Hello, I am proud to announce the immediate availability of Ray 2.3.0 (434 KB).
Most significant change: - add -detect-sequence-files to detect supported files With this option, you just need to put your sequence data files in one directory, and use "mpiexec -n 99 Ray -detect-sequence-files directory. This option will match paired files and everything. What's new: - new option "-run-surveyor" to compare several samples (see Documentation/) - support long reads in -amos option (reported by Bastian Hornung @ wur.nl) - Scaffolder: fix a bug in the formatting of scaffolds (Rob Egan @ Lawrence Berkeley Laboratory) - ElapsedTime.txt is now in tabular format (suggested by James Vincent @ The University of Vermont) - add new sequence file extensions such as .fq.gz (see the manual) - fix a interger overflow for the Bloom filter (thanks to Chien-Chi Lo) - remove the symbolic loop in RayPlatform (reported by Nick Holway) - add the ability to send SIGUSR1 to Ray processes to debug them - use the polytope by default with option -route-messages (instead of the de Bruijn graph) Download link: http://master.dl.sourceforge.net/project/denovoassembler/Ray-2.3.0.tar.bz2 Mirrors: https://github.com/sebhtml/Ray-Releases/raw/master/Ray-2.3.0.tar.bz2 https://bitbucket.org/sebhtml/ray-releases/src/master/Ray-2.3.0.tar.bz2 Thanks ! Sébastien ----- Ticket for the release: https://github.com/sebhtml/ray/issues/194 All changes in between Ray 2.2.0 and 2.3.0: $ git diff --stat -M -C -D v2.2.0..v2.3.0|tail -n1 139 files changed, 9801 insertions(+), 883 deletions(-) Changes in between RayPlatform 1.1.1 and 2.0.0 $ git diff --stat -M -C -D v1.1.1..v2.0.0|tail -n1 129 files changed, 3471 insertions(+), 505 deletions(-) Change log for Ray 2.3.0 (since 2.2.0) f2f9ca1 This is Ray version 2.3.0 c61dcd8 SpuriousSeedAnnihilator: fix some compilation warnings 7156629 add 2.3.0 release 6d61131 build system: fix CMakeList for Ray 5ab3193 SpuriousSeedAnnihilator: fix a bug catched by system tests 5aeb16f Surveyor: fix documentation 63d63ec fix random segmentation fault during edge purging f1dc7a7 fix compilation errors cf37194 build: add libRay.a to the build process daaceb2 Ray Surveyor: add some documentation daa3832 Surveyor: add sample names becfcbe Surveyor: write DistanceMatrix.tsv 732d9b0 Surveyor: write SimilarityMatrix.tsv c5db0da Surveyor: merge Gramian matrix ed1c2a8 Surveyor: give control to StoreKeeper actors for merging 12c8f30 Surveyor: new actor type -> MatrixOwner 943a479 Surveyor: flush buffers and reset them 56b9a6c Surveyor: refactor buffering code a85f80f Surveyor: make space for flushing vertices 59c993d add framework to synchronize mothers 2788a4d compute local Gramian matrix fada683 activate coloring with samples 9fd4e07 storage works now ! 7e2b5b8 use the k-mer length provided in argument b7fa63b add code for StoreKeeper actors c75876d add some methods around the edge set f03afc2 don't spawn Mother without -run-surveyor 620fe88 remove public attributes in Vertex class 412ce31 add aggregation for data sent to storage e0cff32 Surveyor: add StoreKeeper actors 25139a7 Surveyor: connect aggregator actors with storage actors 1c52870 use a buffered reader cf670fc add license to Ray Surveyor files d11c536 send DNA vertices to the aggregator 8c6823b kill actors to actually end computation cdf277d send payloads to aggregator d73acc6 provide the coalescence actor for file actors 519f27b spawn one actor for each genome graph file e4d20d5 add some actor blueprints 857b773 don't mention contigs if no reads are provided 462f5cb add title 5999b3e add index for the documentation 6aaf736 fix the next actor for the first actor bd5a626 process boot signal 0f90feb spawn a Mother actor 616d2a2 disable MPI I/O by default (MPI_IO=n) 9e02902 add option -merge-seeds (disabled by default) 1c6f9f2 add option -ignore-seeds to skip assembly c610ae8 add migration roadmap for the actor model f620d24 add option -debug for '-run-profiler -with-profiler-details' 885e301 fix an integer overflow