[med-svn] [ray] branch master updated (00482e6 -> f10322e)
Sébastien Boisvert
sboisvert-guest at moszumanska.debian.org
Mon Feb 3 19:22:27 UTC 2014
This is an automated email from the git hooks/post-receive script.
sboisvert-guest pushed a change to branch master
in repository ray.
from 00482e6 Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/ray
adds 2aef580 The initial state of the branch upstream must be empty
adds 955666c
adds 76883b0 Moving stuff around
adds 9093c59 Loading a parameter: the directory name
adds 93b583b added a message limit
adds d6b6751 Changes, test1, test2, and test3 are working properly
adds 1c17f41 MPI_Waitall is better
adds 5a19fc3 * possibly proceed separatly for direct and reverse for edges.
adds 02d9a55 * possibly proceed separatly for direct and reverse for edges.
adds 3b66a4b * possibly proceed separatly for direct and reverse for edges. * Resotre add Edges. (find SEGFAULT .)
adds cb446f0 test1, test2, and SRA001125 file 1 load
adds 7938e7a * free message memory
adds 55bcb0f
adds f8f66ba test1 and test2 ok with coverage calculation
adds bf74402 Works ok.
adds 113f490 Sending code
adds 6686b74 Added command for MPICH2
adds 72db23d
adds 3c9cb7a
adds 1e3ad1b
adds 639ecd6
adds 107f7de
adds 800b776
adds 004848a
adds 3d64dca * the seeds are now computed correctly. (need to test stuff in TODO.txt) * parallel code works, but the MPI_Finalize calls hang because of MPI_Barrier calls waiting to complete. * MPI_Send works well because small messages are sent eagerly in Open-MPI 1.4.1. * use can switch back to MPI_Isend by modifying the code.
adds 29964c0 * Fixed problem with Finalize and MPI_Barrier. * The program returns correctly upon completion.
adds 3d79571 * Fixed a bug in building seeds.
adds ce241e4 * will fix these later or never (they are not that important.):
adds 0434b58 Seems ok to me:
adds 94ed43a * Reads get attached now.
adds 38aa15f * Ray returns immediatly if given an invalid configuration file.
adds 370f620 * added version in stdout * tells if the user uses Open MPI.
adds 2ef537b
adds d74ccd7 * Show progress when attaching reads.
adds 335c0c3 * show progress for vertex seeding.
adds b1501c6 No message, just commiting stuff.
adds f52fcef Done: now I have 2*n seeds! yay. * also check that added vertices are 1-in 1-out (work in progress.)
adds bf8a9ea Reduced communication:
adds 207a2ba * Fixed a SEG FAULT when sending large sequences.
adds 96fd599 Updated TODO .
adds 638428c This behavior is correct:
adds 86f9ac8 * The coverage of a vertex is now stored as a 'char', with a maximum of 255.
adds 582eb13 * Edges are stored as a 'char'.
adds f1785e3 * fixed compilation warnings.
adds c5e59e8 * removed cout's SB
adds 8ba5de3 The memory usage is lowered, now each vertex is a (uint64_t,char,char,bool)
adds ae3f256 Summary of today's work:
adds 16e60e5
adds d50e115 Fixed:
adds a501716 * The extension is now done in both direction.
adds eb927f4 fixed compilation warnings
adds 739cc91 * I added constants for allocator's chunk sizes.
adds ce94d8f * only keep seeds with at least 100 nucleotides.
adds 9e6b70d * removed commented code lines in the code.
adds bcf00c4 * FIXED: random mismatches plague seeding? * FIXED: check memory allocation for master... (something to do with vector<Read*> ??)
adds adc3690 * remove Edge class (it was replaced by ReadAnnotation) * replace reads positions with (int,int)
adds 07e683b FIXED:
adds b5921ad Added this feature:
adds cda1aa3 Updated TODO.
adds 66d47b6 Updating TODOs
adds 5839eae Directions are copied.
adds 8620297 * Restored extension. SB
adds 72443b7 Implemented:
adds 91df3e7 Fixed misassembly.
adds 54dffe6 Setting the PERIOD for MPI_Barrier back to 100
adds c851a02 Removed paired-end Class.
adds 0423285 Added the direction class.
adds 52bef94 * removed the line break before the Minimum Coverage * The fusion is implemented in the case of 100% overlapping paths on the same strand.
adds d37209c The fusion has begun.
adds 828ad9e WORKS-FOR-ME:
adds 0856c3f Fixed:
adds f5ef1ad Fixed:
adds 09086f4 Fixed compilation errors.
adds ca2080c Fixed:
adds 36cb5df Fix in README.
adds a421f27 The next milestone:
adds 049eb18 Updated TODO. SB
adds 53b9225 working on a bug it has something to do with Iprobe.
adds 8848929 good .
adds 5205111 * Removed the DUMMY message.
adds 4da9062 Currently investigating the hang.
adds bc86089 The hang is caused by the btl sm.
adds d07b46e Removing ther Makefile for colosse.
adds 8ff66c6 Testing speed limitation.
adds 8bb0da4 Speed regulator works on Llactis with 8 MPI processes.
adds 5784835 * Removed all MPI_Barrier calls from the program (they are broken with shared memory for my application anyway, apparently.)
adds ba789a1 Implemented:
adds 4d53ea6 * added progress when attaching reads.
adds 9b28b19 SRA001125 preliminary results:
adds 6f09a8a * Remove calls to Get_processor_name in code.
adds 69f1599 * Removed time.h and sys/time.h from includes.
adds 49d5406 Debuging on colosse.
adds e054b19 Removed TODO.txt
adds 2f4ae7e Removed the qsub SGE submission script. It does not belong there.
adds da2a1f7 Removing all Barriers.
adds dd9952d Added a detection of MPICH2 turn on Isend when it is the case.
adds 46c7406 Fixed the detection of MPICH2.
adds ead2433 Use shortcut when sending message to self.
adds f07bebd Fixed ticket http://genome.ulaval.ca/seb-trac/trac/ticket/30.
adds 715e127 Detection of MPICH2 and Open-MPI is done.
adds a6a798b Documented the code for MPI implementations.
adds a0b2344 Adding progression in fusion steps. SB
adds 16c0038 * Implemented Ticket #22 (new enhancement) -- possibly use a map<,> to hold information on path lengths. -> this allows a log(N) length extraction instead of the unpopular N. * Fixing #22 fixes #41 ( Ticket #41 (new defect) -- Contigs are duplicated on ls28) * This will presumably eases #37 when colosse.clumeq.ca is not crashed...
adds eebc835 Partial fix for #15 (when complete coverage of a contig invalids it)
adds baebe3d Removed cout's
adds 6e2bdc6 Work in progress.
adds b994544 Debugging stuff.
adds b3d7b9a Added a script to analyse assemblies. Sébastien Boisvert.
adds fcde760 Added segments.
adds 0b41b50 Fixed #47 SB
adds d8d38bd Added the content of the website.
adds 133c258 Moved the content of the site in README.txt
adds 01741ae Updated the README.
adds 92a1ad4 Changed http to https.
adds fb00fda Implemented #45: add a compilation flag for writing things in stdout.
adds 7af5691 Implemented ticket #16.
adds a8b7084 Added endl.
adds c22bf26 Updated the README
adds 969c445 Small changes in the README.txt
adds e75dd88 Added message for SeqAnswers.com
adds 473b737 Added URI.
adds e67047e Updated the text for Seq Answers.com
adds 906ff59
adds b99b0b9 Implemented ticket #52.
adds aac9dd4 Corrected the text.
adds 5bad53f Corrected the README.
adds 638b7c6 Cleaned the code.
adds ab10c1f Added an error message.
adds 8fe4eff Fixed #54: SEGFAULT on SRA001125 unpaired.
adds fe17fa3 Work in progress.
adds f174160 Fixed the duplication of the first contig.
adds 7bcbd15 I only have to make them go together now.
adds fdf9f5d Fixed ticket #53 (Ray produces too much thing for SpPaired)
adds 24fdbf2 Updated year in copyright.
adds 8835a34 Fixed possible infinite loop.
adds 3750293 * disabling cycling for now...
adds 3953ca3 Making some tests.
adds 7e0d895 Removed a false assert (it can be false, but it is not a problem..)
adds c9ecad6 Making some comments.
adds 42f0c99 Fixed compilation error. SB
adds 9357629 Added some comments.
adds f4c666a * Added comments * removed useless files.
adds c1c0e45 Fixed #69 (check if maximum cycling is reached.)
adds 896d981 Removed test. SB
adds 67673cf * Fixed typo in documentation * Added seqanswer thread.
adds b9e793b Work in progress. SB
adds 6ebb83f Sending stuff.
adds 274d29a Working hard on color space!
adds a0e2fef Implemented Distant Segments Graph.
adds 34d6ed3 Testing on SOLiD data, but they seem to be rich in errors...
adds e6ae402 Fixed several SEGFAULTS caused by reads shorter than wordSize
adds 8e3560a Fixed ticket #80. (stop if no peak coverage is observed.)
adds 8a55e56 Implementation of a tip detector.
adds 333c920 Adjusted the maximum coverage using COVERAGE_TYPE.
adds 5965f55 Some patchwork on tip detection!
adds 9540e32 Adding mummer validate script.
adds ae0b406 Fixed SEGFAULT (ticket #84).
adds 518669f Added CoverageDistribution.txt and Parameters.txt to outputs.
adds fbaee42 Implemented BubbleTool. (for tickets #18 and #19)
adds 408a35d Updated RP
adds 41bfebd Fixed a SEGFAULT by reducing the number of members in Machine.
adds 80753d7 Bubble detection tool is online.
adds 9022577 Some work done.
adds 80a9e02 I think I found a good algorithm for homopolymers.
adds 4261b4b Removed alignment of addresses.
adds e8b653f Switching to ls30
adds ccfa49e The algorithm is working out now.
adds 89b6193 Almost done with the bubble detector.
adds 46f7252 Sending work.
adds 511f0d2 Possibly fixed a SEGFAULT. (ticket #86)
adds 0afc533 Fixed bug #86. (SEG FAULT.)
adds 95d25d3 Avoid bubble detection unless the maximum vertices to visit is not reached.
adds efc5420 Created a framework for bubble detection.
adds 5ca5efe Fix of the day for ticket #88 (SpPaired @ k=21 fails).
adds ecdc654 Changes.
adds 0133f84 I misassembled contig now.
adds 9c7087d Added another test.
adds 9246a3c I think this fixed the problem.
adds bab5ec8 Fixed two situations.
adds eed81be Implemented another thing to avoid misassemblies.
adds 707e4d2 Close to version 0.0.4
adds a4d6b7c Updated procedure.
adds a81fff0 Updated wiki.
adds c14b61d Cleared some things written on-screen.
adds 59dffe9 Ticket #92 fixed.
adds 038f0a9 Done with ticket #93.
adds 3087cf7 Started to work on AMOS output (ticket #58)
adds 2ffd784 * added AMOS support (ticket #58) * added support for arguments (ticket #94)
adds 0b628e1 Ticket #94 -- allows on to provide arguments -- is implemented.
adds 1184431 Unified the documentation.
adds 2a07e52 Support for AMOS is finished. #58
adds ab8c96e Fixed a bug.
adds a4eacf2 Updated Release Procedure.
adds 9e84cd2 Corrected a bug for coverage distribution.
adds 58728ea Added a read trimmer to remove letters that are not nucleotides from both ends.
adds fb89818 Fixed crash when one read is provided. (ticket #99)
adds c1c05a5 Working on bubbles.
adds 04b84e9 Fixed a bug in amos output.
adds 76597c8 Working on ticket #100.
adds 8355702 Sending code.
adds b62c188 Adding new scripts.
adds e035e04 This might be a fix for #103.
adds e41f3e5 Changes for today.
adds 7f28cc3 Updated scripts.
adds 91078cf Adding scripts.
adds b4dcdea Updated the wiki.
adds 76ad45f added identifiers. in tests.
adds a3d7d83 Updating the script.
adds 0d0f406 adding scripts directory.
adds a6d51e5 adding scripts.
adds 0826d31 removing script.
adds d3a5bf9 Move things around.
adds 98f848f Updated scripts.
adds 143587b added log files.
adds 3c4be41 adding new scripts.
adds 2ce1251 adding scripts.
adds d32791f adding scripts.
adds f198928 Adding scripts.
adds 268cee4 adding scripts.
adds 08e413d modified scripts.
adds 74ddaa9 Adding scripts.
adds 5a60568 Fix to ticket #105.
adds 4c63e7c adding scripts again.
adds e5181fc Corrected scripts.
adds 9ca65d7 Added additional scripts.
adds 4a08a82 Modified script.
adds 0ceb7bb Corrected scripts.
adds a94414d adding scripts.
adds 6307d49 Adding scripts.
adds 464a2b7 Modified scripts.
adds 70d0c1f Corrected scripts.
adds 0ff8f7c Corrected scripts.
adds c49fcfd Corrected scripts.
adds c942964 corrected scripts.
adds 8905517 Only open Amos file once.
adds 2115edd Skip the first base AND the first color in SOLiD reads.
adds 39b5f0a Fixed ticket #103.
adds fb15602 Fixed ticket #113.
adds ecd51a1 Corrected scripts.
adds de4e4c2 Corrected scripts.
adds 0fb2224 Implementation for vertices, ticket #114.
adds 6562b6d Flushing arcs in groups (ticket #114).
adds 0d5acf9 Started to work on grouping indexing communications.
adds 393cbd1 Added a comment.
adds 4997a61 Added a constant.
adds c099aec This patch is for sequence distribution grouping of communications.
adds 1f68017 Grouping communications for pairing of sequences. (ticket #114)
adds 2f965f7 Investigate the number of elements.
adds caacfd1 Implemented Ticket #115 -- early skipping of 1-coverage vertices in extension
adds 19490d6 Created a component VerticesExtractor (ticket #116)
adds 2675939 Added two constants.
adds cc548aa ticket #117 done.
adds 32808c0 Ticket #116 (new enhancement)
adds 57b70d1 Added a watchdog on the coverage to assess when a maximum coverage is attained.
adds 50a0f89 Implemented Ticket #120 (move computation of sums, counts, and maxs in mapping of reads onto arcs.)
adds a15d18d Fixed a SEG FAULT brought by -ticket #120.
adds 6bfa814 Corrected serious bugs.
adds c938a1e Added a component.
adds 664c679 Investigating ticket #123.
adds 774885e #123 (-DSHOW_CHOICE removal tricks things)
adds f87b69d #116 (create components to reduce the number of C++ lines in a single file.)
adds 8eb592f Added the 'Tron' algorithm, which can replace the 'OpenAssembler' algorithm.
adds f3ef9fd Changes
adds c5cc2af Added a watchdog for repeated vertices.
adds 9115eb2 added a repeated-region watchdog.
adds e009b28 Fixing Makefile.
adds 95447d3 Changed parameters.
adds 6c343b5 #83 (fix compilation errors for 'make test')
adds cd9718e #48 (Fix compilation errors for Simulation tools.)
adds 45ae947 * Fixed basename when the file is in the current directory. * Trim file name if it's too long for simulations.
adds 616818d Corrected scripts.
adds e15e977 Updated a script.
adds a97f080 Added codes for SOLID.
adds 9a92b9a adding scripts
adds 810fd5f Optimizer
adds f868083 Prototype for #126 (new coverage detection based on linear algebra)
adds 529beef #126 (new coverage detection based on linear algebra)
adds 83b7078 Fixed bugs in the new algorithm for coverage detection.
adds 2b553b2 Added documentation on how to use this script.
adds 6df44e2 added code for circular genomes.
adds 748d73a Updated README.txt
adds c913080 Sending updated scripts.
adds f8c15ee Corrected the Makefile
adds 86801c1 Restored the good old coverage detector.
adds a06a5a5 Changed alarm.
adds bef83c9 Restored threshold.
adds 5a77443 Fixed SEGFAULTS
adds fe0fbb1 Ok now.
adds ea00dc9 Updated release procedure.
adds ef20af6 Updated Released procedure.
adds 0dd436e added a change log.
adds cfc7bd8 removed line
adds 745d1a4 Updated version to 0.0.7
adds 7b3d486 Corrected typos.
adds e3ce0ae Multiplicators set to 1.3 are good.
adds 92698c7 Some work for ticket #55.
adds a2b48a3 ticket #55.
adds 3f577a9 Working on ticket #55.
adds aa2df7a Added MPIOPTS in scripts.
adds 81dc819 Improved speed.
adds 257f07a #135 (change multiplicator depending on coverage.)
adds 9ed7571 Working on 0mix14.
adds 1233f1c #136 (add running time in scripts.)
adds a5740cd Corrected a bug.
adds d4db0ad Changed name.
adds 957eb67 Send script.
adds c933205 #116 (create components to reduce the number of C++ lines in a single file.)
adds 447205f Probably a fix for #132 (fix 0mix14-ray)
adds 7bc06b8 #21 (speed hack: when extending reverse-complement paths, only thread reads at the ~1000 last vertices.)
adds bd1a550 Fixed bugs.
adds 3b7024b Single change, but not much.
adds 18cfaf0 1 is not good, remember?
adds 80f8731 Updated the Makefile.
adds 9e696a0 Adding a script.
adds 220ea3f Updated scripts and Makefile.
adds 6c9913c added a watchdog for decision on tips.
adds 31b40ca Introducing watchdogs:
adds 14612d3 Soft watchdog.
adds 678123b Sending data.
adds 803dc98 I am ready to run everything.
adds 53c644b #129 (robustness for arguments parsing)
adds d9fb406 #116 (create components to reduce the number of C++ lines in a single file.)
adds 4b2401a Fixed compilation errors.
adds 2a2f353 Sending modifications.
adds d1fc206 Removed hard-coded thing.
adds b778bf8 sending changes.
adds a8dca52 pre-release of 0.0.7
adds 060059f Changes in scripts.
adds 69e6aad Some work on Splay
adds 3f13272 #150 (pass the allocator to SplayTree when creating them.) SB
adds cd01ea9 #151 (freeze splay tree after vertice distribution)
adds 1242f61 #149 (create an array of splay tree, and hash vertices to place them in)
adds 718459a Small fix.
adds 83e9490 Small changes.
adds a0b8f4e some changes.
adds 975bfae #131 (automatic detection of fragment length and standard deviation)
adds d866f34 #131 (automatic detection of fragment length and standard deviation)
adds 10e2eb0 Working on distances,
adds c573705 Sending code.
adds 2c2b889 #131 (automatic detection of fragment length and standard deviation)
adds 0cd2b53 Updated scripts.
adds 643543c #156 (Group communications for library distances) #158 (se map<int,int> for distance storage in Parameters) #159 (use map<int,int> for distance storage in Machine)
adds c36655d Some small changes.
adds ab6897d Added an option to dump libraries.
adds dc47986 This will fix #162 (find why Ray crashes on mix21 and mix23)
adds e239988 Fixed cabog script.
adds 35a466b Added a script to analyze the quality.
adds 49c2dc4 #162 (find why Ray crashes on mix21 and mix23)
adds 8180ca5 Fixed Makefile.
adds 009389a #163 (add an option to for prefix output)
adds b5af9b5 Now it seems to be ok.
adds eefe82d Removed a blank space.
adds 64faf25 Sending small changes.
adds b9f601c Ready for 0.0.7
adds 94c9e53 Sending README
adds 28732e9 Updating wiki.txt
adds 38e49f2 Moving wiki.
adds f808fd0 Ajout d'un Define.
adds 023c0fb # 446
adds 186264b Enabled -v is default.
adds 5b5d407 Verbose mode.
adds 1018302 make k a tunable parameter
adds 2566500 add reference in Ray
adds 6abbc74 Write the coverage distribution.
adds bc1d97d [boiseb01 at ls28 trunk]$ svn merge -r 3680:3683 http://genome.ulaval.ca/svn/boisvert/Ray/branches/Ray-0.1.0_vector --- Fusion de r3681 à r3683 dans '.': U Machine.cpp U Machine.h U MessageProcessor.cpp U common_functions.h U MessageProcessor.h
adds ec2e430 check the code for extracting edges
adds 7162e4b Adding files.
adds 46323d6 Removed some line breaks.
adds 7a129a4 #164 working on it
adds 6df2f4b #164
adds 0fd514e Added exception when out of memory or requested memory exceeds CHUNK SIZE
adds 541b7dc Added the number of k-mer for a given size.
adds dd0cf7b Updated the release procedure.
adds dc5fe0b Removed a loop.
adds 1316790 COrrected a bug in MPI count
adds b46bf62 Removed a print
adds 409b997 Sending diff.
adds 80ad2c7 SYncing
adds 547fc89 the error was in MessageProcessor
adds 16493d9 cache paired end queries in seed extension
adds fc54155 only do the silly DFS when there are more than one edge LOL
adds af76b19 Moved wiki file.
adds 7c59b46 Now I am ready to face the trials
adds 60206d6 Updated the Makefile.
adds 3c7d7ac Some fixes.
