xMerge branch 'master' of https://github.com/COMBINE-lab/minnow

CMakeLists.txt

@@ -8,14 +8,13 @@ list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake")
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-set(KSW_FLAGS "-march=native -DHAVE_KALLOC")
-set(RBF_CPP_FLAGS "-g -mbmi2 -msse4 -pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function")
-set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") 
+set(RBF_CPP_FLAGS "-pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function -O3")
+#set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") 
 
 #set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wduplicated-branches -Wduplicated-cond -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wnull-dereference -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wrestrict -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") 
 
 
-set(OPT_FLAGS "-O3 -g -ffast-math -fPIC -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing")
+#set(OPT_FLAGS "-O3 -g -ffast-math -fPIC -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing")
 #set(OPT_FLAGS "-fprofile-generate -O3 -DNDEBUG -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing")
 #set(OPT_FLAGS "-fprofile-use -fprofile-correction -O3 -DNDEBUG -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing")
 set(DEBUG_FLAGS "-pg -g -gstabs -no-pie")

README.md

@@ -1,6 +1,10 @@
 [![Build Status](https://travis-ci.org/COMBINE-lab/minnow.svg?branch=master)](https://travis-ci.org/COMBINE-lab/minnow)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/)
+[![Join the chat at https://gitter.im/minnow-sim](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/minnow-sim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
 # Minnow ( read level simulator for dscRNA-seq data)
 
+
 Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or UMI deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-seq (dscRNA-seq) experiment simulation framework.  Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as PCR amplification,  CB (cellular barcodes) and UMI (Unique Molecule Identifiers) selection, and sequence fragmentation and sequencing. 
 
 Minnow is a read level simulator for droplet based single cell RNA-seq data. Minnow simulates the reads by sampling sequences from the underlying de-Bruijn graph (using `--dbg`) of the reference transcriptome or alternatively just samples sequences from the reference transcriptome. As the `--dbg` option also enables other features of the software, it is useful to describe those.
@@ -16,7 +20,11 @@ Minnow is a read level simulator for droplet based single cell RNA-seq data. Min
 [tutorial](https://combine-lab.github.io/alevin-tutorial/2019/running-minnow/)
 
 
-## Installation 
+
+## Installation
+### Via conda 
+`conda install minnow -c bioconda`
+### Manual installation (latest)
 Minnow is written in C++14 and tested in a ubuntu server, please let us know if you have difficulty compiling it in your own machine.
 
 ```console
@@ -93,7 +101,7 @@ The above process are required to be executed sequencially,
 
 for ease of use we uploaded the de-Bruijn graph and reference transcripts are uploaded in zenodo. 
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2556439.svg)](https://doi.org/10.5281/zenodo.2556439)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2556439.svg)](https://doi.org/10.5281/zenodo.2556439) [![Join the chat at https://gitter.im/minnow-sim/community](https://badges.gitter.im/minnow-sim/community.svg)](https://gitter.im/minnow-sim/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 

include/strict_fstream.hpp

@@ -27,7 +27,7 @@ static std::string strerror()
     {
         buff = "Unknown error";
     }
-#elif (_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE
+#elif (_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 || defined(__APPLE__)) && ! _GNU_SOURCE
 // XSI-compliant strerror_r()
     if (strerror_r(errno, &buff[0], buff.size()) != 0)
     {