for the Bloom filter 3dd4ef5 SpuriousSeedAnnihilator: discard self-loops aba4ddd remove debug statements from production builds bba110a update output file to tell user about LibraryData.xml b3e6b07 add support for .fq.gz files in the detection 5b065b0 SpuriousSeedAnnihilator: fix a major in the synchronization code 5c19b7b perform a barrier before gossiping with others 9007778 add a synchronization after state MODE_SHARE_WITH_LINKED_ACTORS 43fb7be perform gossip logic in separate handlers 99b60e0 make sure that any file is not used twice 396a107 add a file named RaySmartCommand for generated options 419474c improve the matching algorithm for option -detect-sequence-files f13d1c8 throw an error message when read counts do not match in paired files 5599b31 improve option -detect-sequence-files to search recursively f51f695 add option -write-plugin-data to write plugin data 6cd5621 don't generate scheduling information without -write-scheduling-data 20d20c1 support long reads in -amos option b47a4ac fix the gossip algorithm for seed merging 02b0111 create a class for managing gossip assets e35f616 add a message regulator for the gossip propagation 6c3017a Merge branch 'master' of git://github.com/sebhtml/ray 9ae63bc register symbols to debug seed merging 5f0801f use a larger Bloom filter e8658d6 fix an integer overflow in the coverage code path 418396c discard self hits at depths greater than 0 74b25d3 add a warning when backtracking fails 14ad4c6 fetch coverage data for seed paths cbeeee3 sort seeds by length 85a348d remove debug messages for seed merging 323f534 actually add the file detector class cd6661b add -detect-sequence-files to detect supported files 5175343 flip the computed paths between shorter seeds too 0d6ed42 don't use a reference to compute the smallest handle 2a7d959 SpuriousSeedAnnihilator: download seeds with the key-value store c493caf use a request to poll progression for seed fetching abdd9bd tested value with ~ 100 KiB and it works well 8892dec add a barrier after seed registration 6d4f59d use char instead of uint8_t for bytes 65dbe0a register all seeds in the key-value store 01fa5df register seeds in the store bba3e35 split the code in smaller methods a5f379d fix a race condition bugs in seed merger 98ea7eb implement an ownership policy for seeds d50a972 use the polytope by default with option -route-messages 801ac38 check path orientation when exploring on the left 96fc956 complete the implementation of the seed merger 459ff84 the code for merging things on the left works 7891d9e design the algorithm for local seed merging from gossips 962cb4c fix 2 compilation warnings 0f302e6 add the solver for the seed merging 11ca496 the gossip algorithm compiles and executes ! b0cf8ac fix a bug in the load method 9a60695 add a new checkpoint called SimpleSeeds 6d29163 implement gossip algorithm for seeds 9d39141 move hasCheckpoint in the initialization because it does file operations 231608b detect loops between two seeds 645a232 validate search results 131bf20 deal with the current path if the depth is not 0 a1e9d26 improve documentation for SFF file loader edf2e2b add a barrier to get deterministic results ba876c0 do a list of symmetric relations d55f088 load and dump graph paths 251fce6 add documentation for the storage engine cbaca9a add a class for path handles e33dd68 add ReadHandle class d374045 add features for transport to kmers f595675 add an interface for carriageable items 60a7402 add a message handler to receive data for relations 026b7bf provide a method to process merging relations cc48eae gather relations between paths bb1ce43 store depth data and query reverse DNA strand c65e677 trace paths between seeds 467d357 reset counters when reusing parallel code paths 743f65d document the Ray API 1649328 register seeds before merging them d0f9c2d query the last vertex in every seed 9528466 replace buggy implementation of buffered reader b18cd50 add a buffered reader for loading sequences d9d935c stop search when too many