adds d9ba95e Add/Change #491 (remove messages that use TAG_HAS_PAIRED_READ)
adds a321624 Add/Change #153 (Use only a int to represent a Read index in PairedRead)
adds b35b22a Add/Change #154 (Use only a int to represent a Read index in ReadAnnotation)
adds 1e36d7d Add/Change #494 (implement a TimePrinter with cool features)
adds b02db8d Added indicator of temporal advancement
adds 9d8a51b Corrected keys, changed them to u64
adds 633209a Sending a small change
adds c106d54 Adding examples.
adds 423b283 Updating scripts.
adds 5edf82a Corrected the Makefile.
adds ff5d111 Moved script.
adds dda3824 Corrected the script.
adds 1e1bac6 Add/Change #495 (group TAG_GET_PAIRED_READ with TAG_REQUEST_READ_SEQUENCE)
adds d7ac69b Simplified extension of seeds.
adds 95a4090 Changed period to 10 for fusion reporting
adds 3aef69c Corrected a critical flaw
adds 6e7a0a3 Remove codename
adds 8996d9b Changed LICENSE file
adds 59cf417 Changed readme file name
adds a88c5c2 Updated files.
adds f73e5e1 The AMOS FILE name is now based on -o option.
adds 9a6baa8 Updated options.
adds 6c9f7be Removing a file
adds 09f2da8 Using 1.4.3 in examples.
adds b6c8a1b Corrected INSTALL
adds 25b0906 Updated NEWS
adds 6039dc1 Add/Change #498 (Do a test by ordering the seeds by the length before processing them.)
adds 19ac364 Sending information.
adds 7bf4f94 Updating Makefile
adds 6debbcd Moved code in code.
adds 0b6009d Removing useless files.
adds 0ff3801 The Makefile is awesome now.
adds 18de70b Updated the Makefile.
adds fd5decc Updating README
adds c420034 Updated released procedure
adds 16d4d60 Updated the Makefile.
adds 89bf261 Removed a debug message.
adds c025ae4 Removing sort, it is useless.
adds 53aad43 Added an example
adds 914df73 Sending commands.
adds b7866b9 sending modifications.
adds 042e0ee corrected TimePrinter
adds 429ee67 Sending small changes
adds 96f8daa Added dates in output of elapsed times.
adds 92cdb1c Updated scripts.
adds 5c735ab removing stuff.
adds f30e60e Adding a script.
adds 7cc7107 Moved scripts.
adds 58f2c7b Added a script.
adds ce63ec7 Adding a script.
adds d58f0e4 Sending news
adds 75d8a39 Updated the NEWS.
adds 2064264 Updated NEWS.
adds c94a148 Sending stuff
adds e5dc6f3 Corrected an output for library computations.
adds 7af7db3 Corrected a bug .
adds cba8313 Version is 0.1.1
adds edb721f Added gnuplot scripts.
adds 214ec10 Added a script to prepare for gnuplot
adds 3225bb2 Adding another script.
adds 274dd4f Add/Change #521 (Do a test with a paired library of 1000 on E. coli.)
adds 16bebb1 Sending configure stuff.
adds 32508bf Removing makefile.
adds 91a43c3
adds 711866c
adds 12e4e0f Adding files.
adds ce179bf Sending stuff.
adds cf5ab61 sending data.
adds ffcf86e Adding a new loader.
adds 3f404c0 sending new file.
adds 2601ad1 Sending code.
adds d249204 Sending new code.
adds 59764e1 AAdd/Change #512 (add support for .gz files)
adds f75f538 Add/Change #525 (add support for .fasta.gz)
adds 2a219c2 Add/Change #526 (left reads are not linked with the right one... this is a bug.)
adds 2994407 APossibly a fix for:
adds 6b014fc Adding a file.
adds 0f69361 Removed memcpy for sending messages to self.
adds 6b5b7c6 Sending code with modifications for regulation.
adds da8853a sending new files
adds 6845e28 the tribe is regulated with a scale of 5 micro-seconds
adds f362e4e Changed it to 15 us.
adds 518a065 Removed the regulator.
adds 84637dd sending diffs.
adds 7d508b1 Add/Change #23 (add an early-stop technology (To speed up the process.))
adds 964306d Add/Change #529 (why is there no message near 'Rank 0: fusion is done.')
adds c0dd371 ASending diff.
adds 14949e9 Debuggng messages.
adds c0060ef Add/Change #537 (do an assertion with message size under 4096 in MPI_Send-utilizing function)
adds 3cb78d4 Add/Change #538 (in Ray, if message is more than 4096 for TAG_REQUEST_READS, send it in chunks)
adds 1155596 Add/Change #540 (use sentinel to remove two messages coupled with TAG_REQUEST_READS)
adds f35ea77 Fixed an infinite loop
adds de178e7 Corrected an error, bug
adds 91b1833 Optimized messages.
adds 013a514 added a comment
adds ae6422e Fixed another pesky bug.
adds 6ede5cd sending stuff.
adds 04bde8a Started to implement the function arrays
adds 84a876a Started to work on this.
adds c57f2da some work
adds 78e6263 Changed the CXXFLAGS to -g
adds aa77c81 updated the makefile
adds d39a7fd Add/Change #539 (optimize the big if/else if/else if in MessageProcessor.cpp, using an array of pointers probably)
adds b6eecdd Add/Change #539 (optimize the big if/else if/else if in MessageProcessor.cpp, using an array of pointers probably)
adds bc1fb79 Add/Change #545 (create MASTER_MODE and SLAVE_MODE in Machine::processData)
adds 4e3d401 sending data
adds 95a8aa0 Checkpoint
adds 9855d8c Almost done.
adds e9a2415 Checkpoint, almost done with ticket 545
adds b9294ac m_master_mode is completed.
adds 254e077 ticket done
adds 9f2942e Add/Change #546 (use an array of method pointers for MASTER_MODE & SLAVE_MODE)
adds 6f9a94d Add/Change #165 ("-i" / "LoadInterleavedPairedEndReads")
adds 8015ad4 Sending a small change
adds 479ca37 Maybe fixed:
adds 268d8b3 Add/Change #549 (in updateDistances, left sequences don't get their sequence updated.)
adds a55df4d Sending diffs.
adds 29e3f4a envoi des données
adds 5548248 Sending code back to the home so I can work on another place.
adds 6f42d1a Sending a preliminary diff.
adds 9506623 Maybe this will fix the problem.
adds 209a975 Corrected visual flaws.
adds 063e0e9 Fixed a bug.
adds 7b57754 fixed compilation errors with MPICH2
adds fd5a4a4 adding two classes
adds f1981a4 Sending Makefile.in
adds 0ef12d5 Now it works with MPICH2 and OpenMPI
adds ab976c1 Small changes.
adds ae535ca sending
adds 79849da Add/Change #558 (make Ray compliant with MPI 2.2, regardless of implementation)
adds fa8f495 Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
adds 49fd29c Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
adds 6783c80 Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
adds 496fcac C'est tout pour aujourd'hui.
adds 49c639d Envoyer un patch de code.
adds 7a9929e Replaced vector<Message> for inbox * outbox with a StaticAllocator.
adds 81080a2 Implemented a RingAllocator for inbox and outbox allocations.
adds ffd5ffb Added regulation for RingAllocator .
adds 5833f77 Small changes.
adds d34bf69 Add/Change #558 (make Ray compliant with MPI 2.2, regardless of implementation)
adds 0ce16f8 * Removed messages replies for send_sequence * ADded a special tag for adding a sequence with a regulator * removed busy-waiting for distribution of fusions * Removed message replies for fusion distribution.
adds aa87b6f Working on Add/Change #497 (add a file for detectDistances and updateDistances)
adds f2946ce Add/Change #497 (add a file for detectDistances and updateDistances)
adds ee04ed4 New code is ready.
adds e30f3fe Moved a script
adds a4cc31d Sending code.
adds b85a33e Add/Change #568 (Dont' load files when indexing reads...)
adds 07b5464 Changed the intervals.
adds fb7c419 Sending diff.
adds 313f6f3 Sending stuff.
adds 5adae4a Now, the verticesExtractor and the EdgeExtractors wait for a reply before continuing.
adds d797e8a Changed the period for seeding from 30000 to 100000
adds a543a7f Add/Change #569 (glue sequences together in the distribution of them.)
adds f0b94b4 Add/Change #570 (flush a destination instead of looping them all)
adds eda5834 Fixed the bug.
adds 4d799a9 Add/Change #571 (send paired information after sending sequences)
adds ad66346 More beautiful output in stdout.
adds 9643693 Add/Change #572 (test on ls30 with MPICH2)
adds 4a0115d Add/Change #572 (test on ls30 with MPICH2)
adds 2df3a8d Now busy-waiting when flushing paired information.
adds af3794e There is a residual bug.
adds 2638ff5 Finally fixed the bug.
adds 4b4bc41 Corrected the TimePrinter so it can print a message every hour.
adds 3f4a759 Management of invalid files.
adds 08d6c8d Fixed the bug:
adds 33c3ea1 Fixed another bug.
adds 34ee5b7 Changed two periods.
adds 39b5792 Adding diff.
adds 43e9188 Added two example scripts.
adds 9f0f43a Sending a BzReader.
adds 1b10957 Add/Change #576 (support bz Files (fastq and fasta))
adds 3d0dfa1 Add/Change #576 (support bz Files (fastq and fasta))
adds 2916e34 Sending new scripts.
adds 5600f1c COrrected a bug for library distribution (size updates)
adds ed0b2ea Added some files for distribution.
adds 3e21f36 Sending a file.
adds 070f729 Renaming file.
adds d8ed11c ggA Add/Change #578 (add installation of scripts with 'make install')
adds 89bf2fd Sending test
adds fb3876b Updated the configure script.
adds cc13ab6 Sending packages.
adds 320655c Added printing of MPI implementation.
adds 97add5c Changed slightly the output.
adds 792437c Printing the number of messages received.
adds dd50209 Added printing of updating distances.
adds 2804231 added +1
adds 6113626 Changed the period.
adds 2eff623 Changed stuff.
adds f003cf4 Adding a file.
adds 3949538 Sending changes.
adds 6773d6e Renamed ChangeLog.
adds bcdc6ea Sending change of license name
adds 65a45a4 Sending DESIGNs.
adds cc8cfe2 Sending stuff.
adds e671285 Changed the place where showStats is called.
adds 668f30f Added busy-waiting for distance updating.
adds 1c03bbb Au revoir message moved.
adds 1944248 Sending correction.
adds 991c576 Adding a script.
adds 74fd75a Adding a script.
adds 47ee904 Add/Change #575 (run Ray with -i on ls30 with MPICH2 & SRA001125)
adds 8e7c960 Small fix.
adds 868f334 Corrected scripts.
adds 0813c6c Sending scripts.
adds bb8082e Add/Change #575 (run Ray with -i on ls30 with MPICH2 & SRA001125)
adds 795efa9 Added sequences in output.
adds 66035d1 ggA Add/Change #581 (run Ray on Pseudomonas -p)
adds 8606925 Add/Change #581 (run Ray on Pseudomonas -p)
adds 05abd83 Added a script for pseudomonas -p
adds 8cbb3a5 ADded the full path for the reference.
adds 58bfc8f Updated the citation
adds 19b5109 Added two directories: one for each implementations.
adds 2a8d153 Moved scripts in directories.
adds ac8ecbf added a file for the sun grid engine.
adds 68c0d10 Add/Change #581 (run Ray on Pseudomonas -p)
adds 10565f6 Sending changes
adds c18d5c5 Add/Change #582 (output a message matrix)
adds 8d67f89 No trimming when the sequence does not come from a file.
adds 7dda7eb Add/Change #582 (output a message matrix)
adds a4cbaaf Add/Change #582 (output a message matrix)
adds 29b95c1 Add/Change #582 (output a message matrix)
adds b3969e6 Add/Change #582 (output a message matrix)
adds 16ea496 Removed a useless output.
adds 697f278 Changed the method name in Parameters for the prefix setting.
adds 2998dcd Updated scripts.
adds 0df5cd6 Modified scripts.
adds 6022b63 Add/Change #581 (run Ray on Pseudomonas -p)
adds dc2e638 Add/Change #584 (Index both read of the pair for paired information)
adds 53d9943 Add/Change #590 (enumc for mpi tags)
adds 81b36ca Add/Change #588 (ENUM FOR master modes)
adds f9f5a35 Add/Change #589 (enum for slave modes)
adds 05f75ea ggA Add/Change #585 (Write the distribution of the libraries too)
adds 24a6b60 adding a script.
adds 9720e4b Moved scripts.
adds 76f2996 Add/Change #585 (Write the distribution of the libraries too)
adds 9d5164b modified a script.
adds 508d59d MOved a line in the output.
adds edf9140 Add/Change #591 (optimize finishFusions (currently O(N^2) LOL)
adds ceb25d4 added the logo.
adds ebed256 Modified scripts.
adds cbcaec0 Moved an output string.
adds d98c617 Removed writting of temporary sequences.
adds c26be4d added a file for paired pseudomonas.
adds 9316380 Fixed
adds 011b6ca Only update paired read is they need it.
adds 3e14f70 «Fixed a compile error.
adds 38c1905 Add/Change #598 (pseudomonas-p.sh has 1 error with HEAD, but 0 with r3846)
adds 6eae6fa Add/Change #598 (pseudomonas-p.sh has 1 error with HEAD, but 0 with r3846)
adds aa2af94 Changed the maximum size of messages to 4000, as suggested by Open-MPI folks.
adds 73d59aa Removed a field.
adds 6acefa9 added regression script. A Add/Change #583 (AUtomate tests with stuff in examples.)
adds 4a6e3c8 Almost ready for release.
adds a26aa73 Corrected the release data in the ChangeLog.
adds c05190e Changed the change log
adds a03535c sending changes
adds d8a51bb Modified scripts.
adds 4cfbd63 Sending new release procedure.
adds 375b8d2 Sending regression.
adds 8c0124a Updating regressions scripts.
adds 20c369c Sending diff: changed 4096 for maxToProcess.
adds 424c103 Sending patch for Library.cpp
adds b6f7b43 Fixed (at least I think I did) the evil bug.
adds ce5c0a6 Now it is fixed (?)
adds 70a217b adding regression.
adds d583793 Modified the regression runner.
adds de2dba4 Problem apparently fixed:
adds 4ed1354 merged the branch.
adds 0d0a0eb Updated the ChangeLog.
adds 7d1b800
adds c54dcd8 Corrected the comments.
adds 33dc093 Add/Change #73 (coli-mpich2-interleaved-bz2.sh has many contigs, but coli-mpich2-interleaved.sh is OK)
adds 9d1348b Corrected a major flaw.
adds b3c4c4f Renamed test.
adds 37090b7 fixed a compilation warning on Sparc V9
adds 9296cc6 sending tested architectures
adds 120c1b7 Adding simple test
adds 836e99c sending x86 as a tested architecture
adds 78fa60c Added architectures.
adds 1ba78e2 Final commit before release.
adds e97ef84 Add/Change #75 (fix compilation warning on SPARC)
adds df1273d Add/Change #78 (test with PowerPC)
adds 8188e57 Corrected the file.
adds 0193c1e Add/Change #67 (add an early-stop technology (To speed up the process.))
adds b1221ba sending a file.
adds 890669a Updated the CHangeLog
adds 6d359cb Removed simple test.
adds 58ef84f Implemented Early-stopping.
adds 05219f4 Worked a little on the early-stopping.
adds b307000 Add/Change #76 (add thanks to René in AUTHORS + Add colosse folks too+ add René for SPARC)
adds ea77dd9 Add/Change #82 (Alert the user if the extension is unknown.)
adds 7a810f2 changelog changed.
adds d10f8b5 removed comparison scripts.
adds 70a2287 sending old version of script.
adds 7de6eb8 aclocal is correct.
adds 2954a73 Au revoir ! % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels Ray & 99 & 2014074 & 20344 & 36482 & 127906 & 0.9873 & 0 & 1 & 0 \\
adds f722122 Add/Change #84 (use printf to make output beautiful with MPICH2)
adds 4156771 Add/Change #79 (Load only 10000 sequence at one instant,)
adds f19864d Fixed a bug
adds 5ca83af Corrected ifdef.
adds 788f694 Fixed configure script.
adds 538a9dd changed cout for printf.
adds f74df5f Fixed an coding error.
adds 470d3d2 new files.
adds 5f6850d Add/Change #88 (code a special arrays for myReads)
adds c7ceaf5 Now the Loader frees its memory.
adds cb539bd Add/Change #89 (misassembly poped back)
adds 5e641f3 Corrected the makefile.
adds 1a00f53 Sending changes.
adds de48bf3 Sending optimization for finishing fusions and for seed extension.
adds 8aec860 Updated finishFusions.
adds 0f8e4b5 Sending code.
adds f5871ef Add/Change #91 (too many contigs for SRA001125)
adds 4770247 Sending code, almost done fixing #91
adds d34fda7 Working on several tickets, but this commit is to allow code to be in scratch.
adds 30681dd Add/Change #96 (Problem with reproducibility of paired distance approximation,)
adds 7d573b2 Removed couts
adds cb4d4be Add/Change #50 (Use only a int to represent a library in PairedRead)
adds 77d17cc Add/Change #93 (remove half seeds, but not before the approximation)
adds 4c77775 Added a script.
adds e3616d5 Add/Change #84 (use printf to make output beautiful with MPICH2)
adds 34920aa Add/Change #79 (Load only 10000 sequence at one instant,)
adds ab15503 Add/Change #79 (Load only 10000 sequence at one instant,)
adds 57591a9 Add/Change #79 (Load only 10000 sequence at one instant,)
adds fc4f2cf Add/Change #79 (Load only 10000 sequence at one instant,)
adds 463a878 Sending new configure script.
adds 137d6ee Sending old configure.ac.
adds 8d5998f Changed the ring size.
adds 3f65981 Sending configure.
adds 32eb237 Sending configure that works.
adds fa4a64c Adding config.h.in
adds bc0aa59 Fixed a bug in loaders:
adds b4200fd added foreign directive.
adds 8110c1e Sending stuff.
adds d73df8f Changed batch size to 1 000 000
adds 5aa9fd1 Sending documentation.
adds 79741dc Add/Change #57 (merge all instances of BufferedData)
adds 6117728 Add/Change #50 (Use only a int to represent a library in PairedRead)
adds a48229e Fixed a printing problem.
adds d2d0db0 Sending code, need to fix the code on SRA001125.
adds f3bdd23 I need to fix the code on SRA001125.
adds 23b1f60 I think the problem is fixed.
adds 2044989 Removed text.
adds 2c55096 Now the mismatches are calculated by mummer too.
adds 024c123 Add/Change #69 (add installation of scripts with 'make install')
adds 360fbeb Add/Change #55 (add a file for finishFusions( and makeFusions)
adds 089c49b Updated changelog.
adds a21dfee Sending information.
adds bfa8244 Add/Change #56 (puts seeding routines in SeedingData)
adds e537fb0 Fixed a bug in the print-latex.sh script.
adds aaa9a10 Sending scripts.
adds dee7371 Sending updates for scripts.
adds b48f8aa Sending code for ls30
adds e890093 Fixed http://genome.ulaval.ca/trac/ticket/113#comment:1
adds 2d1c711 Now it is faster !!!
adds 7de9c30 sending change.
adds f084c86 SOme code for A
adds 8890cea Almost done with this.
adds de58b6c Add/Change #66 (support polymorphic genomes (which data to use, simulated data?))
adds ed7d0ae Removed the number of k-mers in the output.
adds bb81a2c Fixed some problems for polymorphic genomes.
adds ae0d7c3 Removed CHI-Square tests.
adds b474b7d Updated change log.
adds 09d0137 Fixed compilation warnings.
adds 0acf115 Sending debug messages.
adds 48c62ec Sending dummy changes.
adds 9e84c40 Envois des changements:
adds ae678fa Corrected the bug in libraries.
adds e8960b4 Updated CHangeLog
adds 1c87514 Added a crypto file
adds 98c3556 changed the crypto-function
adds 0a06d9f Changed VERTEX_TYPE to uint64_t
adds faa0437 Sending patch to detect the source of the bug.
adds be0edd8 added code for removing node in splay trees.
adds 51e5cbe Added an iterator over forests.
adds fa95808 Add/Change #123 (Implémenter l'algorithme de Jacques: poussin v. pouzin)
adds faae3bb Add/Change #126 (change MODE_ variables for RAY_SLAVE_MODE_)
adds a9d32cb Add/Change #127 (change TAG_ for RAY_MPI_TAG_)
adds b140751 Add/Change #128 (change MASTER_MODE_ for RAY_MASTER_MODE_)
adds ae7e3fe Add/Change #130 (change m_mode for slave_mode)
adds a05b217 Add/Change #131 (add code not to index a read on a vertex that is not in the graph)
adds 440f4f2 Add/Change #132 (add code for not adding an edge if any vertex of the pair does not exist)
adds 217fc8a Add/Change #132 (add code for not adding an edge if any vertex of the pair does not exist)
adds 647ba67 Fixed bugs
adds 9e1698a Au revoir ! % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels Ray & 128 & 2003745 & 15654 & 28294 & 89893 & 0.9829 & 0 & 1 & 0 \\ [boiseb01 at ls30 Open-MPI]$ bash strept-error-ompi.sh |tee log
adds e239cb7 Add/Change #123 (Implémenter l'algorithme de Jacques: poussin v. pouzin)
adds 986ed8c Almost done.
