new FindTranslocation

AUTHORS

@@ -0,0 +1 @@
+Francesco Vezzi francesco.vezzi@scilifelab.se

CMakeLists.txt

@@ -0,0 +1,56 @@
+
+
+cmake_minimum_required (VERSION 2.6)
+project(FRC_aling)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+add_definitions( -Wno-deprecated )
+
+find_package(Boost COMPONENTS  program_options system filesystem REQUIRED)
+
+# set our library and executable destination dirs
+set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
+
+# define compiler flags for all code
+set( CMAKE_BUILD_TYPE Release )
+
+include_directories("${PROJECT_SOURCE_DIR}/src")
+include_directories("${PROJECT_SOURCE_DIR}/lib/")
+include_directories("${PROJECT_SOURCE_DIR}/lib/bamtools/src")
+include_directories( ${Boost_INCLUDE_DIRS} )
+
+
+# sorgenti da compilare
+file(GLOB FRC_FILES
+    ${PROJECT_SOURCE_DIR}/src/FRC_align.cpp
+    ${PROJECT_SOURCE_DIR}/src/data_structures/Contig.cpp
+    ${PROJECT_SOURCE_DIR}/src/data_structures/Features.cpp
+    ${PROJECT_SOURCE_DIR}/src/data_structures/FRC.cpp
+)
+
+# sorgenti da compilare
+file(GLOB FIND_TRANS_FILES
+    ${PROJECT_SOURCE_DIR}/src/FindTranslocations.cpp
+    ${PROJECT_SOURCE_DIR}/src/data_structures/Translocation.cpp
+    ${PROJECT_SOURCE_DIR}/src/common.h
+)
+
+
+add_subdirectory(lib)
+
+# FRC executable
+add_executable(FRC ${FRC_FILES})
+target_link_libraries(FRC ${ZLIB_LIBRARIES})
+target_link_libraries(FRC  BamTools)
+target_link_libraries(FRC ${Boost_LIBRARIES})
+
+
+
+# Find_translocations executable
+add_executable(FindTranslocations ${FIND_TRANS_FILES})
+target_link_libraries(FindTranslocations ${ZLIB_LIBRARIES})
+target_link_libraries(FindTranslocations  BamTools)
+target_link_libraries(FindTranslocations ${Boost_LIBRARIES})
+
+

COPYING

@@ -0,0 +1 @@
+All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).

INSTALL

@@ -0,0 +1,12 @@
+Installation Instructions
+*************************
+
+From the FRCurve directory run:
+
+ mkdir build
+ cd build
+ cmake ..
+ make
+
+You will find the binaries in the main directory under bin. In case of problems the majority of the times there is a problem
+with the local installation of boost.

NEWS

@@ -0,0 +1,2 @@
+
+2014-05-26: New detailed README.md and explicit reference to FindTransolocations

