BayesTyper (v1.2)

.gitignore

@@ -0,0 +1,2 @@
+# Ignore Mac specific files
+.DS_Store

CMakeLists.txt

@@ -14,11 +14,15 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 
-SET(CMAKE_CXX_FLAGS "--std=c++11 -g -Wall -O3 -DBT_VERSION='\"v1.1 ${GIT_LAST_COMMIT_HASH}\"' -lpthread")
+SET(CMAKE_CXX_FLAGS "--std=c++11 -g -Wall -O3 -DBT_VERSION='\"v1.2 ${GIT_LAST_COMMIT_HASH}\"' -lpthread")
 
 FIND_PACKAGE(Boost COMPONENTS program_options system filesystem iostreams REQUIRED)
 message(STATUS ${Boost_LIBRARIES})
+
+add_subdirectory(${CMAKE_SOURCE_DIR}/external/kmc_api)
+add_subdirectory(${CMAKE_SOURCE_DIR}/external/libbf)
 add_subdirectory(${CMAKE_SOURCE_DIR}/src/vcf++)
+add_subdirectory(${CMAKE_SOURCE_DIR}/src/kmerBloom)
 add_subdirectory(${CMAKE_SOURCE_DIR}/src/bayesTyper)
 add_subdirectory(${CMAKE_SOURCE_DIR}/src/bayesTyperTools)
-add_subdirectory(${CMAKE_SOURCE_DIR}/src/bayesTyperTools/scripts)
+add_subdirectory(${CMAKE_SOURCE_DIR}/src/bayesTyperTools/scripts)

external/kmc_api/CMakeLists.txt

@@ -0,0 +1,7 @@
+project(kmc)
+
+SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib)
+
+include_directories(${CMAKE_SOURCE_DIR}/external/kmc_api)
+
+add_library(${PROJECT_NAME} kmc_file.cpp kmer_api.cpp mmer.cpp)

external/libbf/.clang-format

@@ -0,0 +1,41 @@
+---
+AccessModifierOffset: -2
+AlignEscapedNewlinesLeft: false
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackParameters: true
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: false
+ColumnLimit: 80
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 2
+Cpp11BracedListStyle: true
+IndentCaseLabels: true
+IndentWidth: 2
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+
+# Force pointers to the type
+DerivePointerAlignment: false
+PointerAlignment: Left
+
+# Put space after = and after control statements
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+Standard: Cpp11
+UseTab: Never
+BreakConstructorInitializersBeforeComma: false
+...

external/libbf/.gitignore

@@ -0,0 +1,6 @@
+.*swp
+.*swo
+.DS_Store
+build
+doc/gh-pages
+Makefile

external/libbf/CMakeLists.txt

@@ -0,0 +1,20 @@
+# -- Project Setup ------------------------------------------------------------
+
+project(libbf)
+
+SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib)
+
+include_directories(${CMAKE_SOURCE_DIR}/external/libbf)
+
+set(libbf_sources
+  src/bitvector.cpp
+  src/counter_vector.cpp
+  src/hash.cpp
+  src/bloom_filter/a2.cpp
+  src/bloom_filter/basic.cpp
+  src/bloom_filter/bitwise.cpp
+  src/bloom_filter/counting.cpp
+  src/bloom_filter/stable.cpp
+)
+
+add_library(libbf ${libbf_sources})

external/libbf/COPYING

@@ -0,0 +1,28 @@
+Copyright (c) 2016, Matthias Vallentin
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    1. Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+
+    3. Neither the name of the copyright holder nor the names of its
+       contributors may be used to endorse or promote products derived from
+       this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

