Merge branch 'develop'

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.1)
+cmake_minimum_required (VERSION 3.9)
 
 enable_testing()
 
@@ -51,7 +51,7 @@ endif()
 ## Set the standard required compile flags
 # Nov 18th --- removed -DHAVE_CONFIG_H
 set (REMOVE_WARNING_FLAGS "-Wno-unused-function;-Wno-unused-local-typedefs")
-set (TGT_COMPILE_FLAGS "-ftree-vectorize;-funroll-loops;-fPIC;-fomit-frame-pointer;-O3")
+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}")
 
 if (APPLE)
@@ -76,6 +76,8 @@ else ()
   set(GCCVERSION "5.2")
 endif()
 
+include(CheckIPOSupported)
+
 set(THREADS_PREFER_PTHREAD_FLAG ON)
 find_package(Threads REQUIRED)
 

current_version.txt

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

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 = '0.11.1'
+release = '0.11.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/salmon.rst

@@ -428,11 +428,11 @@ traditional rich equivalence classes.  We recommend 4 as a reasonable parameter
 for this option (it is what was used in the range-factorization paper).
 
 """"""""""""""
-``--useVBOpt``
+``--useEM``
 """"""""""""""
 
-Use the variational Bayesian EM algorithm rather than the "standard"
-EM algorithm to optimize abundance estimates.  The details of the VBEM
+Use the "standard" EM algorithm to optimize abundance estimates
+instead of the variational Bayesian EM algorithm.  The details of the VBEM
 algorithm can be found in [#salmon]_.  While both the standard EM and
 the VBEM produce accurate abundance estimates, there are some
 trade-offs between the approaches.  Specifically, the sparsity of
@@ -465,8 +465,8 @@ using VB optimization.
    of the different algorithms is an ongoing area of research.  However, preliminary
    testing suggests that the sparsity-inducing effect of running the VBEM with a small
    prior may lead, in general, to more accurate estimates (the current testing was
-   performed mostly through simulation).  If these results persist through more
-   thorough testing, the VBEM may become the default inference mode in future versions of Salmon.
+   performed mostly through simulation). Hence, the VBEM is the default, and the
+   standard EM algorithm is accessed via the `--useEM` flag.
 
 
 """""""""""""""""""

docker/Dockerfile

@@ -6,7 +6,7 @@ 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 0.11.1
+ENV SALMON_VERSION 0.11.2
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

include/SalmonConfig.hpp

@@ -27,8 +27,8 @@
 namespace salmon {
 constexpr char majorVersion[] = "0";
 constexpr char minorVersion[] = "11";
-constexpr char patchVersion[] = "1";
-constexpr char version[] = "0.11.1";
+constexpr char patchVersion[] = "2";
+constexpr char version[] = "0.11.2";
 constexpr uint32_t indexVersion = 2;
 constexpr char requiredQuasiIndexVersion[] = "q5";
 } // namespace salmon

include/ksw2pp/KSW2Aligner.hpp

@@ -48,6 +48,13 @@ class KSW2Aligner {
   KSW2Aligner(int8_t match = 2, int8_t mismatch = -4);
   KSW2Aligner(std::vector<int8_t> mat);
 
+  int transformSequenceKSW2(const char* const queryOriginal, const int queryLength,
+                            std::vector<unsigned char>& queryTransformed);
+
+  int transformSequencesKSW2(const char* const queryOriginal, const int queryLength,
+                             const char* const targetOriginal, const int targetLength,
+                             std::vector<unsigned char>& queryTransformed,
+                             std::vector<unsigned char>& targetTransformed);
   /**
    * Variants of the operator that require both an explicit type tag to
    * determine the type of alignment to perform, as well as a pointer to