adds ba0be6e sending code
adds 36ba008 Almost done.
adds b8c67c2 From: Sébastien Boisvert <Sebastien.Boisvert.3 at ulaval.ca> To: jacques.corbeil <jacques.corbeil at crchul.ulaval.ca> Cc: francois.laviolette <francois.laviolette at ift.ulaval.ca>, Mario Marchand <Mario.Marchand at ift.ulaval.ca>, Arnaud Droit <arnaud.droit at crchuq.ulaval.ca>, Elenie Godzaridis <elenie.godzaridis.1 at ulaval.ca> Subject: Algorithme de réduction de l'utilisation de la mémoire pour Ray: avancements Date: 10-12-22 02:04:16 PM
adds 87b9cd0 sending stuff.
adds cc8e738 Good job.
adds b875841 Sending stuff.
adds 557e4d3 Deleted EdgesExtractor
adds bd55057 Sending code.
adds df6ea47 Envoi du code
adds 24877fe Fixed the bug.
adds bdb4950 Sending changes.
adds 6f0e46b The bug is that here exists a seed with no reverse-complement seed.
adds 8cfe232 Add/Change #134 (seg fault in trunk while implementing memory usage reduction)
adds d07d8ba Sending some changes.
adds 12d052b Memory usage reduction is working a little.
adds 3d5e24f Sending data
adds ad9ac17 Only one message in the inbox.
adds 456ff33 Possibly fixed a bug.
adds d92c124 the assertion was wrong.
adds 249a06b With memory reducer:
adds 5859e1d Doing a test.
adds 63edbdf Code is operational.
adds 5ec06a6 Seems to work well.
adds 60fb6ce On SRA001125:
adds d391428 Left to do:
adds 4eeda30 Fixed Add/Change #137 (Fatal error in Ray)
adds 5e6eb37 Some changes
adds 691b236 Fixed a compilation warning.
adds 8fd2ff6 Adding scripts + modified errors simulator.
adds b7ab917 Fixed -r option.
adds b6e887a Changed the threshold + swapped a cout for a printf.
adds e98bf84 Modified change log.
adds 54754a8 Updated the change log.
adds 20a8332 Updated RELEASE procedure.
adds be7536d Updated the changelog.
adds 3742ee1 Sending new Makefile.
adds 59e8fa5 Added assertions to track down the bug http://genome.ulaval.ca/trac/ticket/140
adds 5de1310 Add/Change #135 (implement <flushRemainingBuffers>)
adds d2b6bc1 The number of sent messages is below or equal to the number of MPI ranks.
adds d6fb84a Fixed the limit for vertices
adds e1891ad Add/Change #140 (Fatal error in PMPI_Isend: Invalid rank, error stack:)
adds e2c5b47 Fixed a compilation warning.
adds d926a8c Sending chunk allocator, removed realloc in ArrayOfReads.
adds 64f352e Working on
adds a6baf52 Fixed this:
adds e00dd4a Fixed:
adds 73514e2 Removed useless print
adds 676495a Updated the ChangeLog.
adds 54ecc8f Now the paired information is packed.
adds f3615fa The memory reducer is now run at the end of vertices distribution too.
adds 8af56a1 Updated reducer to 10 M
adds de5b4a8 Sending data to root
adds 7cf5fe1 Fixed:
adds ac34695 sending diffs.
adds d91600d Add/Change #151 (Reproduce and fix the bug wherein the number of sent messages overflow the ring buffer.)
adds bbf951a Problem:
adds 4b464af Add/Change #150 (change RAY_MASTER_RAY_SLAVE_ for RAY_MASTER_)
adds bcf5ad0 Add/Change #149 (Group communication (2 instead of 4) for INDEX PAIRED)
adds 3eef730 Fixed a compilation warning.
adds 1b01cc3 Fixed error in compilation.
adds bc53e34 I did some work on the internal buffers.
adds 277916e Debug messages
adds 901d156 Fixed a bug.
adds 513202d Restored message size.
adds f07179b Add/Change #157 (parallel read for input files)
adds 75e1575 Removed pending request
adds 9ce9de3 Fixed a bug in Library.cpp
adds 272090b Reads are now encoded in 2-bits.
adds cccb9b7 SImulators are not compiled now.
adds 0ad71d8 Fixed a bug for maximum number of sequences.
adds 3df81b5 Fixed a critical bug: I had removed a line that should not.
adds b70b4dc Cleaned the code.
adds ae2d90f Updating regressions script.
adds 0c2103e Add/Change #167 (hangs without parameters or with -s or -p with insuficient operands)
adds 22d0af8 Add/Change #167 (hangs without parameters or with -s or -p with insuficient operands)
adds 8f548d1 Added a script to dump commands.
adds c0887c1 Added memory usage dump too.
adds 11a6cf2 Sending sequences.
adds 3c05b01 Removed simulators.
adds 2e8126d Changes
adds 1ea1537 == UPDATE ChangeLog ==
adds e4024fc Add/Change #178 (move scripts in MPICH2 and remove MPICH2 + test with configure script)
adds c744d06 Add/Change #177 (in FusionData::finishFusions(), only fetch paths for -1 up to -1-minimumOverlap)
adds 32ef6d7 Fusions.
adds 58a4a8a Disabled SHOW_CHOICE.
adds 3815362 Now reporting the memory usage for sequences and vertices.
adds e7157b9 ggAChanges
adds 6185a82 Forgot this file.
adds 44643b7 Fixed compilation errors.
adds 549850b added some outputs.
adds 1c548eb Added VirtualCommunicator
adds 6790895 Add/Change #171 (group messages in SeedingData to make it faster)
adds 47fd2ee Add/Change #188 (add Doxygen file)
adds 2f82dee Some work on an event-driven thing.
adds b55a147 Some updates on virtual stuff.
adds bf5f5e9 Some work
adds 335840d Add/Change #171 (group messages in SeedingData to make it faster)
adds 6fd03db works on Strept. but not on E. coli.
adds b460c1d % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 116 & 4551108 & 39233 & 80392 & 176272 & 0.9694 & 0 & 5 & 4 \\
adds e010607 Virtualization of communicators works like a charm.
adds a8c4f68 Add/Change #184 (MessageProcessor::call_RAY_MPI_TAG_GET_PATH_LENGTH(Message*): Assertion `m_fusionData->m_FUSION_identifier_map.count(id)>0' failed.)
adds 5defdc3 Updated the change log
adds 4d1c21a Add/Change #185 (Rank 0 must not gather fusions. Instead, each rank must write them to disk.)
adds f490ca7 Add/Change #186 (adapt the AMOS writer to the parallel writting of contigs.)
adds e685cf4 Adding missing pieces.
adds 98c2054 Updated the INSTALL script.
adds 3984886 Sending fix.
adds fb8efa0 AFlat profile:
adds 1024b5b Flat profile:
adds 28b69d7 kmerAtPosition is no longer among the slowest functions
adds c095d46 Add/Change #193
adds 16c7ab9 Fixed a bug with caching.
adds 08a5354 200, 1000, 10000
adds e3d7749 M trunk/scripts/mummer-validate.rb M trunk/code/FusionData.h M trunk/code/Chooser.cpp M trunk/code/Machine.cpp M trunk/code/OpenAssemblerChooser.cpp M trunk/code/FusionData.cpp M trunk/code/OpenAssemblerChooser.h M trunk/code/ExtensionData.cpp M trunk/code/MessageProcessor.cpp M trunk/code/MyForest.cpp M trunk/code/ExtensionData.h M trunk/code/SplayTree.h M|49175990|ref|NC_000913.2| 65 126025 129764 | 58983 62722 [...]
adds 4df1153 4 libraries
adds f6719f2 With SRA001125
adds 03d6dcc Sending stuff.
adds 503c42a Completion of the assembly: 8 minutes, 17 seconds
adds 93e5c77 Add/Change #153 (Reducer increases memory usage ?? (probably STL, it sucks so much LOL))
adds f87e4fa Removed some leaks.
adds 86f1445
adds be1dbf2 Add/Change #195 (remove the inner loop for doChoice)
adds fbfb8ef Fixed the assembly errors.
adds ea48dd1 Adding file numbers.
adds 3b8f74f added a manual
adds 6cc99cc
adds 36f76b9 Sending stuff.
adds dc4774e Fixed a bug.
adds eeb4c3d % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 79 & 4572091 & 57874 & 126238 & 268486 & 0.9851 & 2 & 8 & 4 \\
adds b7076ba Senidng changes.
adds 37578ce Updated scripts.
adds 5c1d140 Version 1.2.3
adds 2a40f57 Added a grid allocator.
adds 598b0b7 Reduced memory fragmentation in the extension of seeds.
adds 0663f59 Fixed compilation error.
adds f733b4c Missing coverage.
adds 499d553 * Force the packing of structures and classes if using gcc * The memory for sequence reads is reused in the extension of seeds. * Any vertex is stored along its reverse complement. * The Vertex class was stripped to reduce the memory usage.
adds bbd0960 % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 79 & 4592032 & 58126 & 126519 & 269064 & 0.9882 & 3 & 19 & 6 \\
adds 964a433 Fixed makefile.alternate
adds 447dc43 Added the option to pack things up.
adds 6b3ec5f Sending patch.
adds b75fd9e Changements dans le code.
adds 8f69264 Added current vertex in output.
adds 723a4ea Grouped messages in finishing fusions.
adds 936ae8f Fixed:
adds 4456427
adds 879d95b Now ready for another run on the human genome.
adds 2472f4a L1
adds 6eef225 adding a simulator that uses boost
adds a7e47fb The maximumum allowed coverage is now 65535.
adds 006dee4 Work is under way to index reads on the good vertex.
adds 97d0711 % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 93 & 4589864 & 49353 & 101161 & 210313 & 0.9876 & 3 & 11 & 4 \\
adds cd02223 % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 82 & 4593587 & 56019 & 113679 & 269370 & 0.9884 & 2 & 6 & 6 \\
adds 1ef4045 The place where to index a read is carefully choosed now.
adds ab4c43f % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels coli-mpich2.sh.Ray & 79 & 4600771 & 58237 & 126779 & 269428 & 0.9895 & 2 & 7 & 4 \\
adds 1b2a04a Ok ready for paper submission.
adds e680bdb Updated makefile.
adds 9dea8bb Added some verbosity
adds a6b2130
adds 8d36962 Fixed stuff.
adds 827f006 Updated scripts; manual and CHangelog
adds 3d40491 Sending stuff.
adds 97a37cd Updated change log
adds c14c4ef #204 (add VirtualCommunicator in Library.cpp too)
adds 5e1d191 % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels 300-strept.sh.Ray & 78 & 2001927 & 25665 & 45529 & 128021 & 0.9807 & 0 & 1 & 0 \\
adds f3e2c61 Library now uses virtual communications. #204 (add VirtualCommunicator in Library.cpp too)
adds 0cb6df5 NJow I only need to change the number of workers.,
adds 95681f0 #204 (add VirtualCommunicator in Library.cpp too)
adds 1a26404 Ticket done: #204 (add VirtualCommunicator in Library.cpp too)
adds 164e38c Not reproducible
adds a1d588b implemented this:
adds 3d03278 Added entry in changelog.
adds 59e3280 #214 (THere are length-4 sequences with reusing memory) #213 (in the extension, use expiry position for reads too. and remove the inner loop when there is only one choice.)
adds b93a460
adds dfa1730 * A read is not added in the active set if it is marked on a repeated vertex and its mate was not encountered yet.
adds c4bced4 Polished the code a little and added two files for read fetching.
adds 9f1634c RAY_MPI_TAG_SAVE_WAVE_PROGRESSION is grouped with RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE (done)
adds 0cbb1e7 merged RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES and RAY_MPI_TAG_GET_COVERAGE_AND_MARK,
adds 4bdd9b9 merged "RAY_MPI_TAG_GET_COVERAGE_AND_MARK" with "RAY_MPI_TAG_REQUEST_READS",
adds 03385ff * Reads marked on repeated vertices are cached during the extension.
adds 78e3501 removed useless file.
adds 50d9b03 #219 (It hangs at Fusions)
adds f59b45a % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels strept-mpich2.sh.Ray & 89 & 1974326 & 22183 & 39956 & 128050 & 0.9668 & 0 & 0 & 0 \\
adds d577930 #217 (* Reads list for a repeated vertex is cached during the extension.)
adds b766103 Potentially fixed a bug.
adds 246d1d8 [1,0]<stdout>: Beginning of computation: 1 seconds [1,0]<stdout>: Distribution of sequence reads: 59 seconds [1,0]<stdout>: Distribution of vertices & edges: 20 minutes, 58 seconds [1,0]<stdout>: Calculation of coverage distribution: 8 seconds [1,0]<stdout>: Indexing of sequence reads: 27 minutes, 11 seconds [1,0]<stdout>: Computation of seeds: 19 minutes, 37 seconds [1,0]<stdout>: Computation of library sizes: 5 minutes, 43 seconds [1,0]<stdout>: Extension of seeds: [...]
adds 8da1706 Updated version number. <
adds 4ecdf7b Added a disk allocator.
adds 2402a0b Implemented an on-disk allocator.
adds 4cf6755 Optimised the on-disk allocator.
adds e1ffc85 private now
adds b7680d6 Removed the on-disk allocator.
adds ef8a532
adds f60a54c #224 (fetch reads by storing a list of 'mates to meet')
adds 2e96227 Adding the vertex messenger
adds 9783db0 sending stuff. new makefile
adds d5f0735 #224 (fetch reads by storing a list of 'mates to meet')
adds ddab59c Fixed the makefile
adds d5c9839 Sending stuff back to ls30
adds f99c805 #228 (finishing fusions exaust memory)
adds f61f3bd envoi de trucs.
adds 7c0d831 added debug outputs and stuff.
adds ec12534 Added timers.
adds 5fbc173 Fixed a bug. assertion made no sense.
adds be38065 Updated the manual
adds 405516a Call the constructor of timer
adds 225a41f Updated makefile
adds e31d5f3 Fixed a bug regarding timer : 15000 days is impossible.
adds bbba510 Dded code.
adds 2909e01 stop the infinite loop
adds 5f243d0 Catching infinite loop.
adds f9874f4 Added debug messages for IDs:
adds ec159c5 Sending stuff. A * Now a mate is not added if the distance is not OK in the first place
adds 0364b1d Fixed probably the infinite loop.
adds ecf95b4 Envoyer nouvelle version
adds 53f2cd6 Sending stuff.
adds d2384af % & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels L1-L3.sh.Ray & 42 & 4628137 & 110193 & 161412 & 371980 & 0.9974 & 0 & 6 & 0 \\
adds 9ca5436 Activated HUNTBUG Mode
adds b01cee2 Version for unit tests.
adds 628a29a ajout du logo
adds 18e5058 * Changed 'Completion of assembly' to 'Total'
adds 0d4fbba updated the manual
adds 8799acb Recompiled the manual.
adds 4c1e75c Corrected a compilation error.
adds 4da7a01 Added string.h for memcpy
adds 3738ba5 removed large files
adds f2b3767 Corrected the error message for the simulator.
adds 26ef69b Add/Change #238 (Remove the limitation on the maximum number of libraries.)
adds 05254d6 added a marker in the output.
adds e95af63 playing with grid tables.
adds 2565c09 added that mpic++ must be in the path.
adds 7fa8014 Updating manual
adds c5a0627 Ready to launch a computation on the colosse.
adds adeba67 Sending new manual
adds ad276f5 Adding debug messaging for profiling purposes.
adds 5ffabfd The seed coverage is now set to the minimum coverage
adds 8fb5ae5 ajout d'un fichier.
adds c92fe1b Changed the seed coverage.
adds 9abe774 added a real-time timer
adds cca6a35 Sending some work in progress.
adds de82d0a Ticket #259 (new enhancement)
adds ca90c1b Add/Change #261 (design new way to compute seeds)
adds 022308c Fixed a bug in which some vertices would not have coverage values.
adds 1bc21bd Add/Change #262 (some vertices don't have a coverage value in the depth first search)
adds a56f3e8 Fixed bubbles code
adds 5baad61 working on switches for
adds 7b4a5da Removing the configure script.
adds 4a14ba1 sending new code.
adds b723541 Sending code with new makefile
adds 288d9d0 removed files
adds 1eb7d29 New license file
adds 1ebbb12 Add/Change #263 (add a switch to turn on profiler) done
adds 1bad3d8 Add/Change #266 (add a switch to turn one memory usage reporting)
adds d0977c4 Add/Change #264 (add a switch to turn on seed debug mode)
adds 35ae1d8 Add/Change #265 (add a switch to turn on bubble debug mode)
adds c933825 Add/Change #267 (add a flag to show the ending context)
adds 9bb7288 adding profiling scripts.
adds e95a717 New algorithm to find peak.
adds fb65a18 Diff
adds f0bfc23 Add/Change #268 (consider dnGASP coverage)
adds 2c49c79 Ray now writes a file with coverage statistics and a file with library numbers.
adds cee4732 Fixed a bug: out of range.
adds 6b18678 Sending code fix.
adds 66e06b3 Sending new version of peak finder.
adds 09a81b2 possibly fixed a bug regarding ticket #290: manual and automatic detection don't work when mixed...
adds 2b4ffa9 * Ray now writes the statistics for seed lengths to a file.
adds 82b206e Removed the printing of addLibraryData
adds e1ec2ed New algorithm for seeds.
adds a7edd4c #235 scaffolder makes it debug.
adds ba671a9 Working on the scaffolder now.
adds 387898b Pseudocode for the scaffolder link generation
adds 71d1171 Sending code to ls28
adds bfd7430 small change
adds d90a364 There is now only one instance of the Virtual Communicator.
adds e332d6a The Scaffolder now uses the Virtual Communicator.
adds 1ca29ee The slave and master modes are printed The MPI ranks are also printed.
adds 484c07e Great leap forward for my scaffolder.
adds a877b69 The scaffolder is starting to be pretty good.
adds 5c80f92 Example of scaffold links:
adds 936a7c2 4 types out of 8 are done.
adds 5e9ad8f Added some changes for the operating system.
adds e8126c4 Link generator is online.
adds d9aa2ed Updating manual;
adds d0b78f5 Links are now gathered.
adds 161a7a0 The code generates mega-links.
adds 0247c7a Scaffolder is almost finished.
adds 5b6f0fa The scaffolder is operational.
adds 0386471 Scaffolder runs on E coli too.
adds 9c99019 Scaffolder is finished.
adds 2087b14 Sending new code.
adds 945671a New target
adds 221d964 Mmodification to a script.
adds e88cd5f Added these lines at the end:
adds b5ea5e0 Unabling bubbler
adds 2e4e854 Ajout d'un script dans Ray pour calculer des statistiques.
adds 1f919c9 Changed the way the coverage values are computed.
adds 8d4c4a4 New script to validate scaffolds.
adds 5a9740c Renamed the script to ValidateGenomeAssembly.sh
adds 11a1da7 Fixed a bug in the scaffolder.
adds 06fe835 Updated changes.
adds 9e6190e Changed changes.
adds 867c1b0 adding website.
adds c254d8d Nouveau site web
adds 55d9f31 new files.
adds 8ea69a5 moving web site
adds bcda256 updated manual
adds f2a2c22 Sending new version
adds c9b58ed Corrected the code that check scaffolds.
adds c789475 Fixed the script...
adds b01c5fb Added a minimum number of links for scaffolding.
adds 2d1f6ef Removed useless scripts.
adds 446d1b9 Changed merger behavior.
adds 8943f44 [1,0]<stdout>:Check for coli-mpich2.sh.* [1,0]<stdout>: [1,0]<stdout>: % & numberOfContigs &scaffolds & bases & meanSize & n50 & max & coverage & misassembledContigs & misassembledScaffolds & mismatches & indels coli-mpich2.sh.Ray & 78 & 67 & 4597448 & 58941 & 133448 & 285886 & 0.9885 & 3 & 0 & 2 & 4 \\
adds 2aabeca Changed the minimum overlap.
adds 1fc71db Added a strict rule to constraint scaffolding.
adds 42ffed6 300-strept.sh.Ray & 80 & 64 & 1968145 & 24601 & 48138 & 194158 & 0.9669 & 1 & 0 & 1 & 0 \\ coli-mpich2-interleaved.sh.Ray & 77 & 66 & 4595185 & 59677 & 133448 & 285886 & 0.9885 & 3 & 0 & 2 & 4 \\ coli-mpich2.sh.Ray & 77 & 66 & 4595185 & 59677 & 133448 & 285886 & 0.9885 & 3 & 0 & 2 & 4 \\ L1-L3.sh.Ray & 44 & 6 & 4628560 & 105194 & 173963 & 371980 & 0.9976 & 1 & 0 & 1 & 0 \\ pseudomonas-interleaved-bz2.sh.Ray & 85 & 68 & 6234019 & 73341 & 169959 & 573806 [...]
adds 5aaf55f Changed the procedure
adds 477da3d don't print raw link
adds f7eb1db * Fixed a compilation problem in Scaffolder.cpp. Thanks to Volker Winkelmann (University of Cologne). * Changed CC to MPICXX and added lines to compile Ray with Intel's MPI implementation. Thanks to Volker Winkelmann (University of Cologne).
