Activity for Wiktor Franus
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Wiktor Franus committed [d555c7]
Fix unit tests
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Use uppercase letters in k-mers.
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Minor refactors in parameter initialization.
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Add explanation in comment
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Creating reverse compl. sequence now works with lowercase letters as well
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Add strand proper strand recognition for gap sequences. More unit tests.
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Create correspondence file with app' and original contig ids
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Log gap length histograms to files.
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Move links per read counter creation to ContigPairGraph. Use sorted lpr in logger.
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Contigs from file are now loaded only once. Add FileLogger class. Some refactors.
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Add GapInfo struct, log all possible gap sequences into file
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Fix setting gap offset in ContigPairValidator. Still naive approach.
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Minor refactors, code style fixes in scfr
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merge
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Add min_lpr parameter to scfr. Add ContigPairValidator class.
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For each contig pair log links per reads distribution
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Fix setter for min_reads parameter in scfr
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Fix condition in ContigPairMaker, track bridges for contigs, add min_reads parameter.
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Naive gap filling implementation for scfr module.
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Correct some droplist selection n functional tests
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Add instructions of installing Google Mock on Windows
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Update script for building .deb package with web application.
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Rm missing olc test file from tests/Sconscript. Partially fix bst build on Windows
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Uncoment code for starting scaffoldTask related to assemblyTask
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Update .hgignore. Remove sandbox/franus directory
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Unit tests for Scaffolder class. Small refactors. Code documentation.
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Update coverage report generation and doxygen generation
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Add more C++ unit tests, move some c-tor definitions to cpp files
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merge
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Check if kmer size isnt longer that input sequence length
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merge
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More C++ unit tests for scfr
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Add script for generating html with C++ test code coverage
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Fix ajax-django views router
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Update jenkins task for running python tests
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Update scons commands: t=w, cov, syncdb
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Python unit tests for scaffold module, update config.views
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Update scaffolder translations in front-end
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Using same fixture names in multiple files caused Boost.Test bug
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Fix syncdb command in scons
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Minor style fixes
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Remove old file to fix boost include bug
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Save contig id as unit32_t in matepairgraph vertex
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Increase c++ log size to 5MB and turn on rotation of log file
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merge
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Move HashTable*, DnaSequenceRepresentationConverter to common lib
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Remove files after previus move
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Use google::sparse_hash_map with adjacency_list instead of labeled_graph
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merge
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merge
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Add export macros in scfr module
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Update GoogleMock installation steps in README
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More C++ unit tests for scfr module. Use GoogleMock in tests.
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Update README - add manual for installation GoogleMock(GoogleTest) on Ubuntu
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merge
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Represent contig pairs with graph rather than hashmap. Tests for ContigPairMaker
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merge
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Remove compilation error on Windows
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Reorganisation of scfr code into smaller classes
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merge
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merge
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Change mate pairs representation from hashmaps to Boost graph
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Fix logging messages, minor codestyle changes
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Print msgs into logs instead of stdout
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merge
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Sort contigs by length before extending. Some refactors
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merge
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Fix wrong type cast from long to unsigned long
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Split help msg from Parameters class into subclasses. Add help for scfr
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Fix compilation error in scfr, remove some consts from methods
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Fix extending scaffold in left direction
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Saving scaffolds to FASTA
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merge
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Add boost_thread to binary dependiences because it is needed when DEBUG is on
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Rename LOG_CALC_LOC to LOG_CPP_LOC, fix log paths, reorganize cppdefines
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merge
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Extracted k-mers from long reads has FF ->-> orientation
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merge
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update scfr unit tests
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Fix linking error in scons, add .exp and .exe extensions to hgignore
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fix compilation on Windows
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Fix linking in scons, add missing file for scfr test, remove .os file
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Fix compilation error on Windows
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Fix bug: initialize minimum contig length parameter with default value
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Unit tests of Scaffolder
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merge
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Update createScaffold method, works correctly for the first time
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Add ScaffoldParameters, scaffolder can be run from dnaasm exec
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#468 #454 split Parameters class into subclases, use CommandManager in dnaasm exec
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merge
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merge
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move code from createScaffold method to submethods
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fix auto starting scaffolder task after assembly task
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fix scaffolder algorithm
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merge
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use map with parameters when calling scaffolder module from python
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do not link libdnaasm to dbj unit tests
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merge
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merge
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ScaffoldCommand, merge scaffolder module with web app
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