()
 set(WARNING_IGNORE_FLAGS "")
 endif()
 
-if(CONDA_BUILD)
-  message("Building with CONDA_BUILD flag")
-  set(CMAKE_CXX_STANDARD 11)
-  set(CMAKE_CXX_STANDARD_REQUIRED ON)
-  set(CMAKE_CXX_EXTENSIONS OFF)
-  set(CXXSTDFLAG "-std=c++11")
-  set(GCCVERSION "4.8.2")
-else ()
-  set(CMAKE_CXX_STANDARD 11)
-  set(CMAKE_CXX_STANDARD_REQUIRED ON)
-  set(CMAKE_CXX_EXTENSIONS OFF)
-  set(CXXSTDFLAG "-std=c++11")
-  set(GCCVERSION "5.2")
-endif()
+## Prefer static to dynamic libraries
+SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
 
 include(CheckIPOSupported)
 
 set(THREADS_PREFER_PTHREAD_FLAG ON)
 find_package(Threads REQUIRED)
 
+set (ICU_LIBS "")
+set (ICU_INC_DIRS "")
+
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CXXSTDFLAG "-std=c++14")
+set(GCCVERSION "5.2")
+
+if(CONDA_BUILD)
+  message("Building with CONDA_BUILD flag")
+  if (APPLE)
+     # Do we require all these components?  Any others? 
+     find_package(ICU COMPONENTS data i18n io uc REQUIRED)
+     if (ICU_FOUND)
+       message (STATUS "ICU_INCLUDE_DIRS = ${ICU_INCLUDE_DIRS}")
+       message (STATUS "ICU_LIBRARIES = ${ICU_LIBRARIES}")
+     endif()
+     set (ICU_INC_DIRS ${ICU_INCLUDE_DIRS})
+     set (ICU_LIBS ${ICU_LIBRARIES})
+  endif()
+endif()
+
 set (BOOST_CXX_FLAGS "${WARNING_IGNORE_FLAGS} ${CXXSTDFLAG}")
 if (FETCH_BOOST)
    set (BOOST_CXX_FLAGS "${BOOST_CXX_FLAGS} -I${CMAKE_CURRENT_SOURCE_DIR}/external/install/include -L${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib")
 endif()
 
-## Prefer static to dynamic libraries
-SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
-
 ##
 # OSX is strange (some might say, stupid in this regard).  Deal with it's quirkines here.
 ##
@@ -109,7 +140,7 @@ endif()
 set( BOOST_EXTRA_FLAGS "--layout=tagged" )
 ## this get's set differently below if we
 ## are on clang & apple
-set (NON_APPLECLANG_LIBS gomp rt)
+set (NON_APPLECLANG_LIBS gomp)
 
 if(UNIX AND NOT APPLE)
 	set(LIBRT rt)
@@ -156,10 +187,10 @@ if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
     endif()
 
     set (WARNING_IGNORE_FLAGS "${WARNING_IGNORE_FLAGS} -Wno-unused-local-typedefs")
-    set (BOOST_TOOLSET "gcc")
+    set (BOOST_TOOLSET "${CC}")
     set (BOOST_CONFIGURE_TOOLSET "--with-toolset=gcc")
     set (BCXX_FLAGS "${CXXSTDFLAG}")
-    set (BOOST_EXTRA_FLAGS toolset=gcc cxxflags=${BCXX_FLAGS})
+    set (BOOST_EXTRA_FLAGS toolset=${CC} cxxflags=${BCXX_FLAGS})
 # Tentatively, we support clang now
 elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
     set(CLANG TRUE)
@@ -399,6 +430,11 @@ elseif(FETCH_BOOST)
         INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
         #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
 	CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
+        ADD_CUSTOM_COMMAND(
+            OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/tools/build/src/user-config.jam
+            PRE_BUILD
+            COMMAND echo "using gcc : ${CC_VERSION} : ${CMAKE_CXX_COMPILER} ;"
+        )
 	BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
         BUILD_IN_SOURCE 1
         INSTALL_COMMAND ""
@@ -645,27 +681,6 @@ ExternalProject_Add(libstadenio
     INSTALL_COMMAND make install
 )
 
-message("Build system will fetch SPDLOG")
-message("==================================================================")
-ExternalProject_Add(libspdlog
-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
-                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
-                     tar -xzf spdlog-v0.16.1.tar.gz 
-    ##
-    #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
-    #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
-    #TLS_VERIFY FALSE
-    #URL_HASH SHA1=c868b4d1a27c4d9fb3b748f0566a8f0390d83ffb
-    ##
-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog-0.16.1
-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-    CONFIGURE_COMMAND ""
-    BUILD_COMMAND ""
-    BUILD_IN_SOURCE 1
-    INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
-)
-
 set (FAST_MALLOC_LIB "")
 set (HAVE_FAST_MALLOC FALSE)
 

cmake/UnitTests.cmake

@@ -1,5 +1,5 @@
 set(TEST_COMMAND ${TOPLEVEL_DIR}/tests/unitTests)
-execute_process(COMMAND ${TEST_COMMAND}
+execute_process(COMMAND ${TEST_COMMAND} 
 	            WORKING_DIRECTORY ${TOPLEVEL_DIR}/tests
                 RESULT_VARIABLE UNIT_TEST_RESULT
                 )