adds 0b43c57 Removed NEWS
adds 6099e02 Preparing 1.4.1
adds da759ff New variable in the Makefile
adds d531d46 Removed the old Makefile.in
adds e351408 Don't erase fasta files in regressions
adds 2324b19 Don't erase fasta files in regressions
adds 6e91c4b Merge branch 'master' of git at github.com:sebhtml/ray
adds 7c088fe Updated the README file.
adds c3f8322 Added a new class to represent k-mers.
adds 07547b7 Changed uint64_t to Kmer in the code.
adds 7e66e21 Added code/Kmer.o to the Makefile.
adds 7f412d4 The distribution of vertices works with k=31
adds 8241204 moved files
adds 5813765 adapted files to use new paths
adds ca6b385 adapted files to use new paths
adds ae5e763 Fixed the Makefile.
adds 97e80a8 Moved files again.
adds 63a3c45 Fixed k-mer routines so that unit tests are now OK.
adds 055011f Adding the Makefile which is now located in the code directory.
adds 4abc27c Fixed integration test.
adds 24a6fae added a better warning for bad 454 prefix
adds 37aee55 output contigs >= 100 bp, not paths >= 100 vertices
adds 2bb8a07 Moved the AMOS routines in Amos.cpp
adds 9adf879 Now using ReadFetcher.cpp in Amos.cpp to obtain the read markers for a Kmer.cpp
adds 137a64c Fixed a bug in the TLE entries int he AMOS files.
adds 8a3a167 removed the minimum number of links in Scaffolder.cpp
adds 9f35bdb Changed HAVE_ZLIB to HAVE_LIBZ
adds 62b82b6 Fixed a small bug for k-mers longer than 32.
adds 554b58f Fixed a compilation error when -DASSERT is not provided.
adds 8358496 BzReader.cpp and FastqGzLoader.cpp should not be aware of the value of HAVE_LIBZ and HAVE_LIBBZ2.
adds 8a11324 I added a section for compilation options in the Makefile.
adds a3a584c Updated release procedure.
adds c8bb75d Updated the README.
adds 4adced0 Fixed the length of the array that is allocated.
adds d204801 Added a description for MAXKMERLENGTH
adds dfd3629 Added ghostly code to track and kill those pesky bug related to larger k-mers.
adds fbb9fef I catched the renegade with my handy test suite -- I will now fix it.
adds 9eddbeb Fixed the bug, all unit tests pass now.
adds 6dc2100 Added a cool text about P2P technology in Ray.
adds aa00ec5 Found another bug in getOutgoingEdges.
adds db6c6f8 Bug fixed.
adds deeec5d - Updated the README - The Makefile is now devoid of ifeq but remains conditional. It is easier to read that way. - The Makefile is fully operational -- it can *install* Ray somewhere too ! The syntax is based on the makefiles of the linux kernel tree. - Next version will likely be 1.6.0 as MAXKMERLENGTH is a huge feature with *huge* changes to the code base
adds 521da23 Moved some code in directory assembler.
adds ab41540 Moved code in subdirectories -- fixed include paths.
adds 6245da5 Moved all calls to MPI functions in MessagesHandler.
adds 46808d2 Fixed a bug in the VirtualCommunicator.
adds b51185e Ray assembles genomes with MAXKMERLENGTH=64 !
adds 15826e2 The SFF Loader now takes all the sequences, even those that do not match the key sequence.
adds 4df6d69 Fixed element counts for call_RAY_MPI_TAG_REQUEST_VERTEX_READS
adds 6371dde Added the option to compile VirtualNextGenSequencer.
adds 1d8b677 Removed the Instruction manual from the git repository.
adds 0cf16e2 Updated the RELEASE PROCEDURE.
adds 4300f0f Added a warning when the provided k-mer length is higher than KMERMAXLENGTH (k-mer maximum length).
adds 545d514 Edited this file to change the hard-coded maximum k-mer length.
adds 931c8a3 Added a new integration test.
adds c8742d4 Added a script to generate different builds for integration tests.
adds 7c05f05 Only push the warning on MASTER.
adds 45dc0a9 - Ray now estimates the genome length and writes it to RayOutput.CoverageDistributionAnalysis.txt.
adds eb0d5af Updated the ChangeLog
adds d0e7aca Added 2 unit tests for ingoing and outgoing edges with larger k-mers.
adds f1ae768 Unit tests for edges with large k-mers now pass.
adds 6df039e Commented debug-friendly code.
adds c71db6d Added debugging code.
adds d0d8fab Updated scripts to use git and not subversion.
adds b2faea8 Unified the README, now in markdown format.
adds fa7cccb Added doxygen information in the README.md
adds e53ffeb Fixed the README.
adds f2c5ce3 Updated the README.
adds bd00914 Updated the manual.
adds 2175e7a Updated the README. Fixed the Makefile.
adds 397cbd3 - Added the paper in the abstract of the manual. - Remove old build in makeBuilds.sh
adds 3012ee5 Removed the old logo.
adds a94286c Ray works with MAXKMERLENGTH=64 and k-mer length=21, which means that those k-mers are communicated correctly even if the second uint64_t is *useless*.
adds c5dfe6f Integration test for k-mer length=63 works.
adds f922029 Fixed an integer overflow.
adds b879ac2 Fixed CoverageDistribution for Assemblathon-2/Snake
adds 9b6851a The makefile can now install Ray somewhere (PREFIX)
adds fa5df3b Fixed the Makefile.
adds 0743720 Really *fixed* installation
adds 72ad91c Added exit code EXIT_NOMOREMEMORY=42 as suggested by Hannes Pouseele (applied-maths.com).
adds dd08497 Fixed the an access violation on Windows. Bug reported by Hannes Pouseele (applied-maths.com).
adds a63460a Updated change log.
adds d377853 * Fixed compilation errors for Microsoft Visual C++ (xiosbase and stdexcept) Bug reported by Hannes Pouseele (applied-maths.com>)
adds 8f1c58b Removed dependencies of install.
adds becf4a0 Moved the exit which was at the wrong place.
adds 6fc1c14 Cleaned the source code -- removed commented code.
adds 32cf0f2 Documented exit codes in constants.h
adds 630a28c Fixed integration tests for compressed datasets.
adds 080cfed Added compilation options for build-compression.
adds a1fe88d Readded the minimum number of scaffolding links because it reduces the number of scaffolds for a yet unknown reason.
adds b11495f Added documentation for large k-mers.
adds cb4fba7 Updated documentation.
adds 6562651 Added 2 options to the Makefile: GPROF and OPTIMIZE
adds 8344ac2 Fixed compilation error with -pedantic and -Wextra.
adds fe9c196 Optimised some code again.
adds 9f6602d Updated the README.
adds 52645e3 Define MAXKMERLENGTH if it is not defined.
adds 6ab6f1a Fixed some compilation errors under Microsoft Visual Studio 10.0.
adds d8225b1 Moved tests.
adds f000edb Removed inttypes.h as versions prior to Microsoft Visual Studio 10.0 do not support it I believe.
adds 45919fc Fixed some other compilation errors on Microsoft Windows.
adds 1885703 - Moved the simulator outside the tree. - Fixed some compilation errors in Microsoft Visual Studio.
adds 188804c Fixed a compilation error involving stdexcept.
adds d4d2848 - Fixed namespace collision with Message and stdexcept.
adds 14b8371 Added ray_windows.h to LibraryWorker
adds 2fdf8f0 Message also needs stdexcept because it includes mpi.h which I believe check __cplusplus
adds 024435d Finally fixed all compilation errors.
adds 27f416b Ray works on Microsoft Windows and can be compiled with Microsoft Visual Studio 10.0.
adds 238aad8 Added some options in the manual.
adds 5c2922a Fixed a compilation warning for printf with uint64_t.
adds e2bc426 Added documentation of the amos option.
adds 2de854a By default, Ray now displays the options available if parameters are provided or if -help is provided.
adds 44a27a1 Fixed the tiling (TLE) entries in the AMOS file when forwardOffset or reverseOffset are not 0.
adds b689eb9 Changed method name.
adds ee01572 Updated the changelog.
adds 2b7536f Presumably fixed a compilation error on Apple Snow Leopard. Thanks to Anthony Underwood for reporting the bug.
adds 5d13545 Updated change log.
adds 6590dd0 * Added a smoothing routine for the detection of points in the coverage distribution. Thanks to pmiguel on SEQanswers for providing raw data points.
adds 2910a92 Added the processor name for debugging purposes.
adds e81af37 Added option -show-memory-allocations
adds e48b7fd Added an indicator for completion.
adds 8665d6d Changed ifdef linux for ifdef __linux__
adds e130952 * Fixed the showMemoryUsage function. * Fixed uniform distribution of k-mers for k > 32
adds 60d7354 Added a unit test for uniformity.
adds 9b38e4e Added a unit test for uniformity of vertices on ranks.
adds ef77287 Fixed a bug for the seed length distribution written to a file.
adds 11c120c Fixed a bug for the seed length distribution written to a file.
adds ec9673f Changed MAXKMERLENGTH=128 for MAXKMERLENGTH=64 in examples.
adds c8ec3c6 Changed MAXKMERLENGTH=128 for MAXKMERLENGTH=64 in examples.
adds cfd8bc9 Moved the allocator in its own file.
adds 5f39f0b * Fixed a communication problem for k>32.
adds 6bd9458 Optimised run()
adds 0c8f6a2 Added balance for the profiler.
adds df4c197 * Added a progression indicator for scaffolding. * Writting scaffold sequences is now faster.
adds 9eb15a7 Now Ray writes observations for libraries in a file.
adds ce080de Added (some) code documentation.
adds 869f404 Merge branch 'master' of git at github.com:sebhtml/ray
adds a2fc0e8 Modified the code to reduce the number of calls to fopen.
adds f752919 Modified the code that writes scaffolds in FASTA format.
adds a73382b To use 454 mate-pairs in an SFF file, you must extract them and provide Ray with the 2 resulting fastq files.
adds 5842f3c Fixed a compilation error for BzReader.
adds a2c9149 Added some comments in the code.
adds e9e9989 New Ray option: -write-kmers write k-mers, coverage values and arcs to PREFIX.kmers.txt
adds 78c904a Adding experimental support for color-space reads.
adds c2348fb * New experimental option: -color-space for .csfasta files (unstable)
adds cb8ccd5 * Added an assembler panic when no k-mers are found in reads.
adds 5d6032d * Ray can generate an assembly in color space (the resulting assembly is in color space).
adds d8bebd5 Added a small comment to document call_RAY_MPI_TAG_ASK_VERTEX_PATHS.
adds b4c64be Corrected a typo in the eagerness explanation.
adds b94dd2c Documented color-space mode.
adds 43408f7 Edited unit tests to consider changes to the code base.
adds 6fdc94b Added DEBUG=n as default in the Makefile.
adds f9ba492 An additional round of smoothing is now the default.
adds a0eb036 -write-kmers don't write k-mers with coverage of 1
adds 8644d2d Fixed: Sending RAY_MPI_TAG_GET_CONTIG_CHUNK messages fails
adds 9cfac4b Fixed smoothing bug in CoverageDistribution.
adds 2a58dee * New options: -minimumCoverage, -peakCoverage, -repeatCoverage -- provides coverage values automatically.
adds 7872de9 A read can actually be empty after trimming.
adds 12f94cf Fixed a bug in a script that generate Ray commands
adds 2d5d180 Corrected script.
adds f33a60c New C script.
adds f526d10 Created a program to filter qseq files.
adds d220aaf filter-qseq.c is working properly now.
adds 02c1d59 Merge branch 'master' of git at github.com:sebhtml/ray
adds 25ec404 KmerAcademy is a place where all k-mer must transit before making it to the GridTable. Those observed only once remain in the KmerAcademy. This academy is then destroyed.
adds d0a6c2d Memory for low-coverage k-mers (the KmerAcademy) is freed after graph construction.
adds 70802ae The memory usage for optimal read markers is now reported with -show-memory-usage
adds 30d7a77 Merged VertexData with Vertex and merged VertexTable with GridTable
adds f6fd08b * Reduced the memory usage during the building of the graph.
adds 1def137 Added DynamicVector to reduce memory fragmentation
adds bda9226 Fixed a free problem in SeedExtender.cpp when no seeds are available.
adds 3554b8d Added parenthesis for clarity
adds 6d23cc3 Removed segmentation fault
adds 6de4163 Edges pointing to non-existing vertices are now purged
adds 67dcba9 VirtualCommunicator statistics are now reported for BufferedData
adds 945370a Reinstated code for -write-kmers
adds 33c15ec New outputted file: PREFIX.degreeDistribution.txt contains the distribution of degrees in the graph.
adds a757aa6 Cleaned the code by removing MemoryConsumptionReducer (~ -1000 SLOC).
adds 52a0328 Fixed a bug in KmerAcademy
adds 3f2c879 The hashing functions now only take an object, the reverse-complement logic is outside.
adds 55dccf5 The hash tables are now implemented using open addressing with quadratic probing.
adds b431b88 Now using MyHashTable for GridTable
adds 34d0fe7 Implemented a sparse hash map (following the description of Google sparse hash; see structures/MyHashTable.h)
adds 6777ffb Increased the maximum number of reads per message-passing interface rank in Ray
adds 6f504e3 Improved the performance of MyHashTable (running time)
adds 3d0c5c3 Removed data type attribute in Message because it is always 64-bit integers anyway.
adds 8c1ddd3 Added statistics for the new hash table.
adds eb60e40 Added some documentation in the source code of Ray.
adds b9e9088 In MyHashTable, the bitmap is now static instead of dynamically allocated. Furthermore, a group of buckets now contains 64 buckets instead of 48.
adds cbd3b3d Changes: MyHashTable now automatically grows and uses double hashing for open addressing.
adds 5a57c21 Fixed a compilation error for MAXKMERLENGTH>32
adds df93e45 Removed a useless prototype.
adds 5930dde Fixed compilation errors for unit tests.
adds 0d13d7f Fixed a boundary issue with the second hashing function
adds 86ba004 Now, only the MessagesHandler is aware of the message-passing stack (mpi.h and MPI_*). The other folks use the inbox and the outbox to communicate -- or the virtual communicator if they are intelligent.
adds db0f359 Fixed an infinite loop when a file contains no sequences at all.
adds 404ad4c Investigating possible memory fragmentation -- added printing of debug information.
adds 326132a Renamed a directory
adds bb8ad87 Updated unit tests.
adds 56273c9 printStatistics should be called on the k-mer academy, not on the grid table.
adds 2b71038 Created a framework to launch systems tests in parallel on a compute grid
adds 27ff1db Merge branch 'master' of git at github.com:sebhtml/ray
adds edf17af Continued work for the system tests. Mostly script editing.
adds 180e1da Fixed a segmentation fault when one rank has no seeds.
adds 46890f0 System tests can now be done with Sun Grid Engine. Entry point is system-tests/main.sh
adds 150b092 Removed examples directory -- system tests now replace them.
adds c6725c2 A system test can be run outside of a compute grid (cloud) using run-test.sh.
adds f9f4c35 New output file: PREFIX.MessagePassingInterface.txt contains the number of sent messages for each type.
adds d165fa6 Implemented SmartPointer objects to allow defragmentation of memory.
adds 880fa6a Allocating a number of elements, not a number of bytes & fixed a bug for a SmartPointer after deallocate
adds 998e05c Changed the default number of processors for system tests to 30
adds c01b617 Fixed a bug that reported 0 sequence reads for the first file while otherwise handling everything correctly.
adds 8508944 Unstable version of an allocator with real-time defragmentation.
adds 22ab5c8 Removed memmove.
adds 0d0809f Added documentation for getIngoingEdges and getOutgoingEdges
adds 29b0321 Fixed a buffer overflow in getKmerAtPosition, reported by David Eccles (gringer).
adds 36c989d Restored the correct number of cores
adds 9d73ac3 Removed some output in print().
adds 45528ab Fixed a bug in deallocate and added defragment method.
adds 0413e88 Added defragment calls when a core is waiting, testing it.
adds 705b52a Modified defragment to be coherent with the low-granularity of Ray.
adds e8c1cc0 Renamed the Sun Grid Engine runner script for system tests and added the script for testing on a symmetric multiprocessing processing machine.
adds 1bcd6c6 Edited an error message to make it more explicit.
adds 8099ac4 Added a method to obtain the allocated size for a SmallSmartPointer.
adds 08921df Added a method to obtain the allocated size for a SmartPointer.
adds fd01c9c Implemented incremental resizing to allow low latency.
adds f820cfa When all message-passing interface ranks are done computing k-mers (or vertices), the incremental resizing is completed if necessary.
adds 204ec6b Changed the default number of buckets for MyHashTable and changed parameters for incremental resizing.
adds 71889a7 Added m_firstGapStart to speed up the lookup.
adds 45b66f0 Cleaned scripts for Sun Grid Engine
adds 043fc3d Fixed compilation warnings.
adds 9de9cdf Changed the rules for allocation, now more real-time.
adds dd88edd Working on the speed.
adds f6d47aa Fixed a bug that I introduced in ChunkAllocatorWithDefragmentation
adds b7c2804 defragment() now is O(65536).
adds 58c6ddd Added DefragmentationLane class.
adds c5723f8 Fixed a compilation warning.
adds bd62be8 The allocation process is now a little bit faster -- only defragmenting when there are enough gaps.
adds 2fa490b Fixed a bug (KmerAcademy::insert) that effectively doubled the memory usage of the k-mer academy.
adds cacf733 Fixed main-sge.sh.
adds b6dab38 Added a to-do task.
adds 190ec24 Added a task to do.
adds 48dcea9 Documented the main loop of Ray.
adds 73e5b6b Added a to-do task, I think there is memory fragmentation during the selection of optimal read markers.
adds a1c3914 Documented insert().
adds 6aae5b7 Added time complexity.
adds 239b256 Changed maximum execution time.
adds 0e11f62 Fixed 2 segmentation fault bugs in this newly crafted memory allocator.
adds 64bba3b Corrected 2 dead symbolic links.
adds f83e632 Fixed a display bug.
adds 1c44855 Added a new output file called PREFIX.NetworkTest.txt which contains average latency including software overhead.
adds 2d68462 By default, don't pack structures in memory (FORCE_PACKING=n).
adds f075d07 Fixed a display problem.
adds da22f35 Removed a displayed message.
adds 8659ddc Fixed a problem that caused contigs within scaffolds to be 2 times shorter when MAXKMERLENGTH=2.
adds 106cbaa Fixed the computation of the destination for the network test.
adds 090bec2 New thing to do.
adds 414b48e Added -O3 when running the profiler.
adds b132cd3 Removed calls to defragment() outside of DefragmentationGroup.
adds 5aa2526 Added a message indicating that network testing is to be done.
adds e271ee8 Using cout instead of printf to print uint64_t values.
adds c3c7e01 deallocation is faster, so the overall process is faster.
adds c061c36 Fixed a compilation warning.
adds 27c25bc Added host name in network test message.
adds cc0d411 Added a system test for the Illumina MiSeq.
adds fe117c0 Renamed MiSeq system test.
adds f64bb91 Updated version to 1.6.1-rc3
adds 89c6dce Updated R scripts.
adds d8f35e3 Fixed the range.
adds 477d43b Pacific Biosciences long reads now load correctly into Ray systems.
adds 08b2827 Fixed an R script for the plotting boundaries.
adds 852ae1e Moved symbolic links.
adds 6b7a7de Corrected the number of pairs.
adds 34effb4 Updated the change log, version 1.6.1 should be released today.
adds 39a7f6a Added the symbolic link for data-for-system-tests.
adds c3ec6f9 Ray v1.6.1 is code named 'sunray'.
adds 29486fb Using png instead of pdf.
adds 9eabbb7 Now using png instead of pdf.
adds f217fe0 Added log10 scale to library distribution plots.
adds bf1a2a7 Changed a constant in a R script that controls the boundaries.
adds 20f6df7 Added a working prototype in Python for calling library peaks.
adds eab5862 Moved this script because it interferes with system tests.
adds 753046d Merge branch 'master' of github.com:sebhtml/ray
adds 4838cca Library caller prototype works well on all 3 Assemblathon 2 datasets without worrying about persky adaptors, thanks to Optimal Read Markers (TM).
adds 630d762 Fixed the command in a system test.
adds 5fab076 Now working on v1.6.2
adds 4bb20ba Added an entry in the change log for 1.6.2.
adds 7d92f06 Ported the prototype for finding peaks from Python to C++.
adds 7a72aac Ray can find more than one peak in any paired library.
adds bd324ea Now selecting the correct peak to choose the next vertex.
adds 065df3a Choosing the good peak for a paired library if a mate is already available.
adds d652a1c Now Ray uses the maximum peak of a paired library to compute the expiry position of a read.
adds 857c207 Fixed some compilation warning with gcc 4.1.2.
adds 0d6565e Fixed a system test.
adds 2b5f716 Changed the behavior for repeats.
adds 4a4b739 Don't set NSLOTS if already defined.