README.md

@@ -0,0 +1,97 @@
+INSTALLATION
+==============
+
+From the FRCurve directory run:
+- mkdir build
+- cd build
+- cmake ..
+- make
+
+You will find the binaries in the main directory under bin. In case of problems the majority of the times there is a problem
+with the local installation of boost.
+
+
+DESCRIPTION
+==============
+ FRCcurve is a package containing tools to process bam files in order to evaluate and analyze de novo assembly/assemblers and identify Structural Variations 
+ suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects.
+
+ This package contains two tools:
+
+1. FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers
+2. FindTranslocations: tool to identify  chromosomal rearrangements using Mate Pairs
+
+
+FRCbam
+--------------
+ **USAGE: basic, no CE-stats tuning**
+
+1. Assemble your data (n PE libraries and m MP libraries) with your favorite tools. Let us call the assemblies A_tool1, A_tool2, etc.
+2. Align one PE library and one MP library against each of your assemblies (e.g., A_tool1)       
+  1. Use the same parameters
+  2. PE library is mandatory, MP library is highly recommended
+  3. sort and index the generated bam files by coordinate. We will call them A_tool1_PE_lib.bam and A_tool1_MP_lib.bam
+  4. use PE library with largest read coverage (i.e., vertical coverage) and MP with largest spanning coverage (i.e., horizontal coverage)
+3.Run FRCurve for each assembly: 
+```FRC --pe-sam A_tool1_PE_lib.bam --pe-min-insert MIN_PE_INS --pe-max-insert MAX_PE_INS -mp-sam A_tool1_MP_lib.bam  --mp-min-insert MIN_MP_INS --mp-max-insert MAX_MP_INS 
+		--genome-size ESTIMATED_GENOME_SIZE --output OUTPUT_HEADER```
+
+where:
+
+* ```--pe-sam``` A_tool1_PE_lib.bam```: sorted bam file obtained aligning PE library against assembly obtained with tool A;
+* ```--pe-min-insert MIN_PE_INS```: estimated min insert length
+* ```--pe-max-insert MAX_PE_INS``` : estimated max insert length
+* ```--mp-sam A_tool1_MP_lib.bam```: sorted bam file obtained aligning MP library against assembly obtained with tool A;
+* ```--mp-min-insert MIN_MP_INS``` : estimated min insert length
+* ```--mp-max-insert MAX_MP_INS``` : estimated max insert length
+* ```--genome-size ESTIMATED_GENOME_SIZE```: estimated genome size;
+* ```--output OUTPUT_HEADER```: output header;
+
+**IMPORTANT**:
+If ```--genome-size``` is not specified the assembly length is used to compute FRCurve. In order to be able to compare FRCurves
+obtained with different tools (and hence producing slightly different assembly sizes) the same ```ESTIMATED_GENOME_SIZE```
+must be specified.
+
+OUTPUT:
+
+* ```OUTPUT_HEADER_Features.txt```: human readable description of features: contig start end feature_type
+* ```OUTPUT_HEADER_FRC.txt```: FRCurve computed with all the features (to be plotted)
+* ```OUTPUT_HEADER_FEATURE.txt```: FRCurve for the corresponding feature
+* ```OUTPUT_HEADER_featureType.txt```: for each featureType the specific FRCurve
+* ```Features.gff```: features description in GFF format (for visualization)
+* ```OUTPUT_HEADER_CEstats_PE.txt```: CEvalues distribution (for CE_stats tuning)
+* ```OUTPUT_HEADER_CEstats_MP.txt```: CEvalues distribution (for CE_stats tuning)
+
+**USAGE: advanced, CE-stats tuning**
+
+CE-stats are able to identify the presence of insertion and deletion events. Different insert sizes give the possibility to
+identify different events. In order to avoid too many False Positives (or too many False Negatives) a tuning phase is 
+highly recommended.
+
+Once step 3 of USAGE is done, the user can already plot the FRCurves (for all the features or for only some of them).
+CE_stats based features have been computed with default (i.e., not optimal) parameters. Each run of FRCbam produces two
+files: ```OUTPUT_HEADER_CEstats_PE.txt``` and ```OUTPUT_HEADER_CEstats_MP.txt```. These files contain the distribution of the ```CE_values```
+on each assembly. These values must be plotted as suggested in page 3 of Supplementary Material 
+(see http://www.nada.kth.se/~vezzi/publications/supplementary.pdf) to estimate the optimal ```CE_min``` and ```CE_max``` values for 
+ the PE and MP library respectively.
+ Once the optimal parameters are estimated FRCurves must be recomputed for all assemblies (only ```COMPR``` and ```STRECH``` features
+ will change) specifying the following extra parameters:
+
+* ```--CEstats-PE-min CE_PE_MIN```: all position with CE values computed with PE library lower than this are considered compressions
+* ```--CEstats-PE-max CE_PE_MAX```: all position with CE values computed with PE library higher than this are considered expansions 
+* ```--CEstats-MP-min CE_MP_MIN```: all position with CE values computed with MP library lower than this are considered compressions
+* ```--CEstats-MP-max CE_MP_MAX```: all position with CE values computed with MP library higher than this are considered expansions
+
+FindTranslocations
+--------------
+The tool is under constant development. THere will be soon a detailed user guide, for now run the tool with ```--help``` to discover the options.
+
+
+
+
+LICENCE
+==============
+All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3). 
+
+
+

