diff --git a/Makefile b/Makefile
index 2349d469ca926afb5494f31fc6d8f2c074b8c3e9..a594ed5322302961cc510bef43b7d8ee6d3ef1f2 100644
--- a/Makefile
+++ b/Makefile
@@ -9,8 +9,10 @@ OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o))
CXX = g++ -std=c++14
CC = $(CXX)
-# SeqAn
-SEQAN_LIB = ./external/seqan-library-2.2.0/include/
+# SeqAn and Biforst
+SEQAN_INC = ./external/seqan-library-2.2.0/include/
+BIFROST_INC = ./external/bifrost/local/include
+BIFROST_LIB = ./external/bifrost/local/lib
# Date and version number from git
DATE := $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
@@ -19,13 +21,13 @@ CXXFLAGS += -DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\"
# Compiler flags
CXXFLAGS += -DSEQAN_HAS_ZLIB=1 -DSEQAN_DISABLE_VERSION_CHECK
-CXXFLAGS += -W -Wall -pedantic
-CXXFLAGS += -Wno-long-long -Wno-variadic-macros -Wno-unused-result -Wno-class-memaccess -Wno-deprecated-copy -Wno-alloc-size-larger-than
+#CXXFLAGS += -W -Wall -pedantic
+CXXFLAGS += -Wno-long-long -Wno-variadic-macros -Wno-unused-result -Wno-class-memaccess -Wno-deprecated-copy -Wno-alloc-size-larger-than -Wno-subobject-linkage
CXXFLAGS += -march=native -DMAX_KMER_SIZE=64
-CXXFLAGS += -I$(SEQAN_LIB)
+CXXFLAGS += -I$(SEQAN_INC) -I$(BIFROST_INC)
# Linker flags
-LDLIBS = -lbifrost -pthread -lz -rdynamic -DMAX_KMER_SIZE=64
+LDLIBS = -L$(BIFROST_LIB) -l:libbifrost.a -pthread -lz -rdynamic -DMAX_KMER_SIZE=64
# MacOS users might have to comment out the next line
LDLIBS += -lrt
diff --git a/README.md b/README.md
index 255bdd69fce59c271800da3ff3c0328a04830127..f94e9f45305b9c2d9cc0651b89d4e361cf6941cf 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,9 @@ The functions are designed to be chained into a workflow, together with calls to
__The recommended way of running *popins4snake* is using the Snakemake workflow [PopinSnake](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake).__
-You can find installation instructions for all dependencies of the PopinSnake workflow, including instructions for installing popins4snake in the [PopinSnake README file](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake/-/blob/main/README.md).
+<!--
+You can find installation instructions for all dependencies of the PopinSnake workflow, including instructions for installing popins4snake, in the [PopinSnake README file](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake/-/blob/main/README.md).
+-->
@@ -16,9 +18,7 @@ You can find installation instructions for all dependencies of the PopinSnake wo
1. [Requirements](#requirements)
1. [Installation](#installation)
-1. [Usage](#usage)
-1. [Summary of popins4snake functions](#summary-of-popins4snake-functions)
-1. [Help](#help)
+1. [Usage and Functions](#usage-and-functions)
1. [References](#references)
@@ -32,7 +32,9 @@ Prior to the installation make sure your system meets all the requirements:
| C++14 capable compiler | g++ vers. 4.9.2, 5.5.0, 7.2.0, 9.4.0 |
| CMake | >= 2.8.12 (available through Conda) |
-For the default settings of popins4snake a *Bifrost* installation with MAX_KMER_SIZE=64 is required (see below). *Bifrost* is included as a submodule in this repository and comes with a recursive clone. Presently, the conda package of Bifrost does not meet this requirement.
+For the default settings of popins4snake a [*Bifrost*](https://github.com/pmelsted/bifrost) installation with MAX_KMER_SIZE=64 is required (see below).
+Presently, the conda package of Bifrost does not meet this requirement.
+Therefore, *Bifrost* is included as a submodule in this repository.
CMake is required for installing *Bifrost*.
@@ -49,30 +51,17 @@ git clone --recursive https://gitlab.informatik.hu-berlin.de/fonda_a6/popins4sna
```
Next, compile and install *Bifrost* with `MAX_KMER_SIZE=64`. You can either install it globally on your system or locally in your home directory.
-We recommend installing it locally to your home directory in the folder `~/local` by using:
+We here describe how to install it locally in a folder `external/bifrost/local`.
+This is the location, where the `popins4snake` Makefile will look for it by default.
```
-mkdir -p ~/local
cd external/bifrost && mkdir build && cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=~/local -DMAX_KMER_SIZE=64
+mkdir ../local
+cmake .. -DCMAKE_INSTALL_PREFIX=../local -DMAX_KMER_SIZE=64
make
make install
```
-To install *Bifrost* globally, omit the `-DCMAKE_INSTALL_PREFIX=~/local` in the CMake command.
-
-If you follow our recommendation of installing *Bifrost* locally, make sure that the local directory is appended to the relevant system variables.
-Setting these paths is necessary for compiling and running *popins4snake*.
-
-```
-export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:~/local/include/
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/local/lib/
-export LIBRARY_PATH=$LIBRARY_PATH:~/local/lib/
-export PATH=$PATH:~/local/lib/
-```
-
-To make the local install directory (and *Bifrost*) permanently available (for running *popins4snake*), we recommend to add these exports to your `.bashrc`.
-
Now, you can compile *popins4snake*:
```
@@ -87,9 +76,13 @@ The [PopIns2 Wiki](https://github.com/kehrlab/PopIns2/wiki/Troubleshooting---FAQ
-## Usage
+## Usage and Functions
-To get an overview of the functions offered in *popins4snake*, you can run `./popins4snake -h` after installation:
+The recommended way of running *popins4snake* is using the Snakemake workflow [PopinSnake](https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake).
+
+To get an overview of the functions offered in *popins4snake*, you can run `./popins4snake -h` after installation.
+To display the help page of each of the *popins4snake* functions, type `./popins4snake <command> --help`.
+The former will print something similar to this:
```
=====================================================================
@@ -114,16 +107,11 @@ COMMAND
VERSION
0.1.0-a52d4f5, Date: 2022-08-25 14:42:31
-Try `../popins4snake/popins4snake COMMAND --help' for more information on each command.
+Try `./popins4snake COMMAND --help' for more information on each command.
```
-## Summary of *popins4snake* functions
-
-To display the help page of each of the *popins4snake* functions, type `./popins4snake <command> --help`.
-
-
### The `crop-unmapped` function
```
popins4snake crop-unmapped [OPTIONS] sample.bam