adds fdc1bde Merge branch 'master' of git at github.com:sebhtml/ray
adds 8c15d79 Corrected the peak finder.
adds 5a49add Changed to 64 slots.
adds 952dfb8 Don't print the tree.
adds d386173 When the extension is finished, show library peak usage.
adds 3f15314 Don't compute or update peaks for libraries with manually-provided information.
adds f7d9087 Added a coding style file.
adds 982ff04 Updated the coding style.
adds 810187d Corrected a code comment.
adds a2470f2 Moved the configuration of the virtual communicator in Machine.cpp
adds 15ea481 Fixed a compilation error.
adds 9825ecf Implemented parallel file partitioning.
adds 8549758 File partitioning is now performed in parallel.
adds cd8c1af Improved the peak finder when there is no deviation.
adds 1ef868d Created an heuristics module and moved related bits in it.
adds 9c8b02d New experimental heuristics: The Ray NovaEngine.
adds 668ad2f Added a unit test for the NovaEngine.
adds 4471c37 Improved the NovaEngine, but not using it yet. It needs more testing.
adds 1bd4d5a Removed assertion.
adds 862e6dd Removed some messages.
adds 412052b Improved the unit tests for the NovaEngine.
adds 1a8b0e0 Improved the NovaEngine according to unit tests.
adds e704aa1 Simplified the algorithm that finds peak and added 35 unit tests to test it (for various datasets).
adds f7addb4 Added 35 unit tests.
adds 19b3905 Added a symbolic link.
adds 207a193 Added an entry in the changelog.
adds efda9d9 Moved Kmer routines in the class Kmer.
adds 43200b5 Fixed a typo.
adds 88b13a0 Unit tests are now files named test_<test_name>.sh
adds 231dbc9 Added a file describing how to submit a patch.
adds 67a87ed Improved the document about patching.
adds 4372845 Only show nova choices if -show-extension-choice is provided.
adds 9706603 Improved the README for system tests.
adds 20ad18f Added an abstraction layer for the operating system.
adds 9847b9e Added a TODO item.
adds b76e9dd * Added information on unknown nucleotides in the instruction manual.
adds c9e8a5e Added a TODO item.
adds 4b3639f Added a unit test and modified CoverageDistribution.cpp to handle low-coverage datasets.
adds 3fe9fab Removed roughly half of the messages with the MPI tag RAY_MPI_TAG_KMER_ACADEMY_DATA.
adds e1efa6e Fixed a compilation warning.
adds 1c135af Disabling by default the experimental NovaEngine. Results so far are promising !
adds 3696be0 Added 2 scripts for code editing.
adds 1c53c6e Added comments at random places.
adds 0bbd8d3 Removed options in 2 system tests.
adds 73c61bd Fixed a bug in the recently introduced peer-to-peer parallel Partitioner.
adds 5e5edae Option use:NovaEngine enables experimental NovaEngine.
adds 13e5e76 Removed by default the reporting of libraries in stdout.
adds ddeca62 Fixed a bug in the NovaEngine.
adds 9598fda Now using the NovaEngine.
adds af7557e New output files: PREFIX.SequencePartition.txt and PREFIX.NumberOfSequences. Improved the content shown with -help.
adds 8bc58aa Fixed compilation errors with HAVE_LIBZ=y and HAVE_LIBBZ2=y
adds 91359b0 Added options -use-NovaEngine and -show-NovaEngine for debugging purposes.
adds 1902636 Only use NovaEngine when paired information is available.
adds a5e631b New option: -write-seeds which is useful for debugging the code.
adds 182fe2c Added some unit tests for the Ray NovaEngine (for mate-pair reads). Seems to work quite well so far.
adds 9c449be Fixed a compilation warning.
adds d842360 Added a section on how to launch Ray in the manual.
adds 7a3443c Improved the manual.
adds c667133 Added a unit test and fixed NovaEngine to handle it.
adds dac7de5 Modified the extension algorithm to avoid collapsing of repeated k-mers that are near each other in the genome.
adds 3b83d6c Added read placement freezing.
adds bffce62 Merging of similar paths has been modified.
adds d48fa33 Fixed an implementation bug for double hashing.
adds bacc0c7 Fixed comments and assertions for new correct code.
adds 29ab020 Fixed a bug in the incremental resizing algorithm of MyHashTable.
adds 454d5ee Added a test for open addressing.
adds 8ffee2b Merge branch 'master' of github.com:sebhtml/ray
adds 34d1af2 New development option: -show-distance-summary.
adds 798f262 Added debugging option -show-distance-summary.
adds c9aa372 fixing a segfault when no contigs are found
adds 91f3251 Added David Eccles in the README
adds 0811707 Removed email of contributor.
adds a6244b0 Modified the selection engine to that the new unit tests also pass.
adds 1aac7a6 Removed the coverage threshold from the algorithm that finds seeds in the distributed graph. Suggested by David Eccles(gringer) from Max-Planck-Gesellschaft, München.
adds e6c66af Added N50, median, average and largest contig and scaffold lengths in PREFIX.OutputNumbers.txt
adds 8354455 Fixed a compilation errors due to the algorithm library.
adds 83f0e0a Fixed the maximum length of input reads to 65535.
adds ed67f25 Updates in the README.
adds a1233c0 Fixed a recently introduced regression in heuristics (should not choose an invalid choice).
adds 27f24d5 Added a few things in the README.
adds 5a7c941 Implemented a Bloom filter to reduce the memory usage. This is ridiculously good and the false positive rate has no effect whatsoever on Ray thanks to the KmerAcademy.
adds ec0f6d1 Fixed a memory problem in the computation of optimal read markers.
adds f84d308 ExtensionElement objects now contains reads in 2-bit format.
adds 0d1aab0 Fixed a compilation warning with Intel compiler.
adds c63ba4a Fixed a compilation warning with gcc.
adds 5a99139 Fixed a integer overflow.
adds 82f6107 Fixed a compilation Warning.
adds 6ccac7a Flag invalid choices before doing the actual selection.
adds 6a1854a The paired read simulator is now a separate project, see https://github.com/sebhtml/paired-read-simulator
adds fe05cee Added list of working C++ compilers.
adds f23b52d Changed the default number of persistent requests.
adds ac01c27 Modified NovaEngine to pass a new unit test (as well as the old unit tests).
adds 44d2bc8 Extension of seeds if done endlessly until growth stops.
adds 40d1d8a Fixed a bug.
adds dbba521 Added some documentation files.
adds dd5c796 Input opcodes are now shuffled before being utilised.
adds 0f78f4e Fixed which arguments are picked up by opcodes -p and -i.
adds eb13301 Changed the precision of things that go together.
adds 6208303 Fixed a bug in the scaffolder, now more vertices should be investigated.
adds b6e342c Fixed a segmentation fault that occurs in rare cases.
adds 3ece690 Ray merger will merge more things now.
adds c17c1fd RayCommands file is written correctly now.
adds d4e5a25 Fixed N50 when there is only 1 scaffold.
adds 7c2a084 Added skipping events.
adds 6fa20a9 Don't fetch read markers when not needed, use less memory to know is a vertex was assembled.
adds 237339a Only send a RAY_MPI_TAG_ASK_IS_ASSEMBLED message if starting on a seed on flow 1.
adds 5fc8c13 Changed the prototype of VirtualCommunicator::getMessageResponseElements.
adds 1e3490f Modified the order of the steps performed when merging identical paths.
adds 63beff4 Fixed a display problem.
adds c510d96 Added tag counts for option -run-profiler.
adds 60d1ebe Reduced the number of messages with tag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE in SeedExtender.cpp
adds 23f7218 Preparing code for a change.
adds 4822527 Added options -read-checkpoints and -write-checkpoints, this is still in development.
adds 890ba11 Option -write-checkpoints writes all checkpoints.
adds adf7222 -read-checkpoints works with checkpoints <CoverageDistribution>, <GenomeGraph> and <Seeds>.
adds f63590a Checkpoints are now operational.
adds 218546f Checkpoint files are now written in a binary format.
adds e2a2bb6 Added a MANUAL file.
adds 6d29d43 Fixed a messaging bug occuring very rarely.
adds a72d0ec Improved checkpointing messages.
adds a6596ea Added option -test-network-only to only to test the network and return.
adds 5a7b56e Improved checkpointing message.
adds ddf2125 Fixed a bug when no sequence files are provided.
adds 5dd5470 Added checkpoint Partition.
adds 0094fba Added checkpoint Extensions.
adds 6c4fac9 Fixed a hanging problem.
adds aec738a Changed 1 hash function because it was a copy.
adds ee971f5 Read checkpoint before writing it.
adds dcf3eb6 Added a file describing checkpoints.
adds 03cb71f Don't write a checkpoint if it was just read.
adds 37aa1ff Limiting seeds to probably unique vertices.
adds 0034730 Skip a seed if within it during flow 1 and a vertex is already processed.
adds 98dbbd4 Removed unused scripts.
adds d15a0ca Added gmane link in the README
adds 797baef Added -read-write-checkpoints in the changes.
adds 5e09388 Updated the MANUAL.
adds 89ed32b Added option -debug-fusions.
adds ffef055 Updated the ouput of -help option.
adds 1a11ee5 Added checkpoint Sequences.
adds 7f8708f Added an explicit flush.
adds b6aa616 Restored original state.
adds 6a290ce Added additional debugging information.
adds fa809fa Testing symbolic links.
adds 6b6fd7c Removed logo from source.
adds a5ff5c4 Added a Documentation directory.
adds b14a5b7 Removed the manual target from the Makefile.
adds 70c8e92 Changed where is written the binary Ray.
adds 7e04a0a Fixed compilation warnings.
adds 8152dbb Added documentation for the virtual communicator.
adds f11cb16 Added documentation for the virtual processor.
adds 1039128 Added documentation for the network latency.
adds 91799e1 Fixed an argument name.
adds 4897465 Fixed compilation warnings for 32-bit systems.
adds 4eebe61 Introducing the VirtualProcessor class.
adds 8a2be4a Removed MyForest and its iterator minion.
adds 068ce0e Added VirtualProcessor initialization.
adds 952e1a2 Updated Documentation files.
adds 345d267 Added \author tag to all classes.
adds 151028b Migrated some code only utilised by the scaffolder.
adds c6fb5d0 Added INSTALL.txt.
adds 78af599 Adding new files in Documentation/.
adds 7dea079 Added a function to create directories.
adds 8200a28 Merge branch 'master' of github.com:sebhtml/ray
adds d946b29 Fixed compilation warning.
adds db6b8d3 reset() must be called in the constructor.
adds c920e1e Fixed a compilation warning.
adds 26ee554 Updated the path to Ray in system tests.
adds 58e1a6d Modified the behavior of Ray when fusions are generated.
adds b01fe11 Added option -version to Ray.
adds 1048b06 Added scaffolder cases in Documentation/
adds 45ecca1 The ChangeLog file will not be maintained anymore, use ./scripts/dump-ChangeLog.sh
adds 10d3346 Merge branch 'master' of git at github.com:sebhtml/ray
adds 778e0d2 Changed the maximum number of cycles to 16 in merging code.
adds 173a2f3 Removed hard-coded parameter -debug-fusions.
adds b826e68 Added TaskCreator and Merger classes.
adds 75f29f1 Added debugging messages in FusionData.
adds 3547950 Added method hasWorkToDo to VirtualProcessor.
adds d05a902 Added interface Worker for worker classes.
adds 53085bb Restored worker codes.
adds c801302 Added some debugging information for fusions.
adds 84656ae Using the VirtualProcessor for edge purge.
adds 57753e7 Fixed some unit tests by moving scaffolder methods.
adds f778c5b Implemented a new better and simpler merger module -- FusionTaskCreator/FusionWorker.
adds 45280ff Removed OperatingSystem dependency in unit tests.
adds 3cbc5fd Added some debugging information for FusionTaskCreator.
adds 6a5954b Changed the default algorithm in VirtualProcessor -- now using a minimum work unit.
adds 15fc7d1 Added an AUTHORS file.
adds ae4af42 Fixed a machine-state bug in FusionWorker.
adds 80d8fc8 Fixed a state-machine bug in TaskCreator/FusionTaskCreator.
adds e42c2d1 Workers push virtual messages, not real messages.
adds b3b8dde Disabled the reverse-complement copies of extensions.
adds 441d133 Added Joiner code.
adds 9595b0d Added debugging information in JoinerWorker.
adds 1ef78fb Updated a threshold in FusionWorker.
adds 3d49b71 Added selected hit in standard output for JoinerWorker.
adds e53c0cf Now printing hit information in JoinerWorker.
adds e5f0ac7 Joiner software stack now joins otherwise un-joined paths in the distributed graph.
adds e77388e All output files are written in a directory provided with option -o.
adds ef06930 The default is now ASSERT=y in the Makefile.
adds f704b0f Corrected positions in JoinerWorker when on the other strand.
adds 2754a54 Added 3 unit tests for NovaEngine and improved the heuristics.
adds 221e7b4 Implemented the reverse strand case in JoinerWorker.
adds 6538859 Improved heuristics for selection.
adds 32c1384 Corrected the number of flowed vertices in the seed extension.
adds e6a4fd8 Fixed a bug in the virtual processor wherein it was not force-flushing messages when needed.
adds b9fe00b Cleaned some code in the task creator routines for edge purging.
adds fdad4e9 Cleaned some code in the task creator routines for edge purging.
adds 672b5f3 Changed --oneline to --pretty=oneline for compatibility with older versions of git.
adds eaadc7c Modified the Sun Grid Engine job template to erase the directory before running the whole thing.
adds 18edfd0 Fixed the content of a displayed text in the fusion task creator.
adds 77e4a01 Modified the scaffolder routines to check the vertex coverage values in paths.
adds 9150bc1 Removed the minimum number of raw scaffolding links.
adds edbfcd7 The checkpoint ContigPaths is now written on demand.
adds 1db2865 The checkpoint ContigPaths is now fully operational (read and write).
adds 862b5fc Added option -write-contig-paths to write contig paths with coverage values. This is enabled by default.
adds 8dc6766 Fixed the code that counts the number of extended seeds.
adds b5a98d2 RayVersion and RayCommand are now written (a bug was introduced).
adds eb9f8c7 Limiting scaffolding links to vertices that have one parent, one child and a coverage value near the peak.
adds f0fcdd3 Changed the default message size for network testing.
adds 06c7695 Added information in ScaffoldLinks.txt
adds 32646f2 Added non-persistent MPI communication just to compare.
adds 81be6d9 Added the standard deviation in ScaffoldLinks.txt
adds a908567 Implemented a new greedy scaffolding algorithm as discussed with François Laviolette.
adds 21e312c Modified some scaffolding code to obtain the correct side of a contig when it allows both.
adds 1dab4e3 Restored the default number of words in the network test to 500.
adds 5cd9848 Added some documentation for Infiniband.
adds 2afa3cf Updated for ScaffoldLinks.txt format to v2.0.
adds 2828d85 Added more debugging information in the scaffolding test.
adds 53eb012 Fixed scripts to accomodate new prefix directory option.
adds bdf49a2 Fixed an integer overflow in the computation of standard deviations.
adds 95d825d Merge branch 'master' of git at github.com:sebhtml/ray
adds 4e2b599 The number of enabled MPI ranks can be changed during the network test by changing a variable in the source code.
adds 783d522 Fixed a communication problem in MessageProcessor.
adds bc7b314 Added some debugging information for -debug-fusions.
adds 76b0b0d Fixed a bug in JoinerWorker in which two overlapping paths would not be joined together.
adds 0554af1 Regression bug on phix system test fixed.
adds 0df6381 Fixed some divisions by 0 in the scaffolder.
adds 9181dd8 Added assertions and fixed a bug in GridTable.
adds 078148a Added option -debug-scaffolder.
adds 6aa7b59 Removed dependency for clock_gettime.
adds d6b1f5d Added more details in the output of -run-profiler.
adds 7619e84 Added option -show-read-placement.
adds 9779ced Added option -show-communication-events.
adds b63035e Added overlays for option -show-communication-events.
adds c97ea8e Added a communication optimizer with urgent messages.
adds a08888b The option -show-communication-events now shows all messages with overlays too.
adds 58733de Enabled the communication optimizer for the network test too.
adds 7c2d6f6 Fixed a bug in the code that loads the checkpoint GenomeGraph.
adds fd3c033 Added a time period during which other messages are more important than urgent messages.
adds dc196b2 Added option -write-network-test-raw-data.
adds 63a3131 Write raw data for network tests if -test-network-only is provided.
adds 714875d Implemented a round-robin algorithm for the reception of messages.
adds ec32cf4 Merged the persistent communication layer with the round-robin reception.
adds 6b345f9 Changed mpirun to mpiexec as mpiexec is in the standard.
adds f75bfa6 Removed inline code because compilers optimize the code anyway.
adds 57099e3 Disabled persistent communication in the round-robin reception.
adds 0ee6fcc Added comments in the communication layer of Ray.
adds f76e565 Added timer warnings with -run-profiler.
adds d705e55 Reduced the computation granularity for the code that computes reverse-complement extensions.
adds 9bf6e69 Reduced the granularity in call_RAY_SLAVE_MODE_EXTENSION() by cleaning expiration positions.
adds 95f2488 Remove expired reads from the list of unmated reads to reduce the computation granularity.
adds f49a434 Added the compilation option CONFIG_CLOCK_GETTIME for the profiler.
adds 28b2a69 Added granularity summary for option -run-profiler.
adds b388cfc Migrated the version in the Makefile.
adds 41f9603 Fixed some PATH issues in system tests.
adds ddc513c Simplified the release procedure.
adds 1f712cd Fixed PATH problems in unit tests.
adds 2943c44 Updated the manual page.
adds d28e76a Removed data files in unit tests.
adds cb5ebc5 Added option -write-read-markers.
adds 737388b Added option -show-consensus to display read sequences and consensus during the extension.
adds d0e858e Added option -write-marker-summary.
adds 1385f96 New option -write-marker-summary which writes marker files for further inspection.
adds 32b18ee Added some profiling points inside the source code of Ray.
adds 4b9bf54 Added a new output file called ElapsedTime.txt.
adds 1b9764b Added some code to store agreement values during read threading.
adds 64fe9f7 Refactored some code to ease further enhancements.
adds e329c9e Corrected the accuracy of expiry positions.
adds f6f12c6 Added memory usage reporting in the fusion step.
adds 01342a5 Some code refactoring for the extension of seeds.
adds 518e06f Improved the algorithm that compute seeds, less (none) assembly errors are generated.
adds 19d6da3 Added the Open-MPI option -output-filename in system tests.
adds 67be2cc Removed some debugging messages in the creator of fusion tasks.
adds 1648df4 Changed the threshold for the repeated vertices.
adds d1b499a Merge branch 'master' of git at github.com:sebhtml/ray
adds 697e1e1 Added a working prototype router for message routing.
adds 8e3d63a Don't append message statistics when the count is null.
adds 27ce680 Added automatic route generation.
adds 602935c Added option -cores-per-node to help creating better routes with option -route-messages.
adds 470318b Added option -connection-type to specify the type of connections to use with -route-messages.
adds 56d42d4 Added some type definitions and enhanced the routing algorithms.
adds bc7fb0c Assertions are not compiled by default now. (ASSERT=n)
adds 33e9f99 Added relay event counting to avoid hanging code with routes generated with random connections.
adds ac32749 The route from B to A is now computed independently from the route from A to B.
adds 803df88 Routes are now computed by minimizing the relay events for each rank.
adds 0a79c1e Connections not present in routes are removed automatically by the message router.
adds fcccec1 In the network test, the length of the vector is reserved once if raw data are to be stored.
adds 0c47d31 The order in which the routes are computed is now random.
adds d09305d Don't show the final message if the option -test-network-only was provided.
adds ccebd11 Improved the algorithm that generates the random graph for message routing.
adds 22557ff Fixed the number of edges in the complete graph.
adds aeecaa2 Decoupled the creation of the connection graph from the actual message routing.
adds f2ef10e The route are now computed with more verbosity.
adds 6eb972f Implemented de Bruijn message routing.
adds 27f0644 Implemented various types of graphs for message routing.
adds ef9a117 Changed the code so that no routes are computed with de Bruijn routing.
adds bd2f02a The code for de Bruijn routing is now working just fine when the number of ranks is a power of something. Otherwise it does not work as expected.
adds d6f5a19 Optimized isConnected and getNextRankInRoute for de Bruijn routing.
adds 4427ab7 Simplified the code that finds the next vertex in the de Bruijn routing.
adds 525f32c Simplified the implementation of de Bruijn message routing.
adds 242a397 Fixed a bug that created files with strange names (unexpected behavior).
adds 1afbce8 Corrected the number of edges in Routing.Summary.txt.
adds 96d1e8a Implemented message routing with Kautz graphs.
adds 305334f Modified de Bruijn and Kautz graph implementations to avoid copying bytes.
adds 40baffa Added an experimental graph implementation.
adds 41ec0fe Removed a comment in the seed extension code.
adds 8feb467 Added speed indicators and some estimation of remaining time to complete the assembly.
adds 05035f3 Added software components to get speed readouts throughout the seed extension iterations.
adds 39204f5 Added option -routing-graph-degree to change the degree of the routing graph.
