Merge branch 'develop'

.travis.yml

@@ -1,4 +1,7 @@
 #whitelist
+sudo: required
+dist: precise
+
 branches:
     only:
         - master

CMakeLists.txt

@@ -4,10 +4,10 @@ enable_testing()
 
 project (Salmon)
 
-set(CPACK_PACKAGE_VERSION "0.8.2")
+set(CPACK_PACKAGE_VERSION "0.9.0")
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "8")
-set(CPACK_PACKAGE_VERSION_PATCH "2")
+set(CPACK_PACKAGE_VERSION_MINOR "9")
+set(CPACK_PACKAGE_VERSION_PATCH "0")
 set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
@@ -20,13 +20,24 @@ set(CPACK_SOURCE_PACKAGE_FILE_NAME
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
+if( NOT CMAKE_BUILD_TYPE )
+  set( CMAKE_BUILD_TYPE Release CACHE STRING
+       "Choose the type of build, options are: Debug Release."
+       FORCE )
+endif()
+
 if (APPLE)
 set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
 else()
 set (WARNING_IGNORE_FLAGS "")
 endif()
 
+
 set (BOOST_CXX_FLAGS "${WARNING_IGNORE_FLAGS} -std=c++11")
+if (FETCH_BOOST)
+   set (BOOST_CXX_FLAGS "${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})
 
@@ -447,10 +458,10 @@ ExternalProject_Add(libbwa
     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
     #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
     #DOWNLOAD_NAME bwa-master.tar.gz
-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
-                     ${SHASUM} e1665acd44f971f6d8b90c25992c680a7fec0a822268437d6fd4e51dbf603181  bwa-master.tar.gz &&
-                     mkdir -p bwa-master &&
-                     tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
+                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
+                    mkdir -p bwa-master &&
+                    tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
     CONFIGURE_COMMAND ""
@@ -519,7 +530,7 @@ endif()
 ExternalProject_Add(libtbb
 	DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
     DOWNLOAD_COMMAND curl -k -L https://github.com/01org/tbb/archive/2017_U3.tar.gz -o tbb-2017_U3.tgz &&
-                     ${SHASUM} 00a8b2798c498507572e24c2db7bf4896f05b760a38ed9ba566ffd348a7c6cef  tbb-2017_U3.tgz &&
+                     ${SHASUM} 00a8b2798c498507572e24c2db7bf4896f05b760a38ed9ba566ffd348a7c6cef tbb-2017_U3.tgz &&
                      tar -xzvf tbb-2017_U3.tgz
     ##
     #URL https://github.com/01org/tbb/archive/2017_U3.tar.gz 
@@ -638,16 +649,16 @@ 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/v0.12.0.tar.gz -o spdlog-v0.12.0.tar.gz &&
-                     ${SHASUM} 5cfd6a0b3182a88e1eb35bcb65a7ef9035140d7c73b16ba6095939dbf07325b9  spdlog-v0.12.0.tar.gz &&
-                     tar -xzf spdlog-v0.12.0.tar.gz 
+    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.14.0.tar.gz -o spdlog-v0.14.0.tar.gz &&
+                     ${SHASUM} eb5beb4e53f4bfff5b32eb4db8588484bdc15a17b90eeefef3a9fc74fec1d83d spdlog-v0.14.0.tar.gz &&
+                     tar -xzf spdlog-v0.14.0.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-0.12.0
+    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog-0.14.0
     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
     CONFIGURE_COMMAND ""
     BUILD_COMMAND ""
@@ -751,7 +762,6 @@ message("CPACK_SOURCE_IGNORE_FILES = ${CPACK_SOURCE_IGNORE_FILES}")
 # Recurse into Salmon source directory
 add_subdirectory ( src )
 #add_dependencies(salmon RapMap)
-
 # build a CPack driven installer package
 include (CPack)
 

doc/source/salmon.rst

@@ -677,6 +677,7 @@ and/or `carlk@cs.cmu.edu`).  If you encounter any bugs, please file a
 References
 ----------
 
+
 .. [#express] Roberts, Adam, and Lior Pachter. "Streaming fragment assignment for real-time analysis of sequencing experiments." Nature Methods 10.1 (2013): 71-73.
    
