Commit 79a47eef authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.0.5

parent da82e3c8
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test/*.idx
test/*.meta
test/test.out
# Compiled Object files
*.slo
*.lo
*.o
# Compiled Dynamic libraries
*.so
*.dylib
# Compiled Static libraries
*.lai
*.la
*.a
# cmake
CMakeCache.txt
CMakeFiles
cmake_install.cmake
doc/*
bin
Makefile
Cassiopee
test/test_cassiopee
CTestTestfile.cmake
Testing
# reports
cppunit-report.xml
cassiopee.dot
*.png
test/sequence.txt.cass.idx
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>Cassiopee</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
<triggers>clean,full,incremental,</triggers>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.cdt.core.cnature</nature>
<nature>org.eclipse.cdt.core.ccnature</nature>
<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
</natures>
</projectDescription>
cmake_minimum_required (VERSION 2.8)
enable_language(C CXX)
project (Cassiopee)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
link_directories(/usr/local/lib)
set (Cassiopee_VERSION_MAJOR 1)
set (Cassiopee_VERSION_MINOR 0)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_BINARY_DIR ${CMAKE_BINARY_DIR}/bin)
set (PROJECT_DOC_DIR doc)
enable_testing()
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
#add_definitions( -DBOOST_ALL_NO_LIB )
unset(Boost_INCLUDE_DIR CACHE)
unset(Boost_LIBRARY_DIRS CACHE)
set(Boost_USE_STATIC_LIBS OFF)
find_package(Boost REQUIRED COMPONENTS iostreams serialization)
# add a target to generate API documentation with Doxygen
find_package(Doxygen)
if(DOXYGEN_FOUND)
configure_file(${PROJECT_SOURCE_DIR}/Doxyfile.in ${PROJECT_BINARY_DIR}/Doxyfile @ONLY)
add_custom_target(doc ALL
${DOXYGEN_EXECUTABLE} ${PROJECT_BINARY_DIR}/Doxyfile
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
COMMENT "Generating API documentation with Doxygen" VERBATIM
)
endif(DOXYGEN_FOUND)
FIND_PACKAGE(OpenMP)
if(OPENMP_FOUND)
set(USE_OPENMP 1)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
else()
set(USE_OPENMP 0)
endif()
# configure a header file to pass some of the CMake settings
# to the source code
configure_file (
"${PROJECT_SOURCE_DIR}/CassiopeeConfig.h.in"
"${PROJECT_BINARY_DIR}/CassiopeeConfig.h"
)
# add the binary tree to the search path for include files
# so that we will find CassiopeeConfig.h
include_directories("${PROJECT_BINARY_DIR}")
include_directories(${Boost_INCLUDE_DIR})
add_subdirectory (src)
add_subdirectory (test)
1.0.5: 18/11/16 O. Sallou
- bug fix in search with reduction
1.0.4: 08/04/16 O. Sallou
- bug fix in search with reduction
1.0.3: 04/04/15 O. Sallou
- Bug fix on min pattern size to use when limiting index size.
1.0.2: 22/03/15 O. Sallou
- Add -l option to limit the size of the index. If not specified, index will
be done based on pattern length and indels. On next index/search operations
, if -l option or pattern+indel size are longer, index will be rebuild.
1.0.1: 16/04/14 O. Sallou
- Fix case of test failure on a few archs
1.0: First version
License: GNU GPL-3+
Full text is available at http://www.gnu.org/licenses/gpl-3.0.html
Copyright (c) 2013 Olivier Sallou
cassiopee-c
===========
Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem.
It scan an input genomic sequence (dna/rna/protein) and search for a
subsequence with exact match or allowing substitutions (Hamming distance)
and/or insertion/deletions.
This program provides both a binary (Cassiopee) and a shared library.
Index is based on a suffix tree with compression. It is possible to save the
indexed sequence for later use without the need to reindex the whole sequence
(for large data sets).
See Cassiopee -h for all options.
Expected input sequence is a one-line sequence with no header. CassiopeeKnife (see later chapter) can be used to convert Fasta sequences in cassiopee input sequences.
Compilation dependencies
===========
* cppunit
* Google log (glog)
* tree.hh (included):
- Author: kasper.peeters (at) phi-sci.com
- http://tree.phi-sci.com/ under GNU GPL
* libboost-serialization-dev,libboost-iostreams-dev
Runtime dependencies
===================
* Google log (glog)
* libboost-serialization, libboost-iostreams
Compilation
===========
cmake -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_BUILD_TYPE=Debug .
make
Valgrind
=======
valgrind --leak-check=full bin/Cassiopee -s test/sequence.txt -p ggc
Static analysis
==============
CXX=/usr/share/clang/scan-build/c++-analyzer cmake .