adds 5b8850d The mode latency is measured instead of the average during the network test.
adds b86c868 The slave mode is now shown with the speed of Ray.
adds 8c88e47 Added average values for each profiled steps.
adds 29afc18 Added a class for assembly seeds.
adds cbc6229 The seed extension is now done independently from the coverage distribution.
adds c049b76 The peak coverage is not utilised in the read k-mer indexing.
adds d1dd73f The k-mer peak coverage is no longer an issue.
adds 1799f47 Removed the peak coverage dependency in the vertex messenger.
adds 11bfb01 Removed the dependency on the peak coverage from the OpenAssembler engine.
adds b5b719d Removed the repeat coverage from the seed extender.
adds 256bfbf Removed the peak coverage dependency from the bubble objects.
adds f69cc98 Removed the restriction about peak coverage values within the scaffolding bits.
adds 0daec6b Added a script to compile Ray with fancy options.
adds 50433bb Added a maximum number of flow cycles
adds 784071b Created the SwitchMan module and ported the network test code.
adds bb6f959 Added a scripting directory and some methods to the switchman.
adds ccef34f Added design blueprints for Ray Biological Abundances.
adds f91a34f Updated the README.
adds 4afa8d5 Enhanced the layout
adds c524570 Added master switches in the SwitchMan.
adds caad35d New structure for scripting-related files.
adds 5dcb951 Migrated some scripting code in the ScriptEngine.
adds d9ab90e Updated the design ideas for biological abundances
adds 06af89e Added 3 new list for compilation (empty tags, slave modes & master modes).
adds 649f6d8 Implemented contig biological abundances (enabled by default).
adds 9b5d425 The frequency table must be cleared regularly
adds 778e5b0 Moved the license in the main directory.
adds 6353f96 Implemented entry counting for biological abundances.
adds d927f3e Disabled detailed reports and added an option to enable them.
adds b58cfe3 Added option -minimum-contig-length.
adds 5dd6100 Counting sequences to search is now implemented.
adds 33eaf80 Almost done implementing biological abundances.
adds ff6eef5 Biological abundances are now operational.
adds 2e04a0e Files are now written correctly to BiologicalAbundances.
adds 77ccc59 Fixed directory names for option -search.
adds 5a7405e Added speed during the biological abundance computation.
adds 613e231 Switched to BufferedData for buffered messages.
adds c7ed07f Prototyped a use-case for buffering messages in the search engine.
adds 3b660e8 Communications are now buffered in the search engine.
adds af52284 Added the mean k-mer coverage in the list of metrics.
adds 2f4bcef Ray is now tested with these C++ compilers too: pathscale and pgi.
adds 1c52de5 Now using the BufferedData object to compute contig abundances.
adds 0f200e2 Added new MPI tags to eventually distribute more the inputs and outputs.
adds e706b57 Added comments in the virtual communicator.
adds fbb7133 Added some comments in the switchman
adds e80b344 Each rank now writes their own files instead of sending data to master.
adds 8f4d506 Fixed the contig mean coverage and an assertion.
adds 05612c4 Documented the memory management code.
adds 6699516 Fixed a compilation warning with fprintf()
adds a854bcb K-mer coverage depth proportion values are now computed by Ray.
adds bb3bd19 Normalised method names for master modes.
adds 39471f2 Normalised method names for slave modes.
adds e08f957 Renamed the script engine and the nova engine.
adds 76f7224 Changed column names to more verbose ones.
adds 104d1c6 Changed the default to DEBUG=n to disable debugging symbols.
adds 3cef40b Added a machine helper class to delegate things.
adds 8fcf5d2 Moved the code of call_RAY_MASTER_MODE_SEND_COVERAGE_VALUES() in the machine helper.
adds 107cd84 Added slave switches for RAY_MPI_TAG_WRITE_KMERS, RAY_MPI_TAG_EXTENSION_END and RAY_SLAVE_MODE_EXTRACT_VERTICES.
adds d84bb77 Ported the scheduling of the k-mer academy step to the switchman framework.
adds 8b871ee Added a tick logger that outputs in RayOutput/Scheduling/.
adds fb7e471 Added handlers for slave modes, master modes and message tags.
adds 094e3cd Removed the empty tag list.
adds 331ecf4 I separated application code from platform code.
adds ef85cac Ported the code to use slave and master handlers.
adds 012bad9 Now using setObjectHandler() for master and slave methods too.
adds ddc674e I removed reference to Ray in type names in the platform.
adds 1df3882 I added a new class representing a compure core.
adds 2fc48be Added comments for the compute core.
adds dae0f53 Moved all handlers in Machine to MachineHelper.
adds c8e39bf Added a file describing the handler design.
adds 414cb08 Ray is now distributed as Ray Application and Ray Platform.
adds 1c1e520 Ray Platform is now licensed under the LGPLv3.
adds 779277b Ray Platform is now licensed under the LGPLv3.
adds dee142f Now converting bases to upper case if necessary.
adds 13534db Changed the maximum line length for fasta files.
adds 702f832 Now adding the license to installations.
adds ef0d35d Fixed the EXTRAVERSION for beta5.
adds ffb0349 We don't need to configure the virtual communicator twice.
adds 16897a5 Started to implement contig identification.
adds cfbde6c I created a working prototype for contig identification.
adds 4707448 Moved Ray Platform to RayPlatform.
adds 251715a Moved code/Application/* to code/*.
adds 873c356 I removed license notices in scripts.
adds ef2b265 Fixed paths in the README.
adds e5b7df7 Added a README for the Ray Platform.
adds b25c0b2 Added more documentation for the Ray Platform.
adds 15dc1b0 Added an error message in the switchman is not configured properly.
adds acb4521 I explained why latency data files can not be written before the end for everyone.
adds ac48668 Fixed greater-than-1 ratios for contig identifications.
adds de95f5a Cleaned the sorting code.
adds dd3643d Contig identification is now working properly.
adds f701c27 I added threshold to remove some false positives.
adds e1e3ab1 Modified the version to 2.0.0-beta6.
adds d537fe6 I fixed a fatal bug in the search engine for k-mers.
adds b6c9585 Fixed install.sh script.
adds b7010bc Merge branch 'master' of git at github.com:sebhtml/ray
adds bddc377 I fixed a bug in the file creation.
adds b67aa9c I fixed a compilation error with gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1).
adds 8544689 I created a new interface called CorePlugin for modularity.
adds fda31f4 I removed ratio for ticks counts.
adds 775875c I ported the scaffolder, the network test and the message processor to the plugin architecture.
adds cc8d87d I ported MachineHelper, Amos and FusionTaskCreator to the CorePlugin architecture.
adds 45fa8a2 I ported JoinerTaskCreator, Library, Partitioner, SeedingData, and CoverageGatherer to the CorePlugin architecture.
adds 0acc5c1 I simplified the way the ComputeCore is utilised.
adds f89330e I started to work on graph coloring with Ray.
adds 6503855 I removed the mean coverage in the search results.
adds 2361aba I started to implement color virtualization.
adds 5c47e9a I changed the threshold to report something.
adds 75f23e6 K-mers with Ns are not counted anymore by the search engine.
adds 6356dd1 The GenBank identifiers are now detected in files.
adds e6328d2 I added a slave mode for coloring the graph.
adds 96dd355 I implemented virtual colors in Ray.
adds 654f732 Unidentified sequences are not colored.
adds 967e594 I added documentation for virtual colors.
adds b6c03ea Virtual colors with 0 references are recycled.
adds f7030e1 The index in the color set has been removed.
adds e5460ae Physical colors are not embedded in namespaces.
adds 5d90312 Biological abundances are now computed with colors.
adds 5c4134f I removed useless code in allocateVirtualColor().
adds 83fcff9 A set of available handles reduced the time complexity to constant time.
adds 249e667 I corrected performance issues in the graph coloring algorithms.
adds e287f30 Handlers now have only one method called call().
adds 41b45ac The Library plugin now uses adapters.
adds 83826be The Searcher plugin now utilises adapters to register itself.
adds 60583ab The plugin Partitioner now uses adapters (a design pattern) to register itself with the core.
adds 1d7f7ed The plugin NetworkTest now utilises adapters to register with the core.
adds 6cff56f The plugin MessageProcessor now utilises adapters to register with the core.
adds feeef02 The Makefile was updated to add adapters.
adds 21be5d4 The plugin Scaffolder now utilises adapters to register with the core.
adds fa4b070 The plugin MachineHelper now uses adapters to register with the core.
adds a638b5a The plugin Amos now uses adapters to register with the core.
adds e66d032 The plugin FusionTaskCreator now uses adapters to register with the core.
adds 0127585 The plugin SeedingData now uses adapters to register with the core.
adds 8be5ffe The plugin JoinerTaskCreator now utilises adapters to register with the core.
adds d64a43e The plugin CoverageGatherer is now using adapters to register with the core.
adds 5354cdc I fixed the Makefile for adapters.
adds ec9c58b I removed the script engine from the RayPlatform.
adds 97360c8 A plugin now must ask the core to allocate handles.
adds f494d5d Things in the Makefile file in code/ are now grouped per plugin.
adds 59fa124 The plugin SeedExtender is now using adapters to register with the core.
adds e07dac8 Registered plugins are now printed in <RayOutput>/Plugins/*.Plugins.txt.
adds 17b4c36 I added the rank in the SwitchMan.
adds 6c2dedd Ratios for slave mode ticks are not printed anymore.
adds 6a38424 The plugin SequencesIndexer now utilises adapters to register with the core.
adds 576e172 The plugin FusionData now utilises adapters to register with the core.
adds eb53adb The plugin SequencesLoader now uses adapters to register with the core.
adds b47e005 The plugin KmerAcademyBuilder now uses adapters to register with the code.
adds 507d985 The plugin EdgePurger now uses adapters to register with the core.
adds 8ebbf29 The plugin VerticesExtrator now uses adapters to register with the core.
adds edcb9e7 The handle RAY_SLAVE_MODE_COUNT_FILE_ENTRIES is now in the plugin Partitioner.
adds 4b3d9e5 A system of symbol registration was added.
adds 47b2bdc The macros for listing slave modes were removed.
adds e54ad7e Plugins now register their own master modes.
adds bfb8d61 Message tags are now allocated by the core. Plugins have to resolve symbols.
adds 2559f1f The memory allocation types were removed.
adds df2249d RayPlatform now compiles independently without knowledge of an application.
adds 5d234c4 I updated the makefiles.
adds 0f1541a I fixed a bug in setPluginDescription().
adds 3fcfeb3 I added a cmake file for RayPlatform.
adds 02918c5 I added a CMakeLists.txt file for Ray, but it does not work yet.
adds f0921c6 Master switches are now registered by the plugins using the ComputeCore API.
adds ccac002 MessageTag-to-SlaveMode switches are now registered by plugins using the ComputeCore API.
adds 302e877 Added VirtualCommunicator and VirtualProcessor in the plugin list.
adds 12e06de Plugin descriptions are now written in the directory <RayOutput>/Plugin/.
adds ca97465 Reply MessageTag handles are now registered by plugins.
adds efdb36d MessageTag sizes are now registered by plugins.
adds 2e8c28a Plugins now register their next master modes.
adds 72992ee I updated plugin descriptions.
adds c122c58 Don't register plugins before the first call to registerPlugin().
adds c187bbb I fixed a bug in the Makefile files.
adds 3ce4ee1 Fixed the Makefile, yet again.
adds d1f6475 I moved the RayPlatform to another git repository.
adds dba6312 The version of the RayPlatform is now written in a file called RayPlatform_Version.txt.
adds 0fd55f1 The version of RayPlatform is now printed with option -version.
adds 8f8a461 I updated Ray to updates to Ray Platform.
adds bcb603b I removed desired values from call to allocate*Handle().
adds 80eb04b I created application_core/
adds 79fdde4 I created directories plugin_Amos and plugin_CoverageGatherer.
adds cc27625 I removed an extra new line.
adds 57848f3 I created plugin_EdgePurger.
adds 3855f59 Moved files in plugin directories.
adds 79f9cdc Moved license.
adds 6de3cd5 I added a CMakeLists.txt to compile Ray on Microsoft Windows.
adds 955955b I added the code to print virtual color summary.
adds 82b4a0e v2.0.0-rc4
adds 52b333e I fixed the install script again.
adds d10821f The maximum coverage is not set to 2^sizeof(COVERAGE_TYPE)-1
adds feb3b8d Builds are now performed with 4 slots for g++.
adds 7a24a7a The virtual color algorithms should now be faster.
adds 909100c The indexing strategy is now better for virtual colors.
adds 8a297fb I modified the virtual color handle code.
adds 3a0fcb7 I simplified the indexing algorithm.
adds 39f4e0e Unit tests test_invert.sh, test_coverage_distribution.sh and scaffolder_test.sh are now updated.
adds 34ea7b2 I added a progression indicator.
adds 29850da A progression indicator was added for sequence abundances.
adds fa2faa0 I removed calls to seekg() and tellg().
adds ee7a89e I modified the coloring code to fully exploit message multiplexing of RayPlatform.
adds 6fdc748 I added a script to automate product shipment.
adds 7f51552 I refactored the unit test framework.
adds bd95a93 Two bugs were fixed for message multiplexing when coloring.
adds b8bd90a The coloring code is now using stdio.h instead of iostream.
adds aa1572b A header in ScaffoldLinks.txt was added.
adds fd54192 I added uniquely colored assembled k-mer readouts.
adds 053c9c1 I added in-place operations for virtual colors with 1 reference.
adds 0b9422c Colored assembled k-mers need to be in contigs.
adds 81fc9a3 I changed the minimum threshold for nicely assembled.
adds 74db3b7 I added a simple test to weed out false positives.
adds e76e80e I updated the test test_limit_kmer.sh.
adds 75f7a29 Fixed test_novaengine.sh.
adds 363c334 I fixed the test for test_peakFinder.sh.
adds 66d5ed2 I fixed unit-tests/test_uniformity.sh.
adds 176182a Memory usage is now reported by default.
adds b33f3f3 Entries with no colored and assembled k-mers are not written at all.
adds 162fdac Outer distances (insert sizes) are not estimated if there are no paired reads.
adds 2832ae8 I changed the threshold for strangely assembled but colored k-mers.
adds 3b0e5cc The plugin plugin_Searcher now writes distributions too.
adds 6744876 I added unit tests for the algorithm that finds peaks.
adds 7ba87bd A more robust algorithm to detect library peaks is now shipped with Ray.
adds 7db65b4 I added a configuration command for buffers.
adds ca3b3c7 New script to plot colored distributions.
adds 01feee0 I fixed headers of distributions.
adds 21ed820 I removed the threshold for uniquely colored and assembled k-mers.
adds 070bfde I resolved a compilation warning in plugin_Searcher.
adds bea94b9 Code for flagging false positives have been added.
adds e2e202f Buggy correlations are now printed in color plots.
adds 2b73140 I updated the routing tests.
adds 860e948 The CMakeList.txt has been updated to use the new files in RayPlatform.
adds aab0c63 I fixed double-to-int conversions.
adds a6e4811 The script that ships the product is now enhanced.
adds 5a9a7fb mpiexec and exit() are not friends after all.
adds c13d593 HAVE_LIBBZ2=y works as expected now.
adds eabf4c7 The callback call_RAY_MPI_TAG_SEARCHER_CLOSE() was added.
adds b827575 I added some documentation for people who want to submit changes.
adds f92795c Updated script
adds da9272b Updated script
adds f7389d7 Updated script
adds 1b8e19a Updated script
adds 21cb9ef Updated script
adds d1a1b1d Updated script
adds 75b06c5 Updated script
adds 49855ad Updated script
adds d3b51ee Merge branch 'master' of git://github.com/enormandeau/ray
adds 314f6b2 Writing files can not be distributed yet because only rank 0 has some of the required bits.
adds 95b7537 Sequence abundances are now written in a single file per search directory.
adds b68f282 The new directory _Coloring contains a coloring summary.
adds cc570ba I modified the instructions to require signed-off patches.
adds 44dad30 Ray now writes all coloring distributions in XML.
adds 5c49810 Ray now generates a file per directory containing sequence counts.
adds a548a11 I fixed the quality values.
adds 6d9b990 PeakFinder now supports simulated data too.
adds 51214fd I added placeholders to transmit pointers.
adds 44e59ae I modified another part that may cause segmentation faults.
adds 2f37060 I added pack_pointer and unpack_pointer functions.
adds 7e11853 A file containing directories is now created.
adds 1d6fb1f Files containing virtual colors are just too large to be written.
adds 0f8269b Observations are 0 if some quality values are 0.
adds 4059c32 I removed outdated scores.
adds 395353c K-mers with a coverage < 2 are not valid.
adds f8dc6c8 I reduced the complexity of QualityCaller.
adds 87108c8 ColoredPeakCaller is now utilised to weed out false positives.
adds ad67e91 The test suite has moved to a different project.
adds 8bb2d17 Modified the colored peak finder to pass tests.
adds 327ecb6 A bug was fixed for call_RAY_MPI_TAG_REQUEST_VERTEX_READS().
adds a055c64 This commit finally fixes a very critical bug that happens once in a while. This bug is critical and v1.7 is affected. It causes strange behaviors usually leading to segmentation faults or Ray errors.
adds ce97ad6 I modified the peak caller to pass new tests.
adds a7d5ca7 Added a new plugin for phylogeny analyses.
adds c71d7c6 Phylogeny colors are forwarded to call_RAY_MPI_TAG_ADD_KMER_COLOR().
adds 3a7908a The PhylogenyViewer core plugin is now wired.
adds c121d18 Proportions are automatically calculated from now on.
adds 598e646 Physical colors for the phylogeny are fetched from the graph.
adds 5c81439 Taxon are now fetched using the phylogeny colors.
adds 7ff0970 Added some code for syncing taxons across the tribe.
adds 74fd217 The phylogenetic tree is now loaded properly.
adds c6b2dbd Ray now loads taxon names too.
adds a1f9671 K-mer observations are placed in the tree of life.
adds 025394c Only consider assembled k-mers for unknown observations.
adds 700609e Taxon observations are synced with master.
adds 6e17982 Taxon hits are written in a file.
adds 10bb891 I updated the manual.
adds 0f8ca67 The number of responses initially has to be m_size, not 0.
adds bf47449 Taxon observations are now reported along with a proportion and in XML.
adds 85441a8 Ray writes SequenceAbundancesRaw.tsv too.
adds 3a39376 call_RAY_MASTER_MODE_COUNT_SEARCH_ELEMENTS is now the entry point of plugin_Searcher.
adds 50125fc The number of colored k-mers is reported in _DeNovoAssembly for each contig.
adds bf0d6b4 The code that computes the total number of k-mer observations has been fixed.
adds 9ad8cc1 I fixed 3 compilation warnings.
adds 1f14b8d Discovered k-mers in the graph should be sufficient to cover a search entry.
adds a5072e5 A XSL sheet was added for Taxons.xml.
adds 16fb257 I edited the solutions section.
adds 6e1f594 The code contributed by Éric Normandeau is broken and does not work. I restored the old code.
adds 83bb4e0 I added a simple test to filter out some false positives.
adds ab5ad6e The symbols '<' and '>' are not directly allowed in XML files.
adds 72976f0 The sample name was added in _Phylogeny/Taxons.xml.
adds 2b8df21 Biological abundances are now produced in XML.
adds 46302eb The XSL sheets were updated.
adds fda1888 I added file names too.
adds 7098a9e The format of Taxons.txt was updated to include the taxonomic rank too.
adds fa1b99d I added a colored ratio for taxonomy outputs to consider only conserved sequences.
adds fa12265 The XML files with distributions now contain directly the directory and file names.
adds 07f74ad Ray now issues a warning (and an error) is the taxonomic tree contains loops.
adds c4d41a5 The list of pairs from Genome-to-Taxon should not be printed with warnings.
adds 001e3ab A new chunk that prints a warning if a taxon has no parent was added.
adds cd82e5c I fixed the XSL sheet.
adds e17e497 The <coloredProportion> node was added for unknown stuff.
adds 920c376 Recursive counts are now computed too.
adds d5da4b2 All taxons with a non-null recursive count are reported.
adds 23a4ba6 Only 1 XML file is necessary for each search directory. The transformation is done by XSLT.
adds a9d38f8 Two new XSL sheets were created to generate visually appealing tables.
adds 0ce437e A blueprint for l-mers was authored.
adds 547217a The sequence names can not contain special characters reserved for XML.
adds 1e2c9ae Entries are now sorted in the taxon tables.
adds 4c58693 A taxon not being in the tree should not be fatal.
adds cfc9a99 The colored proportions should be constrained to a given rank for better taxonomic profiling.
adds 8eebac0 Reading reference frequencies and color frequency is useful.
adds 7938191 <MPIrank>.CoverageData.xml contains contig coverage values.
adds 8a13338 More details are required for not-a-tree errors.
adds f4d88c9 Paths should not be tested in production settings.
adds 14096a2 1-based positions are easier to understand with a proper file header.
adds 252dfcf Only the printed position should be 1-based.
adds 824c8db The estimated genome length is not very accurate sometimes.
adds 329eec3 Sorted entries are easied to read.
