Activity for Wiktor Kuśmirek
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Wiktor Kuśmirek committed [b06950]
HashTable files removed
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not needed files removed
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tmp files in tmp dir (not in working dir)
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threshold for number of hits while mapping short reads to long reads
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iterative de Bruijn graph dimension added
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threshold for number of hits while mapping contigs to long reads
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local de novo assembling for short reads and contigs moved to cpp module
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local de novo assembling only for short reads moved to cpp module
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split correct file into separate classes
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simple assembly command in cerr module
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rename parameters, new contigs mapping
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bugfix in compressing de Bruijn graph
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added files with scripts to correct ONT data (first version of scripts)
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mapping pair of reads
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paired mapping (only for testing process)
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'correct' files with information about length of the sequence
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first, simple, not working version of mapping short reads to long reads
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cerr added to building process
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cerr branch init
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bugfix in converting k value to K1
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bugfix in dnaasm exec file (console application on Ubuntu)
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bugfix in dnaasm exec file (console application on Ubuntu) [part 2]
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bugfic in ScaffoldParameters class
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dnaasm instead of dmaasm in SConscript
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bugfix in printing help
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fixme
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bugfix'es in parameters (from client layer to cpp module)
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bugfix in client layer while adding alignment task
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merge
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Parameters class used by AlignCommand
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merge Parameters class with AssemblyCommand class
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Parameters class with new names of fields (same as used in django layer)
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updated tests for Parameters class (web version)
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run common library tests
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updated tests for Parameters class (console version)
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parametersService function works with map of parameters
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changes in Parameters class in order to create common params class for console and web application
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merge
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build blast_assembler exec file
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bugfix in compilation on Jenkins
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added tests for Parameters class to testing process
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move Parameters class to common library
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merge
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bugfix in including structure
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cpp/src/common directory added
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rename assembly_main.cpp and assemblypl.cpp files
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extended params in CommandManager by i1_1, i1_2, o1_1 and o1_2
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bugfix in input file path in django layer
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merge
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comment code which throws exception
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running django tests on Ubuntu
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merge
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map of parameters instead values in CommandManager
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statistics for GAGE benchmark
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clean compilation for -std=c++14
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change name of file with statistics
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change name of the packages
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added jenkins job for installing .deb package of dnaasm console application
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change in dnaasm server jenkins job
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another way of setting LD_LIBRARY_PATH
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.deb package for console application
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first version of script to build console application .deb package
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change build .deb package task for jenkins
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new path to .deb package for dnaasm server application
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common library tests in a separate exe
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[bugfix] creating .deb package
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[bugfix] segmentation fault in django tests on Linux
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[bugfix] proper compilation on Linux
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[bugfix] path to lib directory in SConstruct file
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proper path to cpp libs in 'scons t=c' command
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reading from .gz file with unit tests (code review required)
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simple function for recognizing .gz format
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statistics for nanopore reads and canu assembly results (S288c)
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draft of S288c ONT statistics
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statistics for nanopore reads and canu assembly results
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merge
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timeout structure changed to intervals
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merge
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GAGE benchmark's statistics
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statistics for GAGE (rhodobacter sphaeroides)
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merge
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canu assembler howto
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results for model organisms
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better storage of N's chains in contigs in vertex representation
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remove isOriginal_ field from contigs graph
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updated tests for adding mate-pairs to contigs graph
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updated tests for using mate-pairs in extension contigs to scaffolds
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results for S288c
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bugfix in marking connected contigs when pairing contigs using mate-pairs
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results for S288c
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fixes in extending contigs to scaffolds using mate-pairs
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results for S288c
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bugfix in mapping mate-pairs on contigs graph
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append changed to truncate
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first version of using unitigs and contigs in extending contigs to scaffolds by MP
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not adding edges when more than one source/target vertex exists
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results for S288c
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results to C.elegans
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statistics for MP for 3 model organisms for ABySS, Velvet and sspace
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bugfix in kmer output file name
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