Activity for KAnalyze
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Peter Audano posted a comment on ticket #1
Yes, your details are correct with a few caveats. Disk based: By default, KAnalyze fills a memory buffer (k-mer "segment"), sorts and counts it, then dumps it to disk. Then the memory buffer is cleared and the next set of k-mers are counted. Instead of dumping the buffer to disk, it can move it to another place in memory (Option --nodumpseg) and re-allocate the memory buffer. This mode is not recommended unless the machine has lots of memory to work with. In Java, this is also less efficient because...
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Tarang created ticket #1
Help: KAnalyze Configuration
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KAnalyze 2.0.0 has been released!
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KAnalyze 2.0.0 has been released!
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KAnalyze released /v2.0.0/kanalyze-2.0.0-src.tar.gz
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Created outline of the component.
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Filter module and file filter are passing preli...
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Updated GUI components for more general use.
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Updated release notes and added copyright comme...
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Renamed argument parser and made some minor upd...
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Added --stdout and --input to count module.
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Converted stream module and file writers.
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Added binary count writer.
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Rearranged unit tests. Began editing the counte...
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Updated GUI code to make components more reusable.
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Worked out methods for sharing the classloader ...
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Filter module architecture complete. No filters...
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Added screenshot to images.
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Merge branch 'stdio' into prefilter
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Prepaing for help system import.
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Converted KmerUtil to process large k-mers.
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Added timed put/take methods to BoundedQueue.
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Made FilterComponent and filters generic, but n...
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Added filter component to count module. Still n...
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Updated ReleaseNotes, fixed minor layout bug wi...
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Pre-1.0.0 build (NOT to be released!). Testing ...
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Added --stdin and --input options to stream mod...
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Filter code in place. Modules need code to run it.
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Updated GUI components for more general use.
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Added dynamic library loading with --lib and --...
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KmerUtil complete and passing unit tests; Binar...
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Merge branch 'dev' into prefilter
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Merge branch 'dev' into prefilter
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Updated comments on the bounded queue.
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Merge branch 'dev' into prefilter
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Fixed errors in Linux launch scripts, and the c...
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Added quality filtering.
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Applied a major update to the count writer (dyn...
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Ported LongHashSet to KmerHashSet (LongHashSet ...
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Fixed bug in count GUI. The file field of the e...
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Updated manual.
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Threaded sort implemented, but it performs worse.
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Added '.fas' as a FASTA extension in FASTA and ...
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Fixed some Javadoc comment issues.
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Made several changes preparing for the next rel...
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Count component unit test passing.
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Updated batching constants.
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Added minimizer, a minimizer indexed binary fil...
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Updated manual. Fixed bug in KmerIndexComponent...
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v1.0.0dev7
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K-mer and k-mer count batching is implemented a...
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Fixed minor bugs in KAnalyze.
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Added shutdown hook to attempt faster shutdown ...
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Unbuildable commit: Reader buffering is in prog...
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Created a sequence name table that will discard...
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Updated tests and added k-mer array sort to Kme...
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Performance tweaking.
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Large k-mer update compiles and runs. Serious p...
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Updated default class loader.
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Fixed bug in KmerUtil sorting.
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Count component compiles. Moved KmerUtil to uti...
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Fixed deadlock bugs in sequence readers when st...
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Fixed bugs in the IKC reader and writer.
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Merge branch 'bigmer' into multisplit
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Fixed minor issues with IKC headers.
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Non-working build: Completed initial work on se...
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Non-working build; Added and updated batch and ...
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Changed Constants to KAnalyze constants, and ma...
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Fixed pause while allocating large k-mer array ...
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Count module is more re-usable, new kmer file w...
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Count module runs and generates results for bas...
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Fixed bugs in KmerUtil sort().
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Made HelpRunException a RuntimeException.
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Added writers (need to test), completed IKC rea...
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Initial work on count components. Split compile...
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KmerUtil is now an abstract class with minimize...
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Updated k-mer sort algorithm and created optimi...
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v1.0.0.dev8
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Updated default class loader for methods to use...
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v2.0.0
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Merge branch 'bigmer' into multisplit
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Sequence readers complete and unit tests are pa...
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Was not writing temporary files to the location...
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Updated threaded sort and Split Component synch...
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KAnalyze reads all sequences from FASTA and FASTQ files. Are you doing something...
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Bill Wright posted a comment on discussion General Discussion
An suggestions about how to handle a multi-FASTA file with more than one sequence...
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Added FASTA format writer.
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Updated JUnit JAR files.
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v 0.9.7
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v0.9.6
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Added hex output example to the manual.
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Added output format option to the count module ...
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Updated citation module. Added scripts and docu...
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Fixed DEC format (classes and constants were mi...
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Release 0.9.7
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v0.9.7
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