adds ea5ac56 The code that fetches the base name of a virtual file system path is buggy.
adds a2332af Two new XSL sheets can fetch the most abundant phylum and family taxons.
adds f1941c0 The plugin GenomeNeighbourhood (compatible with RayPlatform) produces a sophisticated bird's-eye view of a sample's DNA.
adds 9546ae9 The plugin GenomeNeighbourhood is not linked with the rest.
adds 49606ff The design for computation of neighbourhoods is written.
adds 23f4d26 The CMakeList.txt file is now correct.
adds 0b3da75 Exploration of the graph highlights path relationships.
adds c213717 Fetching the number of paths is a good step for implementing neighbourhood discovery.
adds 128995e Detailed information is not required in the standard output.
adds 648bc66 Paths are fetched with message passing to get neighbourhoods.
adds b5315ba The code that gets neighbourhoods is almost operational.
adds 654e79a Nearby paths are detected automatically.
adds 735fba5 The exploration stops locally when something gets in the way.
adds 33f2dc2 Left neighbours are communicated to master.
adds 2021a22 Right neighbours are communicated too.
adds d0cca35 The final list for neighbours is agglomerated on master.
adds 57f18c5 A new output file called NeighbourhoodRelations.txt is created.
adds ab52623 Position is strand-specific.
adds 6be91a3 New XSL sheets are necessary to convert taxonomic profiling XML files.
adds 4672530 This is Ray release candidate 5.
adds 20991d4 The CMake file was updated.
adds 6fba705 GC content can be useful when plotting contig coverage depths.
adds 5970b23 The new option -one-color-per-file will force Ray to use one color per file.
adds 57b7344 The manual page was updated.
adds 79c3fda Input/output file operations are faster in "append" mode than in normal mode. One of the reasons is that one can not use fseek in "append" mode. Calls to fseek are ignored in "append" mode.
adds 59c547d Using append mode makes operations faster.
adds 32402ff The XML files for contig coverage are generated with a few input/output operations.
adds d331115 The sequence abundance XML files are now written with buffered input/output operations.
adds d8da889 The input/output operations for contig identifications are grouped for better performance.
adds b949513 I added a comment for getWriter()
adds 89cae09 More documentation was added.
adds 1cb0ed7 The buffer size for input/output operations on the file system is 32 MB.
adds d5c6b35 File system operations are buffered for colored coverage distributions.
adds 26403e3 File intput/output operations for taxons are buffered.
adds 397ffe0 Contig lengths are written to disk using buffering.
adds ec152b1 Contigs.fasta is written using buffering.
adds c00e01d Scaffolds.fasta is now written with buffering in mind.
adds 3cec107 Scaffold links are written to disk with buffering.
adds 4978a3f Scaffold lengths and scaffold components are written to disk with buffering.
adds b28bad4 I changed CONFIG_FILE_IO_BUFFER_SIZE to 16 MB.
adds 5323b54 Memory usage will be reported during the joining of paths.
adds 0a6d460 The number of assembled k-mers was added.
adds 13ff64e A progression indicator was added for the network test.
adds 31775b3 The total number of colored k-mers and k-mer observations are now computed too.
adds a997244 I added a XSL sheet to fetch proportions.
adds ca5004b Progression indicators were added for scaffolding.
adds b60c8e9 A integer overflow was fixed in the scaffolder.
adds 5348165 The buffering code was optimized.
adds f679548 The neighbourhood file is generated with buffering.
adds 7dd116f I added a guide for message routing.
adds fbd01da I created another XSL sheet for sequence abundances.
adds c2f150a I fixed a integer overflow in the profiler.
adds a9756b2 Total counts for parts of the distributed graph are shared correctly.
adds fbd8119 I increased the sensitivity of the method while not changing the specificity (which is very high).
adds 593758b I added <totalColoredKmerObservations> and <totalColoredKmers> to XML objects.
adds 43ee453 I disabled the plugin for neighbourhoods since it is buggy.
adds 19c1838 This is an experimental patch to accelerate one of the slowest computational steps of Ray. Basically, the patch tells Ray instances that completed previously to not try to do anything else after completion.
adds a004fd7 I added the Number of k-mers in the distributed de Bruijn graph.
adds a8110bf Support was added for a EMBL_CDS namespace.
adds 91b4843 The backbone for a GeneOntology CorePlugin is ready.
adds e91bfa6 The CorePlugin GenomeNeighbourhood is reinstated, but it is still disabled.
adds 0c54728 4 compilation warnings were weeded out.
adds 53495ad A variable shadowing caused a compilation error on OS X using openmpicxx. This was reported by Adam Caldwell. This is fixed now.
adds cf7c753 Ray now counts colors related to EMBL_CDS objects.
adds f491c68 Two bugs were fixed. Hangs could be encountered depending on the mood of the compiler.
adds 56a8e4d The period for reporting to the user the progression of loading sequences was changed.
adds dc6a063 Gene ontology annotations are loaded by Ray.
adds 54a39c6 The code path should continue as usual for de novo assemblies.
adds 0dca45c Biological signal for ontology terms are extracted from the de Bruijn graph.
adds 32e2adf I ported the plugin GeneOntology to the new macro commands.
adds a9200a5 A compilation warning was fixed regarding a comparison between two integers.
adds 17895e5 Ontology terms are counted and synchronized.
adds 455566f The documentation of Ray was updated to include gene ontology profiling.
adds 64ab206 Ray now produces gene ontology profiling.
adds 150e09b Gene ontology profiles are now generated in a compact format too.
adds 4fa04f1 A missing header was added.
adds 7457c1e The switchman handle should not be in the plugin MessageProcessor.
adds 99dbebc A missing header was added.
adds 96ddc3b Callback methods are public by convention.
adds efbe721 Plugins interact indirectly with the compute core using adapters, which are a design pattern. These adapters are now created automatically using macro commands provided by RayPlatform.
adds 06f735e Old declarations and implementations of adapters were removed from the tree.
adds 3f94610 I fixed a linking error when ASSERT is not provided.
adds 1e6ff4c The CMakeLists.txt file was updated.
adds 2039f50 This is Ray version v2.0.0-rc6 (release candidate 6). The code name for v2.0.0 is "Dark Astrocyte of Knowledge".
adds 2045ab1 I forgot to update the manual.
adds 2b5319a This patch fixes a bug that makes Ray hangs.
adds d8e8554 Any k-mer should only be counted at most once for each gene ontology term.
adds a4df091 I added proportions for gene ontology terms.
adds 919f095 I fixed a division by zero.
adds 3a495ce I updated the formula for computing proportions of DNA sequences.
adds 55756df Relationships are now loaded from the gene ontology file.
adds 6ffc940 The paths to the root are written to the XML file too.
adds 75b25dc Proportions are now available automatically in the gene ontology TSV file too.
adds 2f4a2c0 I created a XSL sheet to convert the gene ontology Terms.xml file to TSV.
adds dc19ce1 Domains are loaded from gene ontology, and depths are computed too.
adds 2b9332a Gene ontology information is extracted for each domain.
adds 6a4ca25 The total number of observations used for computing g ne ontology proportion considers only a single namespace.
adds 4dd51d1 A bug was fixed for the synchronization of counts. The master rank does not need to send anything to itself.
adds 30b79bc I fixed a bug occuring when -gene-ontology Operand1 Operand2 was not at the end.
adds dab0b3a K-mer observations are not required to be assembled to be used.
adds 99e893a Profile files for taxonomy are automatically generated.
adds af47f74 Some code was added to derefence alternate identifiers for gene ontology analysis. Also, profile files are generated for gene ontology too.
adds 0979439 Profile files are also produced with -search option.
adds 8253bd7 The number of dereferenced handles was added.
adds 6dae9cc I added the brandname to profile files.
adds 51ab01a I removed the superfluous branding.
adds ae054e3 This change set fixes a bug introduced in the commit 19c1838382cda4bcc19dffcdc25745a076ffc38a. This bug caused some contigs to be wrongly duplicated in the assembly. The bug was introduced on Sat Apr 21 23:22:21 2012 -0400. To solve it, the code path introduced is now disabled, but its effect remains because of the reduced number of cycles.
adds 88668dd A critical bug was fixed in the gene ontology plugin. The bug caused proportions to be wrong because the synchronization was not occuring before writing files
adds 5ce6a7b I added the percentage of assembled k-mers for each genome of interest.
adds 4c11abf A new XSL sheet was created to obtain the assembled proportions for genomes.
adds c1f25c5 A bug concerning the file name for -write-kmers was fixed.
adds 4eece00 I added more details to an obscure error message in Ray.
adds 2688f0d The code was polished and more information was added when the strange error occurs.
adds 30ee3e7 I added more information to zero in on the bug.
adds 40b9641 A elusive bug that caused runtime problems was finally solved.
adds 504f912 These data types were added to avoid elusive bugs: LargeIndex LargeCount PathHandle ReadHandle MessageUnit.
adds c71116d The maximum number of message tags was moved in RayPlatform.
adds 7443278 This is Ray v2.0.0-rc7.
adds bcef79a I fixed again the CMAKELIST file.
adds ec56e55 Deprecated parameters were removed from the help page.
adds 63e7166 I added an error message for unknown extensions.
adds 7c52141 The code that put together paths was modified to avoid creating misassemblies.
adds b617b03 ParallelPaths.txt contains parallel path data.
adds b9a2c2f Ray v2.0.0-rc8 has even less misassemblies (Ray v2.0.0-rc7 had so few already).
adds 459f26f The options for using checkpointing features requires a directory.
adds 95f4589 A new option is available to disable read recycling.
adds 8c95040 The release procedure was updated.
adds 91052b3 Patch information was updated.
adds dcc7389 Routing strategies were updated.
adds 7102b16 A compilation warning was removed for an integer comparison.
adds 048ba76 The peak finder should detects simulated data as well.
adds 22d4ec0 The multiplicator used for spawning read helpers was changed from 2.0 to 1.5. This should remove any assemblies and should not affect contiguity.
adds d96047c This change set improves the fidelity of Ray when computing peak coverage for short seeds (let's say that a short seed has a length lower than 512 vertices).
adds 4b48157 This solves a division by 0.
adds 2243df7 Floating numbers must not be stored with the integer type 'int'.
adds 6adeef3 This is Ray v2.0.0.
adds 2a065f8 The copyright was updated to add 2012.
adds 174f800 When there are 508 reads and 32 MPI ranks, the number of reads per rank is 508/32= 15. Therefore, assuming a perfect division read number 495 would be on MPI rank 33 (495/15 = 33). This makes Ray crash. This change set corrects this.
adds d090bf1 A list of releases was added.
adds f128c5b The codename of the next release will be "Ancient Granularity of Epochs".
adds 9857b2e An assertion was added for the performance scaled messaging related bug.
adds 063d86b Two assertions were added to detect possible message corruption.
adds a519e0c The help page was update to add the data reliability option. Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca>
adds 538550f The peak finder was modified to pass new tests.
adds c369574 Scaffolder is not required when using unpaired reads.
adds f15baa3 I edited the guide to submit changes.
adds de88a97 Patch Koala: Added an option (-use-maximum-seed-coverage) so that higly-covered seeds can be ignored.
adds c9fd5dd The manual now includes the new option for overly-covered seeds.
adds 4ecdd82 A error was fixed in the file that says how to submit changes.
adds 3520e56 The return statement was misplaced in a recent patch.
adds 8154067 I added the names 'Ray Méta', 'Ray Communities', and 'Ray Ontologies'.
adds a0ac2e7 An assertion was added to make sure that data is not overwritten.
adds dc516eb Searcher: added verbose statements
adds ebe9210 Searcher: fixed a race condition
adds 7365e49 Searcher: added a missing value.
adds 51775a1 SeedExtender: moved system calls inside this plugin
adds 0b6bf36 SeedExtender: modified the code for hot skipping
adds b7a839a SeedExtender: implemented hot skipping
adds 2e53ba0 Parameters: 4 options were added to change distributed storage behavior.
adds 20edb56 Documentation: Ray can be run with a single configuration file containing options.
adds d3cffdf The default load factor threshold was changed to 0.75.
adds b92ff8a The methods setKey() and getKey() were added to KmerCandidate and Vertex classes for compatibility with MyHashTable.
adds 96a489a If the hash table is verbose, ask it to display its status.
adds ca261b1 NetworkTest: added the option -skip-network-test to skip the network test.
adds 4ac0ff7 Added a new option to enable genome neighbourhood calculation. The option is -find-neighbourhoods
adds fa22b73 I added some code to detect windows 32 bits and windows 64 bits.
adds e3c5928 More parameters for compilation can be provided with EXTRA=...
adds 06d5591 Porting Ray to the new RayPlatform: removed macro calls in .h files.
adds d528530 Porting Ray to the new RayPlatform: removed remaining codes in .h.
adds 746681d Porting Ray to the new RayPlatform: removed token 'generated_automatically'.
adds 31b0788 Porting Ray to the new RayPlatform: added CreatePlugin and BindPlugin instructions.
adds 43137b4 Porting Ray to the new RayPlatform: updated the macro names in C++ plugin files.
adds 3633413 Porting Ray to the new RayPlatform: removed adapter from plugin class definitions.
adds c13e1bd Porting Ray to the new RayPlatform: remove calls to setObject.
adds d46428d Porting Ray to the new RayPlatform: Ray compiles with the simplified RayPlatform adapters now.
adds 95ea5c0 I removed handlers from the cmake file.
adds 17d7185 Updating the manual.
adds 7eb7775 SeedExtender: changed the verbosity period.
adds f6a55ea Removed some output from the computation of seeds.
adds 4ddb312 The manual was updated to include pointers to documentation.
adds 12d7c89 If you run Ray with a configuration file (mpiexec -n 4 Ray Ray.conf) you can start comments with the '#' symbol like in python.
adds eb77dc7 Information to compile Ray with gcc was added.
adds 05f17a4 The default number of buckets is now 1048576. The default number of buckets per group is still 64, so that is only 16384 groups with almost no memory usage because it is sparse.
adds de27b5c This fixes a input/output bug for the Ray configuration file.
adds 5005de5 The code that randomizes the arguments was removed because it can lead to bugs. This also simplifies checkpointing.
adds 991c42d The edge purging should be done in a massively parallel way unless the option -write-kmers was provided.
adds 2765a4c Corrected the tet that determines the quality control results. There was too much false negatives. The returned value is more reliable now.
adds 9685a0d Merge branch 'master' of https://github.com/plpla/ray into pl
adds 163eabc I added a script to build Ray with link time optimization.
adds 368d739 The EXTRA commands are also given to the linking command.
adds d54427b I added -fwhole-program for better optimization.
adds 608b9c0 I added compilation flags for compression.
adds 404cd50 I added instructions to build Ray with link time optimization.
adds b27abbe NetworkTest: the number of test messages is now constant regardless of the number of MPI ranks in the communicator.
adds 8b4e434 application_core: added a call to obtain a string configuration token.
adds e6e68be KmerAcademyBuilder: option -bloom-filter-bits can sets the number of bits.
adds 752ad1c KmerAcademyBuilder: Bloom filter has 64 M bits by default.
adds 4cd2c65 Merge branch 'master' of github.com:sebhtml/ray
adds 7340772 Merge branch 'master' of github.com:sebhtml/ray
adds f3e3ff1 SequencesLoader: added a 'please wait' before counting entries in a file.
adds ff6d829 SequencesLoader: a bz2 file can contain many compressed streams. Each of them needs to be opened, read (until BZ_STREAM_END), and closed.
adds 3422d36 application_core: bugs were fixed in the configuration routines.
adds 3879d25 GeneOntology: removed the use of argv
adds 2bef656 Merge branch 'master' of github.com:sebhtml/ray
adds 268e219 Fixed an integer overflow in the distributed storage engine.
adds c6d91f8 Merge branch 'master' of github.com:sebhtml/ray
adds 1e6719e A path with 0 k-mers has 0 nucleotides, not 0-k+1.
adds 07d481e Merge branch 'master' of github.com:sebhtml/ray
adds f27154d A new routing graph is available: the hypercube.
adds 0fd2dac Documentation: documented the hypercube features of Ray.
adds b428853 core: the default number of buckets is now 268435456 per rank.
adds 92f2995 scaffolder: it can be disabled with -disable-scaffolder
adds a559b40 normalized option names with -enable-* and -disable-*
adds e0f88db documentation: moved assembly options up
adds 7fd5f7e core: added documentation for class Parameters.
adds 47410c0 SeedingData: -use-minimum-seed-coverage changes the minimum
adds 6171892 documentation: added missing operands in the manual and -help page
adds ee1186d core: Ray -version provides more compile flags like popcnt and sse
adds 7703091 SeedingData: seeds can not contain k-mers with too low coverage
adds c69f2b7 build: the C++ standard is C++ 1998. gcc -ansi provides that
adds c10cecd Searcher: large integer constants needs ULL for portability
adds a812fc9 SeedExtender: added additional information for an error
adds dda2d53 MessageProcessor: k-mer data messages should never be discarded
adds ae1e69c VerticesExtractor: don't flush while waiting for messages
adds dc65e18 KmerAcademyBuilder: only send the forward k-mer, not the lower
adds f744b41 VerticesExtractor: improved the code quality for easier reading
adds 4e763bb MessageProcessor: don't discard k-mers while receiving messages
adds f4ac1e4 VerticesExtractor: store twin edges in a single source
adds 228ef20 EdgePurger: any edge is removed only if a end is not in the graph
adds 905722b MessageProcessor: removed a call to a private attribute
adds 5b75e2f Documentation: added a document about profiling Ray
adds e671d31 Documentation: added information about elapsed time
adds ae05454 BuildSystem: added a strip command to reduce the memory footprint
adds aa42e01 BuildSystem: replaced -ansi with -std=c++98 for more verbosity
adds 2334be6 Documentation: updated the author file
adds 4209dc6 KmerAcademyBuilder: removed the k-mer academy
adds 06d281d VerticesExtractor: this module extracts vertices to add edges
adds 290544f Merge branch 'kill-kmer-academy'
adds 4047bb1 MessageProcessor: new text to show when the Bloom filter is created
adds 5ab026c KmerAcademyBuilder: added the number of set bits in the Bloom filter
adds 6323f5b MessageProcessor: added a warning when the oracle is half full
adds a5f323b KmerAcademyBuilder: the Bloom filter can have any number of bits
adds 0cdd884 Merge branch 'bloom-features'
adds b5213c9 MessageProcessor: coverage depth starts at 1 with Bloom filters
adds 4fbaea1 MessageProcessor: the thresold is 50.0 (50.0%), not 0.5
adds 5179279 KmerAcademyBuilder: added the number of filtered k-mers
adds a034922 Merge branch 'bug-hunting'
adds c7602f2 application_core: added routing with a convex regular polytope
adds 6b7b54e NetworkTest: the number of exchange can be changed with -exchanges
adds 3e07cb1 Documentation: added options for a 64-rank polytope
adds 972a92e Documentation: updated the taxonomy documentation
adds 933d7dc NetworkTest: added average round trip latency
adds 0a6c79c scripts: initial version of a script to create NCBI taxonomy
adds a25cb5c scripts: download NCBI bacterial genomes too
adds e1d5c73 Merge branch 'master' of github.com:sebhtml/ray
adds a0e07e0 Documentation: added documentation for NCBI taxonomy
adds 9a52772 Documentation: simplified the usage of the tool to pull NCBI data Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca>
adds afd5a95 scripts: the script that pulls NCBI data is almost ready
adds 223d2a1 scripts: the script that pulls NCBI stuff is ready
adds 4bcd490 Documentation: added information about XML files
adds 015fe19 Partitioner: also create a file FilePartition.txt
adds d1935ac MachineHelper: don't run the AMOS code path if not necessary
adds 9444844 Parameters: throw a warning when distances are invalid
adds 2ee566a Merge branch 'for-seb-September-2012'
adds d8a8d73 Searcher: fixed a race condition where a message was lost
adds 16877ad Calls to deprecated methods were eliminated.
adds 80c83ca This is Ray v2.1.0-rc0 "Ancient Granularity of Epochs"
adds c6f2289 Searcher: browsing the distributed colored de Bruijn subgraph
adds d1aeb8d Searcher: find or create a virtual color from physical colors
adds 42be6ac Searcher: added physical color in SequenceAbundances.xml
adds cc00ad9 Searcher: fixed assertion code
adds 75194b5 scripts: don't ship the example and only ship the bz2 distribution
adds fcd8150 SequencesLoader: fixed the scope of a buffer
adds ac55873 Searcher: removed debug messages from stable release
adds 13efb22 Documentation: added more documentation for gene ontology.
adds beb565a Searcher: fixed buffer overflow
adds 28e9401 Searcher: fixed compilation warnings
adds c96f752 Searcher: GraphBrowsing.xml needs -one-color-per-file
adds 282548e This is the branch for Ray v2.1.0-rc1
adds 89d43d5 Related git repositories were added in the README.