external/libbf/README.md

@@ -0,0 +1,168 @@
+**libbf** is a C++11 library which implements [various Bloom
+filters][blog-post], including:
+
+- Basic
+- Counting
+- Spectral MI
+- Spectral RM
+- Bitwise
+- A^2
+- Stable
+
+[blog-post]: http://matthias.vallentin.net/blog/2011/06/a-garden-variety-of-bloom-filters/
+
+Synopsis
+========
+
+    #include <iostream>
+    #include <bf.h>
+
+    int main()
+    {
+      bf::basic_bloom_filter b(0.8, 100);
+
+      // Add two elements.
+      b.add("foo");
+      b.add(42);
+
+      // Test set membership
+      std::cout << b.lookup("foo") << std::endl;  // 1
+      std::cout << b.lookup("bar") << std::endl;  // 0
+      std::cout << b.lookup(42) << std::endl;     // 1
+
+      // Remove all elements.
+      b.clear();
+      std::cout << b.lookup("foo") << std::endl;  // 0
+      std::cout << b.lookup(42) << std::endl;     // 0
+
+      return 0;
+    }
+
+Requirements
+============
+
+- A C++11 compiler (GCC >= 4.7 or Clang >= 3.2)
+- CMake (>= 2.8)
+
+Installation
+============
+
+The build process uses CMake, wrapped in autotools-like scripts. The configure
+script honors the `CXX` environment variable to select a specific C++compiler.
+For example, the following steps compile libbf with Clang and install it under
+`PREFIX`:
+
+    CXX=clang++ ./configure --prefix=PREFIX
+    make
+    make test
+    make install
+
+Documentation
+=============
+
+The most recent version of the Doxygen API documentation exists at
+<http://mavam.github.io/libbf/api>. Alternatively, you can build the
+documentation locally via `make doc` and then browse to
+`doc/gh-pages/api/index.html`.
+
+Usage
+=====
+
+After having installed libbf, you can use it in your application by including
+the header file `bf.h` and linking against the library. All data structures
+reside in the namespace `bf` and the following examples assume:
+
+    using namespace bf;
+
+Each Bloom filter inherits from the abstract base class `bloom_filter`, which
+provides addition and lookup via the virtual functions `add` and `lookup`.
+These functions take an *object* as argument, which serves a light-weight view
+over sequential data for hashing.
+
+For example, if you can create a basic Bloom filter with a desired
+false-positive probability and capacity as follows:
+
+    // Construction.
+    bloom_filter* bf = new basic_bloom_filter(0.8, 100);
+
+    // Addition.
+    bf->add("foo");
+    bf->add(42);
+
+    // Lookup.
+    assert(bf->lookup("foo") == 1);
+    assert(bf->lookup(42) == 1);
+
+    // Remove all elements from the Bloom filter.
+    bf->clear();
+
+In this case, libbf computes the optimal number of hash functions needed to
+achieve the desired false-positive rate which holds until the capacity has been
+reached (80% and 100 distinct elements, in the above example). Alternatively,
+you can construct a basic Bloom filter by specifying the number of hash
+functions and the number of cells in the underlying bit vector:
+
+    bloom_filter* bf = new basic_bloom_filter(make_hasher(3), 1024);
+
+Since not all Bloom filter implementations come with closed-form solutions
+based on false-positive probabilities, most constructors use this latter form
+of explicit resource provisioning.
+
+In the above example, the free function `make_hasher` constructs a *hasher*-an
+abstraction for hashing objects *k* times. There exist currently two different
+hasher, a `default_hasher` and a
+[`double_hasher`](http://www.eecs.harvard.edu/~kirsch/pubs/bbbf/rsa.pdf). The
+latter uses a linear combination of two pairwise-independent, universal hash
+functions to produce the *k* digests, whereas the former merely hashes the
+object *k* times.
+
+Evaluation
+----------
+
+libbf also ships with a small Bloom filter tool `bf` in the test directory.
+This program supports evaluation the accuracy of the different Bloom filter
+flavors with respect to their false-positive and false-negative rates. Have a
+look at the console help (`-h` or `--help`) for detailed usage instructions.
+
+The tool operates in two phases:
+
+1. Read input from a file and insert it into a Bloom filter
+2. Query the Bloom filter and compare the result to the ground truth
+
+For example, consider the following input file:
+
+    foo
+    bar
+    baz
+    baz
+    foo
+
+From this input file, you can generate the real ground truth file as follows:
+
+    sort input.txt | uniq -c | tee query.txt
+       1 bar
+       2 baz
+       2 foo
+
+The tool `bf` will compute false-positive and false-negative counts for each
+element, based on the ground truth given. In the case of a simple counting
+Bloom filter, an invocation may look like this:
+
+    bf -t counting -m 2 -k 3 -i input.txt -q query.txt | column -t
+
+Yielding the following output:
+
+    TN  TP  FP  FN  G  C  E
+    0   1   0   0   1  1  bar
+    0   1   0   1   2  1  baz
+    0   1   0   2   2  1  foo
+
+The column headings denote true negatives (`TN`), true positives (`TP`), false
+positives (`FP`), false negatives (`FN`), ground truth count (`G`), actual
+count (`C`), and the queried element. The counts are cumulative to support
+incremental evaluation.
+
+License
+========
+
+libbf comes with a BSD-style license (see [COPYING](COPYING) for details).

external/libbf/aux/macports/README

@@ -0,0 +1,9 @@
+Add the line
+
+    file:///path/to/this/directory
+
+to /opt/local/etc/macports/sources.conf *before* the rsync source and run
+
+    sudo portindex
+
+in the same directory where this README is located.