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 0
 VERSION_MINOR 11
-VERSION_PATCH 2
+VERSION_PATCH 3

doc/source/alevin.rst

@@ -19,7 +19,7 @@ Alevin requires the following minimal set of necessary input parameters (general
 * ``-1``: CB+UMI file(s), alevin requires the path to the *FASTQ* file containing CB+UMI raw sequences to be given under this command line flag. Alevin also supports parsing of data from multiple files as long as the order is the same as in `-2` flag.
 * ``-2``: Read-sequence file(s), alevin requires the path to the *FASTQ* file containing raw read-sequences to be given under this command line flag. Alevin also supports parsing of data from multiple files as long as the order is the same as in `-1` flag.
 * ``--dropseq / --chromium``: the protocol, this flag tells the type of single-cell protocol of the input sequencing-library.
-* ``-i``: index, file containing the salmon index of the reference transcriptome, as generated by `samlon index` command.
+* ``-i``: index, file containing the salmon index of the reference transcriptome, as generated by `salmon index` command.
 * ``-p``: number of threads, the number of threads which can be used by alevin to perform the quantification, by default alevin utilizes *all* the available threads in the system, although we recommend using ~10 threads which in our testing gave the best memory-time trade-off.
 * ``-o``: output, path to folder where the output gene-count matrix (along with other meta-data) would be dumped.
 * ``--tgMap``: transcript to gene map file, a tsv (tab-separated) file --- with *no header*, containing two columns mapping of each transcript present in the reference to the corresponding gene (the first column is a transcript and the second is the corresponding gene).

doc/source/conf.py

@@ -57,7 +57,7 @@
 # The short X.Y version.
 version = '0.11'
 # The full version, including alpha/beta/rc tags.
-release = '0.11.2'
+release = '0.11.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

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 0.11.2
+ENV SALMON_VERSION 0.11.3
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,2 +1,3 @@
 #! /bin/bash
-docker build -t combinelab/salmon:0.11.2 .
+SALMON_VERSION=0.11.3
+docker build -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

include/AlevinOpts.hpp

@@ -58,6 +58,8 @@ struct AlevinOpts {
   bool useCorrelation;
   // don't run EM flag
   bool doEM;
+  // Avoid segfaults based on no whitelist mapping
+  bool debug;
   // perform naive deduplication
   bool naive;
   // perform eqclass level analysis instead of gene or txp level minsets

include/BAMQueue.tpp

@@ -553,6 +553,9 @@ inline bool BAMQueue<FragT>::getFrag_(UnpairedRead& sread, FilterT filt) {
             !(bam_flag(sread.read) & BAM_FUNMAP) and
             sread.transcriptID() >= 0) {
             haveValidRead = true;
+            bool isFwd = !(bam_strand(sread.read));
+            int32_t startPos = bam_pos(sread.read); 
+            sread.libFmt = salmon::utils::hitType(startPos, isFwd);
         }
 
         if (!haveValidRead) { 

include/CollapsedCellOptimizer.hpp

@@ -32,6 +32,10 @@ using tgroupweightvec = std::vector<double>;
 namespace bfs = boost::filesystem;
 using SCExpT = ReadExperiment<EquivalenceClassBuilder<SCTGValue>>;
 
+struct CellState {
+  bool inActive;
+};
+
 class CollapsedCellOptimizer {
 public:
   using VecType = std::vector<tbb::atomic<double>>;
@@ -65,11 +69,12 @@ void optimizeCell(SCExpT& experiment,
                   std::deque<std::pair<TranscriptGroup, uint32_t>>& orderedTgroup,
                   std::shared_ptr<spdlog::logger>& jointlog,
                   bfs::path& outDir, std::vector<uint32_t>& umiCount,
-                  spp::sparse_hash_set<uint32_t>& skippedCBcount,
+                  std::vector<CellState>& skippedCBcount,
                   bool verbose, GZipWriter& gzw, size_t umiLength, bool doEM,
                   bool quiet,std::atomic<uint64_t>& totalDedupCounts,
                   spp::sparse_hash_map<uint32_t, uint32_t>& txpToGeneMap,
-                  uint32_t numGenes, bool txpLevel, bool naive, bool eqClassLevel);
+                  uint32_t numGenes, bool txpLevel, bool naive, bool eqClassLevel,
+                  bool inDebugMode);
 
 using VecT = CollapsedCellOptimizer::SerialVecType;
 

include/EquivalenceClassBuilder.hpp

@@ -161,9 +161,9 @@ class EquivalenceClassBuilder {
       totalCount += kv.second.count;
     }
 
-    logger_->info("Computed {} rich equivalence classes "
+    logger_->info("Computed {:n} rich equivalence classes "
                   "for further processing", countMap_.size());
-    logger_->info("Counted {} total reads in the equivalence classes ",
+    logger_->info("Counted {:n} total reads in the equivalence classes ",
                   totalCount);
     return true;
   }
@@ -178,10 +178,10 @@ class EquivalenceClassBuilder {
       countVec_.push_back(kv);
     }
 
-    logger_->info("Computed {} rich equivalence classes "
+    logger_->info("Computed {:n} rich equivalence classes "
                   "for further processing",
                   countVec_.size());
-    logger_->info("Counted {} total reads in the equivalence classes ",
+    logger_->info("Counted {:n} total reads in the equivalence classes ",
                   totalCount);
     return true;
   }

include/GZipWriter.hpp

@@ -49,7 +49,8 @@ class GZipWriter {
   bool writeAbundances(std::vector<double>& alphas,
                        std::vector<Transcript>& transcripts);
 
-  bool writeAbundances(std::string bcName,
+  bool writeAbundances(bool inDebugMode,
+                       std::string bcName,
                        std::vector<double>& alphas);
 
   template <typename ExpT>