vertices were visited 16f82bc add some code to explore the graph ed99ccd add architecture to merge seeds e0e90c8 change the next version number to 2.3.0 (like on github) 51a12d8 add preliminary code to merge short seeds 49516ec add distributor 31251b4 add distributors e773917 SequencesLoader: use a buffer of4M for fastq.gz files too 7d4a4cb SequencesLoader: add readahead in the fastq loader c49deee Searcher: fix column names for Contigs.tsv 77270af Scaffolder: fix a bug in the formatting of scaffolds 606be2a fix the script to build Ray with LTO 349db6f reduce the verbosity of offset computation 688490c enable MPI I/O features by default in Ray plugins 0f8342d Add -IRayPlatform in Makefile a4e630f Checkpoint : Write the checkpoints in blocs c7ac118 Write ElapsedTime.txt with tabulation 9f42ec2 remove debug statements and update the manual 96cc13c SequencesLoader : add new extensions support f6a5a94 Merge branch 'master' of git://github.com/sebhtml/ray 3839145 Change the method to writing the information into the kmers.txt file 126a9e3 fix the link-time-optimization build script 0d80656 working on v2.2.1 3bf0659 fix a interger overflow for the Bloom filter All change log for RayPlatform 2.0.0 (since 1.1.1) 9f19ad0 this is RayPlatform 2.0.0 3b30d54 preformat illustration 16556e7 documentation: move README to README.md 33745bc add RayPlatform Plugin API documentation 018bcd0 communication: return pointer to bytes when fetching buffer 5c9b39f add a sentinel for tags 0648ffb add the RayPlatform Actor Playground 2aeeba1 add a wrapper to read lines from text files 772a7f0 fix license text for the actor model 4dc04a8 add LGPL statements in source files ac87112 set source and destination actors for MPI messages too 9ae258d run until all actors died 8e7b315 enable payloads that are not multiple of 8 bytes 7019fef use MPI_BYTE for MPI calls (instead of MPI_UNSIGNED_LONG_LONG) e558117 don't repeat the MPI datatype b4c166c copy content from actor buffer to RayPlatform buffer 9622eb0 Internally, store message buffers as bytes f4ae852 fix compilation warnings in the key-value store bc55991 add the padding because we always need actors 589a272 fix a regression caused by wrong assertion 3b3baf1 fix the routing code paths for actors fca0bff allow messages to be sent between actors 37ec5da boot actors when starting the computation d41a5d2 add actor model features 1bb67ce add debugging feature: sending SIGUSR1 toggle debug mode d04afaa show debug window at tick number 0 with -debug d2d8f73 flush a message when iteration over workers ends 2e14fce add memory usage values to debug Ray on titan 76f7c84 add memory usage during profiling 5131590 fix a compilation bug c6b7052 add a function to check if a file is a directory 342ea4d fix a compilation warning (uninitialized variable) with g++ 4.8.0 19d3875 memory: register debugging information for dirty buffers 1707226 show buffer states when a dirty buffer warning occurs 937c889 add a function to get the entries in a directory fb94c1e store: use references in the public API 487a3b8 store: fix a bug in offsets 6089e26 KeyValueStore: the code is ready for production fcf80cb the key-value store is ready, mostly 821ec88 implemented the messaging code for data store operations 0a65458 use char instead of uint8_t for interface 4f94518 add a memory allocator inside the data store 0a678a3 add implementation for the key-value store c3c2628 add a draft of the key-value store API ade4b30 move CarriageableItem in the framework e2eed96 add a method to close a slave mode in the API a486b72 add more information when compiling with -DCONFIG_SWITCHMAN_VERBOSITY d78e7ec core: fix a messaging bug that caused undefined behaviors 7d1c50c enhance the building process 72af0e4 Remove the sym link to RayPlatform f527caa Write into ElapsedTime.txt with tabulation ------------------------------------------------------------------------------ Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. 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