 .. [#roberts] Roberts, Adam, et al. "Improving RNA-Seq expression estimates by correcting for fragment bias." Genome Biology 12.3 (2011): 1.

docker/Dockerfile

@@ -1,12 +1,13 @@
 # image: COMBINE-lab/salmon
 # This dockerfile is based on the one created by
 # Titus Brown (available at https://github.com/ctb/2015-docker-building/blob/master/salmon/Dockerfile)
+#FROM insilicodb/bioconductor 
 FROM ubuntu:16.04
 MAINTAINER salmon.maintainer@gmail.com
 
 ENV PACKAGES git gcc make g++ cmake libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev curl unzip autoconf
-ENV SALMON_VERSION 0.8.2
+ENV SALMON_VERSION 0.9.0
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

include/AlignmentGroup.hpp

@@ -2,64 +2,63 @@
 #define ALIGNMENT_GROUP
 
 extern "C" {
-#include "io_lib/scram.h"
 #include "io_lib/os.h"
+#include "io_lib/scram.h"
 #undef max
 #undef min
 }
 
-
 // Cereal includes
-#include "cereal/types/vector.hpp"
 #include "cereal/archives/binary.hpp"
+#include "cereal/types/vector.hpp"
 
-#include <vector>
-#include "SalmonMath.hpp"
 #include "ReadPair.hpp"
+#include "SalmonMath.hpp"
+#include <vector>
 
-template <typename FragT>
-class AlignmentGroup {
-    public:
-        AlignmentGroup() : read_(nullptr), isUniquelyMapped_(true) { alignments_.reserve(10); }
-        AlignmentGroup(AlignmentGroup& other) = delete;
-        AlignmentGroup(AlignmentGroup&& other) = default;
-        AlignmentGroup& operator=(AlignmentGroup& other) = delete;
-        AlignmentGroup& operator=(AlignmentGroup&& other) = delete;
+template <typename FragT> class AlignmentGroup {
+public:
+  AlignmentGroup() : read_(nullptr), isUniquelyMapped_(true) {
+    alignments_.reserve(10);
+  }
+  AlignmentGroup(AlignmentGroup& other) = delete;
+  AlignmentGroup(AlignmentGroup&& other) = default;
+  AlignmentGroup& operator=(AlignmentGroup& other) = delete;
+  AlignmentGroup& operator=(AlignmentGroup&& other) = delete;
 
-        void setRead(std::string* r) { read_ = r; }
-        std::string* read() { return read_; }
+  void setRead(std::string* r) { read_ = r; }
+  std::string* read() { return read_; }
 
-        inline std::vector<FragT>& alignments() { return alignments_; }
-        void emplaceAlignment(FragT&& p) { alignments_.emplace_back(p); }
-        void addAlignment(FragT& p) { alignments_.push_back(p); }
+  inline std::vector<FragT>& alignments() { return alignments_; }
+  void emplaceAlignment(FragT&& p) { alignments_.emplace_back(p); }
+  void addAlignment(FragT& p) { alignments_.push_back(p); }
 
-        void clearAlignments() {
-            alignments_.clear();
-            isUniquelyMapped_ = true;
-        }
+  void clearAlignments() {
+    alignments_.clear();
+    isUniquelyMapped_ = true;
+  }
 
-        inline bool& isUniquelyMapped() { return isUniquelyMapped_; }
-        inline size_t numAlignments() { return alignments_.size(); }
-        inline size_t size() { return numAlignments(); }
+  inline bool& isUniquelyMapped() { return isUniquelyMapped_; }
+  inline size_t numAlignments() { return alignments_.size(); }
+  inline size_t size() { return numAlignments(); }
 
-        template <typename Archive>
-        void serialize(Archive& archive) {
-            archive(alignments_);
-        }
+  template <typename Archive> void serialize(Archive& archive) {
+    archive(alignments_);
+  }
 
-        /**
-         *  Sort the alignments by their transcript ids
-         */
-        inline void sortHits() {
-            std::sort(alignments_.begin(), alignments_.end(),
-                    [](const FragT& x, const FragT& y) -> bool {
-                        return x->transcriptID() < y->transcriptID();
-                     });
-        }
+  /**
+   *  Sort the alignments by their transcript ids
+   */
+  inline void sortHits() {
+    std::sort(alignments_.begin(), alignments_.end(),
+              [](const FragT& x, const FragT& y) -> bool {
+                return x->transcriptID() < y->transcriptID();
+              });
+  }
 
-    private:
-        std::vector<FragT> alignments_;
-        std::string* read_;
-        bool isUniquelyMapped_;
+private:
+  std::vector<FragT> alignments_;
+  std::string* read_;
+  bool isUniquelyMapped_;
 };
 #endif // ALIGNMENT_GROUP