Tests
=====
bin/test_cassiopee
or
cd test; ctest -V
Tree graph generation
=====================
API provides the graph method to generate a cassiopee.dot file.
To generate the image from the file:
dot -Tpng cassiopee.dot > cassiopee.png
Documentation
============
doxygen bin/Doxyfile
BUGS
====
CassiopeeKnife
=============
Convert an input Fasta sequence in a cassiopee input format (one line sequence
with no header).
TODO
====
COPYRIGHT
========
See license file.
Code under src/tree from http://tree.phi-sci.com/, copyright kasper.peeters@phi-sci.com
Notes on how this package can be tested.
────────────────────────────────────────
This package can be tested by executing
sh run-unit-test
in order to confirm its integrity.
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
.TH CASSIOPEE "1" "April 2014" "Cassiopee Version 1.0" "User Commands"
.SH NAME
cassiopee \- manual page for Cassiopee Version 1.0
.SH SYNOPSIS
.B cassiopee
\fI[Options]\fR \fB<sequence>\fR
.SH DESCRIPTION
.SS "Usage:"
.HP
\fB\-l\fR: maximum index depth / maximum pattern size
.HP
\fB\-u\fR: save index for later use
.HP
\fB\-s\fR: sequence to index
.HP
\fB\-p\fR: pattern to search
.HP
\fB\-f\fR: file containing pattern to search
.HP
\fB\-o\fR: output file
.HP
\fB\-r\fR: apply tree reduction
.HP
\fB\-m\fR: search mode: 0=DNA, 1=RNA, 2=Protein
.HP
\fB\-a\fR: allow alphabet ambiguity search
.HP
\fB\-n\fR: max consecutive N allowed matches in search
.HP
\fB\-e\fR: max substitution allowed matches in search
.HP
\fB\-i\fR: max indel allowed matches in search
.HP
\fB\-g\fR: generates a dot file of the graph
.HP
\fB\-d\fR: max depth of the graph
.HP
\fB\-t\fR: output format: 0:tsv (default), 1:json
.HP
\fB\-x\fR: minimum position in sequence
.HP
\fB\-y\fR: maximum position in sequence
.HP
\fB\-v\fR: show version
.HP
\fB\-h\fR: show this message
debian/tmp/usr/bin/cassiopee usr/bin
debian/tmp/usr/bin/cassiopeeknife usr/bin
debian/cassiopee.1
debian/cassiopeeknife.1
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
.TH CASSIOPEE "1" "April 2014" "Cassiopee Version 1.0" "User Commands"
.SH NAME
cassiopeeknife \- this tool is part of the cassiopee library
.SH DESCRIPTION
.SS "Usage:"
.HP
\fB\-s\fR: sequence to convert
.HP
\fB\-o\fR: output file
.HP
\fB\-v\fR: show version
.HP
\fB\-h\fR: show this message
cassiopee (1.0.5-2) UNRELEASED; urgency=medium
* Team upload.
[ Nadiya Sitdykova ]
* add autopkgtest test
-- Nadiya Sitdykova <rovenskasa@gmail.com> Wed, 23 Aug 2017 20:52:25 -0400
cassiopee (1.0.5-1) unstable; urgency=medium
* New upstream release bug fix release
-- Olivier Sallou <osallou@debian.org> Fri, 18 Nov 2016 11:30:40 +0100
cassiopee (1.0.4+dfsg-1) unstable; urgency=medium
* New upstream bug fix release
-- Olivier Sallou <osallou@debian.org> Wed, 09 Mar 2016 18:13:25 +0100
cassiopee (1.0.3+dfsg-3) unstable; urgency=medium
* Team upload
* Gcc-5 transition
Closes: #796732
* Enhance long description of doc package
* cme fix dpkg-control
* DEP5
* Add doc-base control file
* Enhance manpages
-- Andreas Tille <tille@debian.org> Mon, 31 Aug 2015 08:28:40 +0200
cassiopee (1.0.3+dfsg-2) unstable; urgency=medium
* Remove timestamp from doc for reproductibility builds (Closes: #787765).
- d/patches/HTML_timestamp-option
thanks to Maria Valentina Marin <marivalenm@gmail.com>
-- Olivier Sallou <osallou@debian.org> Fri, 05 Jun 2015 08:19:31 +0200
cassiopee (1.0.3+dfsg-1) unstable; urgency=medium
* New upstream release fixing a bug
-- Olivier Sallou <osallou@debian.org> Sat, 04 Apr 2015 22:33:05 +0100
cassiopee (1.0.2+dfsg-1) unstable; urgency=medium
* New upstream release
* d/control: Standards 3.9.6
-- Olivier Sallou <osallou@debian.org> Sun, 22 Mar 2015 10:27:53 +0100
cassiopee (1.0.1+dfsg-3) unstable; urgency=medium
* d/control: remove unnecessary dep, managed by shlibs.
