burkhard-morgenstern · smortezah · Nov 17, 2019 · Nov 17, 2019 · Nov 17, 2019 · Nov 17, 2019
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,6 @@ slope-spam.exe
 out.dmat
 pattern
 paper
+Slope-SpaM.pdf
+Mash.pdf
+chapter3.pdf
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -37,43 +37,43 @@ target_link_libraries(slope-spam
     stdc++fs
 )
 
-add_executable(slope-spam-test
-    $<TARGET_OBJECTS:slope-spam-common>
-    src/config.test.cpp
-    src/main.test.cpp
-    src/string.test.cpp
-    src/spam/pattern.test.cpp
-    src/spam/wordlist.test.cpp
-)
-
-target_include_directories(slope-spam-test PRIVATE
-    ${CMAKE_SOURCE_DIR}/third_party/catch2/single_include
-)
-
-target_link_libraries(slope-spam-test
-    ${CMAKE_THREAD_LIBS_INIT}
-    fmt::fmt
-    stdc++fs
-)
-
-add_test(slope-spam-test slope-spam-test)
-
-add_executable(generator
-    src/generator.cpp
-)
-
-add_executable(simulate
-    $<TARGET_OBJECTS:slope-spam-common>
-    src/simulate.cpp
-    src/generator.cpp
-)
-
-target_compile_definitions(simulate
-    PRIVATE -DGENERATOR_NO_MAIN
-)
-
-target_link_libraries(simulate
-    ${CMAKE_THREAD_LIBS_INIT}
-    fmt::fmt
-    stdc++fs
-)
+# add_executable(slope-spam-test
+#     $<TARGET_OBJECTS:slope-spam-common>
+#     src/config.test.cpp
+#     src/main.test.cpp
+#     src/string.test.cpp
+#     src/spam/pattern.test.cpp
+#     src/spam/wordlist.test.cpp
+# )
+
+# target_include_directories(slope-spam-test PRIVATE
+#     ${CMAKE_SOURCE_DIR}/third_party/catch2/single_include
+# )
+
+# target_link_libraries(slope-spam-test
+#     ${CMAKE_THREAD_LIBS_INIT}
+#     fmt::fmt
+#     stdc++fs
+# )
+
+# add_test(slope-spam-test slope-spam-test)
+
+# add_executable(generator
+#     src/generator.cpp
+# )
+
+# add_executable(simulate
+#     $<TARGET_OBJECTS:slope-spam-common>
+#     src/simulate.cpp
+#     src/generator.cpp
+# )
+
+# target_compile_definitions(simulate
+#     PRIVATE -DGENERATOR_NO_MAIN
+# )
+
+# target_link_libraries(simulate
+#     ${CMAKE_THREAD_LIBS_INIT}
+#     fmt::fmt
+#     stdc++fs
+# )
diff --git a/Mash.pdf b/Mash.pdf
diff --git a/README.md b/README.md
@@ -1,55 +1,58 @@
-# About
+# Slope-SpaM &nbsp;&nbsp;&nbsp;&nbsp; [![Codacy Badge](https://api.codacy.com/project/badge/Grade/ebcd8da0747b48da84693965306a4ac8)](https://www.codacy.com/manual/smortezah/Slope-SpaM?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=burkhard-morgenstern/Slope-SpaM&amp;utm_campaign=Badge_Grade) ![GitHub repo size](https://img.shields.io/github/repo-size/burkhard-morgenstern/Slope-SpaM) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](LICENSE)
 
 `Slope-SpaM` estimates phylogenetic distances between two DNA sequences. More precisely, for a set of input sequuences in FASTA format, it estimates all pairwise Jukes-Cantor distances. That is, for each pair of sequences it estimates the average number of substitutions per sequence positions that have occurred since the sequences have evolved from their last common anchestor. The output of the program is a matrix with these pairwise distances in phylip format.
 
 To estimate the phylogenetic distance between two DNA sequences, Slope-SpaM calculates the number of word matches for two different word lengths k_min and k_max. Instead of words, so-called spaced-words may be used, i.e. words containing wildcard characters at certain positions specified by the user. To this end, a binary pattern representing "match positions" ('1') and "don't-care positions" ('0') has to be provided as input to the program.
 
-If spaced words are used, two binary patterns with k_min match positions and k_min match positions are used by shortening the input pattern specified by the user (i.e. by using suitable prefixes of this pattern). 
+If spaced words are used, two binary patterns with k_min match positions and k_max match positions are used by shortening the input pattern specified by the user (i.e. by using suitable prefixes of this pattern). 
 
