Hello, Ray v1.6.1 codename 'sunray' is available for download.
http://denovoassembler.sourceforge.net/download.html List of changes: = 1.6.1 'sunray' = 2011-07-14 * Presumably fixed a compilation error on Apple Snow Leopard. Thanks to Anthony Underwood for reporting the bug. * Added a smoothing routine for the detection of points in the coverage distribution. Thanks to pmiguel on SEQanswers for providing raw data points. * Changed ifdef linux to ifdef __linux__. * Fixed the showMemoryUsage function. * Fixed uniform distribution of k-mers for k > 32 -- there was a bug in an hashing function. Thanks to Adrian Platts (McGill University) for reporting this. * Fixed a bug for the seed length distribution written to a file. * Changed MAXKMERLENGTH=128 for MAXKMERLENGTH=64 in examples. Thanks to Adrian Platts (McGill University) for reporting this. * Fixed a communication problem for k>32. * Added a progression indicator for scaffolding. * Writting scaffold sequences is now faster. * New option: -write-kmers writes k-mers, their counts and the arcs linking them. * New experimental option: -color-space for .csfasta files. Ray can generated color-space contigs but the feature is mostly untested. * Added an assembler panic when no k-mers are found in reads. * New options: -minimumCoverage, -peakCoverage, -repeatCoverage -- provides coverage values automatically. Otherwise these are automatically selected as usual. * Reduced the memory usage during the building of the graph using a k-mer academy. Once the graph is ready, memory for k-mers occuring once is freed. * New outputted file: PREFIX.degreeDistribution.txt contains the distribution of degrees in the graph. Most vertices should have an ingoing degree of 1 and an outgoing degree of 1. * Cleaned the code by removing MemoryConsumptionReducer. * The hash tables are now implemented using open addressing with double hashing (from The Art of Computer Programming by Donald Knuth) * Implemented a sparse hash map (following the description of Google sparse hash; see structures/MyHashTable.h) * New output file: PREFIX.MessagePassingInterface.txt contains the number of sent messages for each type during an assembly run. * System tests are now in system-tests * Implemented SmartPointer objects to allow defragmentation of memory. * Implemented real-time defragmentation for SmartPointer objects. * Implemented incremental resizing to allow low latency when an hash table needs to grow. * Fixed a buffer overflow in getKmerAtPosition, reported by David Eccles (gringer) from Max-Planck-Gesellschaft, München. * Added a new output file called PREFIX.NetworkTest.txt which contains the average latency including software overhead. * Fixed some compilation warning on 32-bit GNU/Linux. * Tested Ray on the Intel Atom processor. Sébastien ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