-- Olivier Sallou <osallou@debian.org> Tue, 27 May 2014 07:36:52 +0200
cassiopee (1.0.1+dfsg-2) unstable; urgency=medium
* Fix missing Depends (Closes: #749302).
* Remove hard coded runtime dependencies (Closes: #749303).
-- Olivier Sallou <osallou@debian.org> Mon, 26 May 2014 12:57:58 +0200
cassiopee (1.0.1+dfsg-1) unstable; urgency=low
* New upstream release to fix FTBS on some archs (test failure)
-- Olivier Sallou <osallou@debian.org> Mon, 14 Apr 2014 09:25:54 +0200
cassiopee (1.0+dfsg-1) unstable; urgency=low
* Initial release (Closes: #743930)
-- Olivier Sallou <osallou@debian.org> Tue, 08 Apr 2014 12:59:31 +0200
Source: cassiopee
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9.0.0),
cmake,
doxygen,
libboost-serialization-dev,
libboost-iostreams-dev,
libgoogle-glog-dev,
libcppunit-dev
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cassiopee/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cassiopee/trunk/
Homepage: https://github.com/osallou/cassiopee-c
Package: cassiopee
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Description: index and search tool in genomic sequences
Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem. It scans an input
genomic sequence (dna/rna/protein) and search for a subsequence with
exact match or allowing substitutions (Hamming distance) and/or
insertion/deletions.
.
This package contains the cassiopee and cassiopeeknife tools.
Package: libcassie-doc
Architecture: all
Section: doc
Depends: ${misc:Depends},
libjs-jquery
Description: documentation for cassiopee library
Cassiopee index and search library C implementation. It is a complete
rewrite of the ruby Cassiopee gem. It scans an input genomic sequence
(dna/rna/protein) and search for a subsequence with exact match or
allowing substitutions (Hamming distance) and/or insertion/deletions.
.
This package contains the doxygen generated documentation for the
cassiopee library for development.
Package: libcassie1v5
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Conflicts: libcassie1
Replaces: libcassie1
Description: library implementating search algorithms
Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem. It scans an input
genomic sequence (dna/rna/protein) and search for a subsequence with
exact match or allowing substitutions (Hamming distance) and/or
insertion/deletions.
Package: libcassie-dev
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
libcassie1v5 (= ${binary:Version})
Description: library and headers for development
Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem. It scans an input
genomic sequence (dna/rna/protein) and search for a subsequence with
exact match or allowing substitutions (Hamming distance) and/or
insertion/deletions.
.
This package contains the header files for development.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: cassiopee
Source: https://github.com/osallou/cassiopee-c
Files-Excluded:
deps
Files: *
Copyright: 2013 IRISA, Olivier Sallou <osallou@irisa.fr>
License: GPL-3+
Files: src/tree/tree.hh
Copyright: 2001-2011 Kasper Peeters <kasper@phi-sci.com>
License: GPL-3
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Files: src/tree/tree_util.hh
Copyright: 2001-2009 Kasper Peeters <kasper@phi-sci.com>
License: GPL-3+
Files: debian/*
Copyright: 2014 Olivier Sallou <osallou@debian.org>
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
License: GPL-3+
On Debian systems, the complete text of the GNU General Public
License version 3 can be found in "/usr/share/common-licenses/GPL-3".
README.md
debian/README.test
debian/tests/run-unit-test
test/test2.fasta.cass
debian/tmp/usr/lib/libcassie.so usr/lib
debian/tmp/usr/include usr/include
Document: libcassie-doc
Title: Cassiopee Documentation
Author: Olivier Sallou <osallou@irisa.fr>
Abstract: Cassiopee index and search library C implementation.
It is a complete rewrite of the ruby Cassiopee gem. It scans an input
genomic sequence (dna/rna/protein) and search for a subsequence with
exact match or allowing substitutions (Hamming distance) and/or
insertion/deletions.