lib/CMakeLists.txt

@@ -0,0 +1,12 @@
+project( BamTools )
+
+# BamTools version information
+set (BamTools_VERSION_MAJOR 2)
+set (BamTools_VERSION_MINOR 0)
+set (BamTools_VERSION_BUILD 5)
+
+# add our includes root path
+include_directories( bamtools/src )
+
+# list subdirectories to build in
+add_subdirectory( bamtools/src/api )

lib/bamtools/CMakeLists.txt

@@ -0,0 +1,65 @@
+# ==========================
+# BamTools CMakeLists.txt
+# (c) 2010 Derek Barnett
+#
+# top-level
+# ==========================
+
+# set project name
+project( BamTools )
+
+# Cmake requirements
+cmake_minimum_required( VERSION 2.6.4 )
+
+# Force the build directory to be different from source directory
+macro( ENSURE_OUT_OF_SOURCE_BUILD MSG )
+    string( COMPARE EQUAL "${CMAKE_SOURCE_DIR}" "${CMAKE_BINARY_DIR}" insource )
+    get_filename_component( PARENTDIR ${CMAKE_SOURCE_DIR} PATH )
+    string( COMPARE EQUAL "${CMAKE_SOURCE_DIR}" "${PARENTDIR}" insourcesubdir )
+    IF( insource OR insourcesubdir )
+        message( FATAL_ERROR "${MSG}" )
+    ENDIF( insource OR insourcesubdir )
+endmacro( ENSURE_OUT_OF_SOURCE_BUILD )
+
+ensure_out_of_source_build( "
+  ${PROJECT_NAME} requires an out of source build.
+  $ mkdir build 
+  $ cd build
+  $ cmake ..
+  $ make 
+(or the Windows equivalent)\n" )
+
+# set BamTools version information
+set( BamTools_VERSION_MAJOR 2 )
+set( BamTools_VERSION_MINOR 3 )
+set( BamTools_VERSION_BUILD 0 )
+
+# set our library and executable destination dirs
+set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
+set( LIBRARY_OUTPUT_PATH    "${CMAKE_SOURCE_DIR}/lib" )
+
+# define compiler flags for all code
+set( CMAKE_BUILD_TYPE Release )
+add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
+
+# -----------------------------------------------
+# handle platform-/environment-specific defines
+
+# If planning to run in Node.js environment, run:
+# cmake -DEnableNodeJS=true
+if( EnableNodeJS )
+    add_definitions( -DSYSTEM_NODEJS=1 )
+endif()
+
+# If running on SunOS
+if( "${CMAKE_SYSTEM_NAME}" MATCHES "SunOS" )
+    add_definitions( -DSUN_OS )
+endif()
+
+# -------------------------------------------
+
+# add our includes root path
+include_directories( src )
+
+# list subdirectories to build in
+add_subdirectory( src )

lib/bamtools/LICENSE

@@ -0,0 +1,22 @@
+The MIT License
+
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

lib/bamtools/README

@@ -0,0 +1,60 @@
+--------------------------------------------------------------------------------
+README : BAMTOOLS
+--------------------------------------------------------------------------------
+
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
+
+I.   Learn More
+
+II.  License
+
+III. Acknowledgements
+
+IV.  Contact
+
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
+
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
+
+https://github.com/pezmaster31/bamtools/wiki
+
+Join the mailing list(s) to stay informed of updates or get involved with 
+contributing:
+
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
+
+--------------------------------------------------------------------------------
+II. License :
+--------------------------------------------------------------------------------
+
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+    Michael Stromberg
+
+See included file LICENSE for details.
+
+--------------------------------------------------------------------------------
+III. Acknowledgements :
+--------------------------------------------------------------------------------
+
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
+
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
+
+Feel free to contact me with any questions, comments, suggestions, bug reports,
+    etc.
+
+Derek Barnett
+Marth Lab
+Biology Dept., Boston College
+
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools