Fix unit tests
Use uppercase letters in k-mers.
Minor refactors in parameter initialization.
Add explanation in comment
Creating reverse compl. sequence now works with lowercase letters as well
Add strand proper strand recognition for gap sequences. More unit tests.
Create correspondence file with app' and original contig ids
Log gap length histograms to files.
Move links per read counter creation to ContigPairGraph. Use sorted lpr in logger.
Contigs from file are now loaded only once. Add FileLogger class. Some refactors.
Add GapInfo struct, log all possible gap sequences into file
Fix setting gap offset in ContigPairValidator. Still naive approach.
Minor refactors, code style fixes in scfr
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Add min_lpr parameter to scfr. Add ContigPairValidator class.
For each contig pair log links per reads distribution
Fix setter for min_reads parameter in scfr
Fix condition in ContigPairMaker, track bridges for contigs, add min_reads parameter.
Naive gap filling implementation for scfr module.
Correct some droplist selection n functional tests
Add instructions of installing Google Mock on Windows
Update script for building .deb package with web application.
Rm missing olc test file from tests/Sconscript. Partially fix bst build on Windows
Uncoment code for starting scaffoldTask related to assemblyTask
Update .hgignore. Remove sandbox/franus directory
Unit tests for Scaffolder class. Small refactors. Code documentation.
Update coverage report generation and doxygen generation
Add more C++ unit tests, move some c-tor definitions to cpp files
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Check if kmer size isnt longer that input sequence length
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More C++ unit tests for scfr
Add script for generating html with C++ test code coverage
Fix ajax-django views router
Update jenkins task for running python tests
Update scons commands: t=w, cov, syncdb
Python unit tests for scaffold module, update config.views
Update scaffolder translations in front-end
Using same fixture names in multiple files caused Boost.Test bug
Fix syncdb command in scons
Minor style fixes
Remove old file to fix boost include bug
Save contig id as unit32_t in matepairgraph vertex
Increase c++ log size to 5MB and turn on rotation of log file
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Move HashTable*, DnaSequenceRepresentationConverter to common lib
Remove files after previus move
Use google::sparse_hash_map with adjacency_list instead of labeled_graph
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Add export macros in scfr module
Update GoogleMock installation steps in README
More C++ unit tests for scfr module. Use GoogleMock in tests.
Update README - add manual for installation GoogleMock(GoogleTest) on Ubuntu
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Represent contig pairs with graph rather than hashmap. Tests for ContigPairMaker
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Remove compilation error on Windows
Reorganisation of scfr code into smaller classes
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Change mate pairs representation from hashmaps to Boost graph
Fix logging messages, minor codestyle changes
Print msgs into logs instead of stdout
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Sort contigs by length before extending. Some refactors
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Fix wrong type cast from long to unsigned long
Split help msg from Parameters class into subclasses. Add help for scfr
Fix compilation error in scfr, remove some consts from methods
Fix extending scaffold in left direction
Saving scaffolds to FASTA
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Add boost_thread to binary dependiences because it is needed when DEBUG is on
Rename LOG_CALC_LOC to LOG_CPP_LOC, fix log paths, reorganize cppdefines
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Extracted k-mers from long reads has FF ->-> orientation
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update scfr unit tests
Fix linking error in scons, add .exp and .exe extensions to hgignore
fix compilation on Windows
Fix linking in scons, add missing file for scfr test, remove .os file
Fix compilation error on Windows
Fix bug: initialize minimum contig length parameter with default value
Unit tests of Scaffolder
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Update createScaffold method, works correctly for the first time
Add ScaffoldParameters, scaffolder can be run from dnaasm exec
#468 #454 split Parameters class into subclases, use CommandManager in dnaasm exec
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move code from createScaffold method to submethods
fix auto starting scaffolder task after assembly task
fix scaffolder algorithm
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use map with parameters when calling scaffolder module from python
do not link libdnaasm to dbj unit tests
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ScaffoldCommand, merge scaffolder module with web app