 For more details, check our [paper](https://www.biorxiv.org/content/10.1101/527515v1).
-
-# Installation
 
-The installation requires `cmake` (>= 3.8.2) and a C++17 compliant C++ compiler. Use the following commands to install `Slope-SpaM`:
+## Installation
+The installation requires CMake >= 3.8.2 and a C++17 compliant compiler.
+
+### Linux / macOS
+CMake v3.15.5 can be downloaded [here](https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5-Linux-x86_64.sh) for Linux, and [here](https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5-Darwin-x86_64.dmg) for macOS. Use the following commands to install `Slope-SpaM`; the binaries will be provided in the `bin/` folder:
 
 	git clone --recursive https://github.com/burkhard-morgenstern/Slope-SpaM
 	cd Slope-SpaM
 	mkdir build
 	cd build
 	cmake -DCMAKE_BUILD_TYPE=Release ..
 	make
+	mkdir ../bin
+	mv slope-spam slope-spam-test generator simulate ../bin
 
 If the default compiler available does not support C++17, the compiler can be set to e.g. GCC 8 using:
 
 	cmake -DCMAKE_C_COMPILER=gcc-8, -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_BUILD_TYPE=Release ..
 
-# Example Usages
+### Windows 10
+After installing `wsl` (Windows Subsystem for Linux), you can use the same commands as for Linux/macOS.
+
+## Example Usages
 
 	./slope-spam -o out.dmat -p 10101001010101111111101010101001111111111000111 multi_fasta_file.fasta
 	./slope-spam -o out.dmat -k=11,14 multi_fasta_file.fasta
 	./slope-spam --as-reads -o out.dmat reads1.fasta reads2.fasta
 	./slope-spam --help
-
-# Options
 
-Option | Description
-:---: | :---
--o, --output | The output file. Ignored if multiple inputs are given.
--p, --pattern | The binary word pattern used to create wordlists from sequences. May only include '0' and '1' characters.
--k, --kmer-lengths | Comma-separated list of wordlengths to consider when calculating the distance between two sequences.
--a, --as-reads | Comma-separated list of wordlengths to consider when calculating the distance between two sequences.
--h, --help | Show help.
-input files... | Fasta files or directories of fasta files to process. If more than one input file is given, the option output is ignored. Instead for each .fasta file a .dmat file and for each directory a .dir.dmat file with the same name is created. If --as-reads is not specified, one output matrix is created for each input file. If --as-reads is specified, one output matrix using each input file as a single sequence is created.
+## Options
+| Option                        | Description |
+| ---                           | ---         |
+| -o, --output <img width=600/> | The output file. Ignored if multiple inputs are given. <img width=600/> |
+| -p, --pattern                 | The binary word pattern used to create wordlists from sequences. May only include '0' and '1' characters. |
+| -k, --kmer-lengths            | Comma-separated list of wordlengths to consider when calculating the distance between two sequences. |
+| -a, --as-reads                | Comma-separated list of wordlengths to consider when calculating the distance between two sequences. |
+| -h, --help                    | Show help. |
+| input files...                | FASTA files or directories of FASTA files to process. If more than one input file is given, the option output is ignored. Instead for each .fasta file a .dmat file and for each directory a .dir.dmat file with the same name is created. If --as-reads is not specified, one output matrix is created for each input file. If --as-reads is specified, one output matrix using each input file as a single sequence is created. |
 
-## License
-
-Copyright © 2019 - Alexander Linne
+### License
+Copyright © 2019 Alexander Linne
 
 License GPLv3+: GNU GPL version 3 or later.
 
 This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at <http://gnu.org/licenses/gpl.html>.
 
-## Contact
-
+### Contact
 In case of bugs or unexpected errors don't hesitate to send me a mail: [email protected]
-
diff --git a/bin/generator b/bin/generator
diff --git a/bin/simulate b/bin/simulate
diff --git a/bin/slope-spam-test b/bin/slope-spam-test
diff --git a/bloom/Makefile b/bloom/Makefile
@@ -0,0 +1,39 @@
+#
+# Open Bloom Filter Master MakeFile
+# By Arash Partow - 2000
+#
+# URL: http://www.partow.net/programming/hashfunctions/index.html
+#
+# Copyright Notice:
+# Free use of this library is permitted under the guidelines
+# and in accordance with the most current version of the
+# Common Public License.
+# http://www.opensource.org/licenses/cpl1.0.php
+#
+
+COMPILER         = -c++
+OPTIMIZATION_OPT = -O3
+OPTIONS          = -pedantic-errors -ansi -Wall -Wextra -Werror -Wno-long-long $(OPTIMIZATION_OPT) -o
+LINKER_OPT       = -L/usr/lib -lstdc++
+
+BUILD+=bloom_filter_example01
+BUILD+=bloom_filter_example02
+BUILD+=bloom_filter_example03
+
+all: $(BUILD)
+
+bloom_filter_example01: bloom_filter.hpp bloom_filter_example01.cpp
+	$(COMPILER) $(OPTIONS) bloom_filter_example01 bloom_filter_example01.cpp $(LINKER_OPT)
+
+bloom_filter_example02: bloom_filter.hpp bloom_filter_example02.cpp
+	$(COMPILER) $(OPTIONS) bloom_filter_example02 bloom_filter_example02.cpp $(LINKER_OPT)
+
+bloom_filter_example03: bloom_filter.hpp bloom_filter_example03.cpp
+	$(COMPILER) $(OPTIONS) bloom_filter_example03 bloom_filter_example03.cpp $(LINKER_OPT)
+
+clean:
+	rm -f core *.o *.bak *stackdump *#
+
+#
+# The End !
+#