Section: Science/Biology
Format: html
Index: /usr/share/doc/cassiopee/html/index.html
Files: /usr/share/doc/cassiopee/html/*
#DOCS#
doc/html usr/share/doc/cassiopee
usr/share/javascript/jquery/jquery.js usr/share/doc/cassiopee/html/jquery.js
debian/tmp/usr/lib/libcassie.so.1 usr/lib
debian/tmp/usr/lib/libcassie.so.1.0.0 usr/lib
Subject: remove timestamp from generated doc
Description: timestamp prevents complete reproductibility testing,
so remove timestamp from Doxygen generated doc
Author: Maria Valentina Marin <marivalenm@gmail.com>
Bug:787765
Forwarded: yes
Last-Updated: 2015-06-05
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -932,7 +932,7 @@
# page will contain the date and time when the page was generated. Setting
# this to NO can help when comparing the output of multiple runs.
-HTML_TIMESTAMP = YES
+HTML_TIMESTAMP = NO
# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
# files or namespaces will be aligned in HTML using tables. If set to
#HTML_timestamp-option
#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
# This has to be exported to make some magic below work.
export DH_OPTIONS
#include /usr/share/cdbs/1/class/cmake.mk
%:
dh $@
override_dh_clean:
dh_clean
rm -rf doc
override_dh_install:
rm -f doc/html/jquery.js
dh_install
Tests: run-unit-test
Depends: @
Restrictions: allow-stderr
#!/bin/sh -e
pkg=cassiopee
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test* .
gunzip -r *
cassiopee -p ggtt -s test2.fasta.cass -o test.out -r -g
# Compulsory line, this is a version 3 file
version=3
opts="dversionmangle=s/\+dfsg//g" \
https://github.com/osallou/cassiopee-c/tags .*/v?(\d\S*)\.tar\.gz
set(Cassie_VERSION_STRING ${Cassiopee_VERSION_MAJOR}.${Cassiopee_VERSION_MINOR}.0)
add_library(cassie SHARED cassiopee.cxx)
set_target_properties(cassie PROPERTIES VERSION ${Cassie_VERSION_STRING} SOVERSION ${Cassiopee_VERSION_MAJOR})
add_executable(cassiopee cassie.cxx)
add_executable(cassiopeeknife knife.cxx)
target_link_libraries(cassie glog ${Boost_LIBRARIES} )
target_link_libraries(cassiopee cassie glog ${Boost_LIBRARIES} )
target_link_libraries(cassiopeeknife cassie glog ${Boost_LIBRARIES} )
# add the install targets
install (TARGETS cassiopee DESTINATION bin)
install (TARGETS cassiopeeknife DESTINATION bin)
install (FILES "${PROJECT_BINARY_DIR}/CassiopeeConfig.h"
DESTINATION include)
install (TARGETS cassie DESTINATION lib)
set(HS Cassiopee.h tree/tree.hh tree/tree_util.hh)
MACRO(INSTALL_HEADERS_WITH_DIRECTORY HEADER_LIST)
FOREACH(HEADER ${${HEADER_LIST}})
STRING(REGEX MATCH "(.*)[/\\]" DIR ${HEADER})
INSTALL(FILES ${HEADER} DESTINATION include/${DIR})
ENDFOREACH(HEADER)
ENDMACRO(INSTALL_HEADERS_WITH_DIRECTORY)
INSTALL_HEADERS_WITH_DIRECTORY(HS)
This diff is collapsed.
// the configured options and settings for Cassiopee
#define Cassiopee_VERSION_MAJOR @Cassiopee_VERSION_MAJOR@
#define Cassiopee_VERSION_MINOR @Cassiopee_VERSION_MINOR@
#define use_openmp @USE_OPENMP@
#define SUFFIX_CHUNK_SIZE 10
\ No newline at end of file
This diff is collapsed.
// A simple program that computes the square root of a number
#include <stdio.h>
#include <glog/logging.h>
#include <unistd.h>
#include <libgen.h>
#include <algorithm>
#include "Cassiopee.h"
using namespace std;
void showUsage() {
fprintf(stdout,"Usage:\n");
fprintf(stdout,"\t-l: maximum index depth / max pattern size\n");
fprintf(stdout,"\t-u: save index for later use\n");
fprintf(stdout,"\t-s: sequence to index\n");
fprintf(stdout,"\t-p: pattern to search\n");
fprintf(stdout,"\t-f: file containing pattern to search\n");
fprintf(stdout,"\t-o: output file\n");
fprintf(stdout,"\t-r: apply tree reduction\n");
fprintf(stdout,"\t-m: search mode: 0=DNA, 1=RNA, 2=Protein\n");
fprintf(stdout,"\t-a: allow alphabet ambiguity search\n");
fprintf(stdout,"\t-n: max consecutive N allowed matches in search\n");
fprintf(stdout,"\t-e: max substitution allowed matches in search\n");
fprintf(stdout,"\t-i: max indel allowed matches in search\n");
fprintf(stdout,"\t-g: generates a dot file of the graph\n");
fprintf(stdout,"\t-d: max depth of the graph\n");
fprintf(stdout,"\t-t: output format: 0:tsv (default), 1:json\n");
fprintf(stdout,"\t-x: minimum position in sequence\n");
fprintf(stdout,"\t-y: maximum position in sequence\n");
fprintf(stdout,"\t-v: show version\n");
fprintf(stdout,"\t-h: show this message\n");