adds c895300 Ray v2.1.0
adds 765aa3d Social networks were added to the release procedure
adds 7fe93d5 Code names of old releases were added
adds f641553 Merge branch 'master' of git://github.com/sebhtml/ray into upstream
adds eb605b7 Imported Upstream version 2.1.0
new a38ff74 Imported Upstream version 2.3.0
new 768eb84 Merge tag 'upstream/2.3.0'
new f10322e Package for Ray version 2.3.0 (release 1)
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CMakeLists.txt | 293 +--
Documentation/454.txt | 0
Documentation/AMAZON_EC2.txt | 0
Documentation/Blue_Gene_Q.txt | 5 +
Documentation/COMPILERS.txt | 0
Documentation/CodingStyle.txt | 15 +-
Documentation/Distributed-Storage-Engine.txt | 15 +-
Documentation/Illumina.txt | 0
Documentation/IonTorrent.txt | 0
Documentation/Migration-to-the-Actor-Model.txt | 56 +
Documentation/PacBio.txt | 0
Documentation/Profiling.txt | 2 +-
Documentation/RELEASE_PROCEDURE.txt | 12 +-
Documentation/Ray-Surveyor.md | 58 +
Documentation/Releases.txt | 54 +-
Documentation/Routing.txt | 57 +-
Documentation/SOLiD.txt | 0
Documentation/VISUAL_STUDIO.txt | 0
Documentation/Very-Large-Jobs.txt | 5 +-
Documentation/index.markdown | 3 +
MANUAL_PAGE.txt | 78 +-
Makefile | 260 +--
README.md | 54 +-
RayPlatform/Documentation/Actor-Model.txt | 13 +
RayPlatform/Documentation/DebugMode.txt | 18 +
RayPlatform/Documentation/Gates.txt | 41 +
RayPlatform/Documentation/Handlers.txt | 18 +-
RayPlatform/Documentation/MiniRanks.txt | 329 ++++
RayPlatform/Documentation/Torus.txt | 37 +
RayPlatform/Documentation/plugins.txt | 70 +
LICENSE.txt => RayPlatform/GPL-3.0.txt | 0
RayPlatform/LICENSE | 3 +
RayPlatform/Makefile | 25 +-
RayPlatform/Makefile.shared-gcc | 3 -
RayPlatform/{README => README.md} | 20 +-
RayPlatform/RayPlatform/actors/Actor.cpp | 114 ++
RayPlatform/RayPlatform/actors/Actor.h | 75 +
RayPlatform/RayPlatform/actors/Playground.cpp | 211 ++
RayPlatform/RayPlatform/actors/Playground.h | 81 +
.../communication/BufferedData.cpp | 17 +-
.../{ => RayPlatform}/communication/BufferedData.h | 13 +-
RayPlatform/RayPlatform/communication/Message.cpp | 389 ++++
RayPlatform/RayPlatform/communication/Message.h | 176 ++
.../RayPlatform/communication/MessageQueue.cpp | 291 +++
.../RayPlatform/communication/MessageQueue.h | 169 ++
.../communication/MessageRouter.cpp | 152 +-
.../communication/MessageRouter.h | 36 +-
.../communication/MessagesHandler.cpp | 832 +++++---
.../communication/MessagesHandler.h | 122 +-
.../communication/VirtualCommunicator.cpp | 58 +-
.../communication/VirtualCommunicator.h | 18 +-
.../{ => RayPlatform}/communication/mpi_tags.cpp | 8 +-
.../{ => RayPlatform}/communication/mpi_tags.h | 10 +-
RayPlatform/{ => RayPlatform}/core/ComputeCore.cpp | 751 +++++--
RayPlatform/{ => RayPlatform}/core/ComputeCore.h | 148 +-
.../core/MiniRank.cpp} | 16 +-
.../Worker.h => RayPlatform/core/MiniRank.h} | 41 +-
.../{ => RayPlatform}/core/OperatingSystem.cpp | 115 +-
.../{ => RayPlatform}/core/OperatingSystem.h | 25 +-
RayPlatform/RayPlatform/core/RankProcess.h | 323 ++++
.../{ => RayPlatform}/core/master_modes.cpp | 8 +-
RayPlatform/{ => RayPlatform}/core/master_modes.h | 8 +-
RayPlatform/{ => RayPlatform}/core/slave_modes.cpp | 9 +-
RayPlatform/{ => RayPlatform}/core/slave_modes.h | 8 +-
RayPlatform/{ => RayPlatform}/core/statistics.cpp | 9 +-
RayPlatform/{ => RayPlatform}/core/statistics.h | 6 +-
RayPlatform/{ => RayPlatform}/core/types.h | 19 +-
.../{ => RayPlatform}/cryptography/crypto.cpp | 32 +-
.../cryptography/crypto.h} | 24 +-
RayPlatform/RayPlatform/files/FileReader.cpp | 179 ++
RayPlatform/RayPlatform/files/FileReader.h | 60 +
.../handlers/MasterModeExecutor.cpp | 36 +-
.../handlers/MasterModeExecutor.h | 28 +-
.../RayPlatform/handlers/MasterModeHandler.h | 106 +
.../handlers/MessageTagExecutor.cpp | 34 +-
.../handlers/MessageTagExecutor.h | 31 +-
.../RayPlatform/handlers/MessageTagHandler.h | 101 +
.../handlers/SlaveModeExecutor.cpp | 33 +-
.../{ => RayPlatform}/handlers/SlaveModeExecutor.h | 30 +-
.../RayPlatform/handlers/SlaveModeHandler.h | 102 +
.../memory/ChunkAllocatorWithDefragmentation.cpp | 11 +-
.../memory/ChunkAllocatorWithDefragmentation.h | 11 +-
.../memory/DefragmentationGroup.cpp | 11 +-
.../memory/DefragmentationGroup.h | 9 +-
.../memory/DefragmentationLane.cpp | 9 +-
.../{ => RayPlatform}/memory/DefragmentationLane.h | 8 +-
RayPlatform/RayPlatform/memory/DirtyBuffer.cpp | 72 +
RayPlatform/RayPlatform/memory/DirtyBuffer.h | 56 +
.../{ => RayPlatform}/memory/MyAllocator.cpp | 27 +-
RayPlatform/{ => RayPlatform}/memory/MyAllocator.h | 15 +-
.../memory/ReusableMemoryStore.cpp | 9 +-
.../{ => RayPlatform}/memory/ReusableMemoryStore.h | 6 +-
RayPlatform/RayPlatform/memory/RingAllocator.cpp | 536 +++++
.../{ => RayPlatform}/memory/RingAllocator.h | 73 +-
RayPlatform/{ => RayPlatform}/memory/allocator.cpp | 13 +-
RayPlatform/{ => RayPlatform}/memory/allocator.h | 6 +-
.../{ => RayPlatform}/plugins/CorePlugin.cpp | 8 +-
RayPlatform/{ => RayPlatform}/plugins/CorePlugin.h | 58 +-
.../{ => RayPlatform}/plugins/RegisteredPlugin.cpp | 15 +-
.../{ => RayPlatform}/plugins/RegisteredPlugin.h | 9 +-
.../{ => RayPlatform}/profiling/Derivative.cpp | 15 +-
.../{ => RayPlatform}/profiling/Derivative.h | 9 +-
.../RayPlatform/profiling/ProcessStatus.cpp | 102 +
RayPlatform/RayPlatform/profiling/ProcessStatus.h | 28 +
.../{ => RayPlatform}/profiling/Profiler.cpp | 14 +-
RayPlatform/{ => RayPlatform}/profiling/Profiler.h | 6 +-
.../{ => RayPlatform}/profiling/TickLogger.cpp | 10 +-
.../{ => RayPlatform}/profiling/TickLogger.h | 8 +-
.../{ => RayPlatform}/profiling/TimePrinter.cpp | 39 +-
.../{ => RayPlatform}/profiling/TimePrinter.h | 17 +-
.../{ => RayPlatform}/routing/ConnectionGraph.cpp | 55 +-
.../{ => RayPlatform}/routing/ConnectionGraph.h | 38 +-
.../routing/GraphImplementation.cpp | 9 +-
.../routing/GraphImplementation.h | 8 +-
.../routing/GraphImplementationComplete.cpp | 8 +-
.../routing/GraphImplementationComplete.h | 8 +-
.../routing/GraphImplementationDeBruijn.cpp | 9 +-
.../routing/GraphImplementationDeBruijn.h | 9 +-
.../routing/GraphImplementationExperimental.cpp | 9 +-
.../routing/GraphImplementationExperimental.h | 9 +-
.../routing/GraphImplementationGroup.cpp | 9 +-
.../routing/GraphImplementationGroup.h | 8 +-
.../routing/GraphImplementationKautz.cpp | 9 +-
.../routing/GraphImplementationKautz.h | 9 +-
.../routing/GraphImplementationRandom.cpp | 9 +-
.../routing/GraphImplementationRandom.h | 8 +-
.../routing/Polytope.cpp} | 69 +-
.../Hypercube.h => RayPlatform/routing/Polytope.h} | 21 +-
RayPlatform/RayPlatform/routing/Torus.cpp | 558 ++++++
.../Hypercube.h => RayPlatform/routing/Torus.h} | 77 +-
.../{ => RayPlatform}/scheduling/SwitchMan.cpp | 39 +-
.../{ => RayPlatform}/scheduling/SwitchMan.h | 28 +-
.../{ => RayPlatform}/scheduling/TaskCreator.cpp | 9 +-
.../{ => RayPlatform}/scheduling/TaskCreator.h | 12 +-
.../scheduling/VirtualProcessor.cpp | 18 +-
.../scheduling/VirtualProcessor.h | 13 +-
RayPlatform/{ => RayPlatform}/scheduling/Worker.h | 11 +-
RayPlatform/RayPlatform/store/CarriageableItem.h | 61 +
RayPlatform/RayPlatform/store/KeyValueStore.cpp | 604 ++++++
RayPlatform/RayPlatform/store/KeyValueStore.h | 177 ++
.../RayPlatform/store/KeyValueStoreItem.cpp | 105 +
RayPlatform/RayPlatform/store/KeyValueStoreItem.h | 50 +
.../RayPlatform/store/KeyValueStoreRequest.cpp | 66 +
.../RayPlatform/store/KeyValueStoreRequest.h | 54 +
.../{ => RayPlatform}/structures/MyHashTable.h | 18 +-
.../structures/MyHashTableGroup.h | 9 +-
.../structures/MyHashTableIterator.h | 9 +-
RayPlatform/{ => RayPlatform}/structures/MyStack.h | 8 +-
.../{ => RayPlatform}/structures/SplayNode.h | 8 +-
.../{ => RayPlatform}/structures/SplayTree.h | 20 +-
.../structures/SplayTreeIterator.h | 26 +-
.../{ => RayPlatform}/structures/StaticVector.cpp | 17 +-
.../{ => RayPlatform}/structures/StaticVector.h | 16 +-
RayPlatform/common.mk | 120 +-
RayPlatform/communication/Message.cpp | 85 -
RayPlatform/communication/Message.h | 92 -
RayPlatform/git.txt | 1 -
RayPlatform/github.txt | 1 -
RayPlatform/handlers/MasterModeHandler.h | 42 -
RayPlatform/handlers/MessageTagHandler.h | 46 -
RayPlatform/handlers/SlaveModeHandler.h | 42 -
RayPlatform/memory/RingAllocator.cpp | 222 ---
RayPlatform/tag.txt | 1 -
code/{plugin_Amos => Amos}/Amos.cpp | 59 +-
code/{plugin_Amos => Amos}/Amos.h | 27 +-
code/Amos/Makefile | 3 +
.../CoverageDistribution.cpp | 10 +-
.../CoverageDistribution.h | 8 +-
.../CoverageGatherer.cpp | 148 +-
.../CoverageGatherer.h | 20 +-
code/CoverageGatherer/Makefile | 4 +
.../EdgePurger.cpp | 109 +-
.../{plugin_EdgePurger => EdgePurger}/EdgePurger.h | 37 +-
.../EdgePurgerWorker.cpp | 8 +-
.../EdgePurgerWorker.h | 20 +-
code/EdgePurger/Makefile | 4 +
code/Example/Example.cpp | 273 +++
code/Example/Example.h | 117 ++
code/Example/Makefile | 3 +
.../FusionData.cpp | 95 +-
.../{plugin_FusionData => FusionData}/FusionData.h | 35 +-
code/FusionData/Makefile | 3 +
.../FusionTaskCreator.cpp | 27 +-
.../FusionTaskCreator.h | 43 +-
.../FusionWorker.cpp | 31 +-
.../FusionWorker.h | 20 +-
code/FusionTaskCreator/Makefile | 4 +
.../GeneOntology.cpp | 41 +-
.../GeneOntology.h | 38 +-
.../KeyEncoder.cpp | 11 +-
.../KeyEncoder.h | 8 +-
code/GeneOntology/Makefile | 4 +
code/{plugin_GeneOntology => GeneOntology}/types.h | 0
.../GenomeNeighbourhood.cpp | 53 +-
.../GenomeNeighbourhood.h | 33 +-
code/GenomeNeighbourhood/Makefile | 5 +
.../Neighbour.cpp | 2 +-
.../Neighbour.h | 5 +-
.../NeighbourPair.cpp | 5 +-
.../NeighbourPair.h | 5 +-
.../JoinerTaskCreator.cpp | 32 +-
.../JoinerTaskCreator.h | 39 +-
.../JoinerWorker.cpp | 169 +-
.../JoinerWorker.h | 22 +-
code/JoinerTaskCreator/Makefile | 4 +
.../BloomFilter.cpp | 20 +-
.../BloomFilter.h | 5 +-
.../Kmer.cpp | 188 +-
.../Kmer.h | 94 +-
.../KmerAcademyBuilder.cpp | 48 +-
.../KmerAcademyBuilder.h | 32 +-
code/KmerAcademyBuilder/Makefile | 5 +
code/{plugin_Library => Library}/Library.cpp | 182 +-
code/{plugin_Library => Library}/Library.h | 46 +-
.../LibraryPeakFinder.cpp | 8 +-
.../LibraryPeakFinder.h | 2 +-
code/{plugin_Library => Library}/LibraryWorker.cpp | 22 +-
code/{plugin_Library => Library}/LibraryWorker.h | 18 +-
code/Library/Makefile | 5 +
.../MachineHelper.cpp | 720 ++++---
.../MachineHelper.h | 179 +-
code/MachineHelper/Makefile | 3 +
code/Makefile | 35 -
code/MessageProcessor/Makefile | 3 +
.../MessageProcessor.cpp | 782 ++++----
.../MessageProcessor.h | 307 ++-
code/Mock/Makefile | 5 +
code/Mock/Mock.cpp | 47 +
.../cryptography/crypto.h => code/Mock/Mock.h | 25 +-
code/{application_core => Mock}/Parameters.cpp | 447 ++++-
code/{application_core => Mock}/Parameters.h | 42 +-
.../common_functions.cpp | 110 +-
code/{application_core => Mock}/common_functions.h | 37 +-
code/{application_core => Mock}/constants.h | 82 +-
code/NetworkTest/Makefile | 3 +
.../NetworkTest.cpp | 108 +-
.../NetworkTest.h | 33 +-
code/Partitioner/Makefile | 3 +
.../Partitioner.cpp | 118 +-
.../Partitioner.h | 30 +-
code/PathEvaluator/Makefile | 3 +
code/PathEvaluator/PathEvaluator.cpp | 113 ++
code/PathEvaluator/PathEvaluator.h | 68 +
code/Scaffolder/Makefile | 8 +
.../Scaffolder.cpp | 562 +++++-
.../{plugin_Scaffolder => Scaffolder}/Scaffolder.h | 98 +-
.../ScaffoldingAlgorithm.cpp | 28 +-
.../ScaffoldingAlgorithm.h | 13 +-
.../ScaffoldingEdge.cpp | 5 +-
.../ScaffoldingEdge.h | 8 +-
.../ScaffoldingLink.cpp | 4 +-
.../ScaffoldingLink.h | 2 +-
.../ScaffoldingVertex.cpp | 5 +-
.../ScaffoldingVertex.h | 10 +-
.../SummarizedLink.cpp | 8 +-
.../SummarizedLink.h | 9 +-
code/{plugin_Searcher => Searcher}/ColorSet.cpp | 5 +-
code/{plugin_Searcher => Searcher}/ColorSet.h | 2 +-
.../ColoredPeakFinder.cpp | 8 +-
.../ColoredPeakFinder.h | 2 +-
code/{plugin_Searcher => Searcher}/ContigHit.cpp | 2 +-
code/{plugin_Searcher => Searcher}/ContigHit.h | 8 +-
.../ContigSearchEntry.cpp | 2 +-
.../ContigSearchEntry.h | 6 +-
.../DistributionWriter.cpp | 7 +-
.../DistributionWriter.h | 5 +-
code/Searcher/Makefile | 11 +
.../QualityCaller.cpp | 5 +-
code/{plugin_Searcher => Searcher}/QualityCaller.h | 6 +-
.../SearchDirectory.cpp | 29 +-
.../SearchDirectory.h | 9 +-
code/{plugin_Searcher => Searcher}/Searcher.cpp | 97 +-
code/{plugin_Searcher => Searcher}/Searcher.h | 99 +-
.../VirtualKmerColor.cpp | 5 +-
.../VirtualKmerColor.h | 5 +-
.../BubbleData.h | 15 +-
.../BubbleTool.cpp | 8 +-
.../BubbleTool.h | 11 +-
.../Chooser.cpp | 7 +-
.../Chooser.h | 7 +-
.../DepthFirstSearchData.cpp | 24 +-
.../DepthFirstSearchData.h | 18 +-
.../Direction.cpp | 13 +-
.../Direction.h | 10 +-
.../ExtensionData.cpp | 44 +-
.../ExtensionData.h | 42 +-
.../ExtensionElement.cpp | 37 +-
.../ExtensionElement.h | 24 +-
code/SeedExtender/Makefile | 14 +
.../NovaEngine.cpp | 5 +-
.../NovaEngine.h | 5 +-
.../OpenAssemblerChooser.cpp | 6 +-
.../OpenAssemblerChooser.h | 6 +-
.../ReadFetcher.cpp | 15 +-
.../ReadFetcher.h | 14 +-
.../SeedExtender.cpp | 464 +++--
.../SeedExtender.h | 108 +-
.../TipWatchdog.cpp | 4 +-
.../TipWatchdog.h | 8 +-
.../VertexMessenger.cpp | 25 +-
.../VertexMessenger.h | 15 +-
code/SeedingData/GraphPath.cpp | 743 +++++++
code/SeedingData/GraphPath.h | 154 ++
code/SeedingData/Makefile | 9 +
code/SeedingData/PathHandle.cpp | 128 ++
code/SeedingData/PathHandle.h | 69 +
.../SeedWorker.cpp | 286 ++-
.../SeedWorker.h | 62 +-
.../SeedingData.cpp | 330 ++--
.../SeedingData.h | 56 +-
.../DynamicVector.h | 7 +-
.../IndexerWorker.cpp | 14 +-
.../IndexerWorker.h | 19 +-
code/SequencesIndexer/Makefile | 9 +
.../PairedRead.cpp | 18 +-
.../PairedRead.h | 12 +-
.../ReadAnnotation.cpp | 20 +-
.../ReadAnnotation.h | 10 +-
.../SequencesIndexer.cpp | 38 +-
.../SequencesIndexer.h | 39 +-
.../ArrayOfReads.cpp | 7 +-
.../ArrayOfReads.h | 6 +-
code/SequencesLoader/BufferedReader.cpp | 206 ++
code/SequencesLoader/BufferedReader.h | 66 +
.../BzReader.cpp | 17 +-
.../BzReader.h | 8 +-
.../ColorSpaceDecoder.cpp | 39 +-
.../ColorSpaceDecoder.h | 8 +-
.../ColorSpaceLoader.cpp | 36 +-
.../ColorSpaceLoader.h | 26 +-
code/SequencesLoader/ExportLoader.cpp | 108 ++
.../ExportLoader.h} | 45 +-
code/SequencesLoader/FastaBz2Loader.cpp | 51 +
.../FastaBz2Loader.h} | 37 +-
code/SequencesLoader/FastaGzLoader.cpp | 53 +
.../FastaGzLoader.h} | 42 +-
.../FastaLoader.cpp | 10 +-
.../FastaLoader.h | 23 +-
code/SequencesLoader/FastaLoaderForReads.cpp | 49 +
.../FastaLoaderForReads.h} | 41 +-
.../FastqBz2Loader.cpp | 44 +-
.../FastqBz2Loader.h | 36 +-
code/SequencesLoader/FastqGzLoader.cpp | 305 +++
code/SequencesLoader/FastqGzLoader.h | 75 +
code/SequencesLoader/FastqLoader.cpp | 134 ++
.../FastqLoader.h} | 46 +-
code/SequencesLoader/Loader.cpp | 154 ++
.../Loader.h | 64 +-
code/SequencesLoader/LoaderFactory.cpp | 50 +
code/SequencesLoader/LoaderFactory.h | 77 +
code/SequencesLoader/LoaderInterface.cpp | 54 +
.../LoaderInterface.h} | 43 +-
code/SequencesLoader/Makefile | 25 +
.../Read.cpp | 52 +-
.../Read.h | 18 +-
code/SequencesLoader/ReadHandle.cpp | 100 +
code/SequencesLoader/ReadHandle.h | 58 +
code/SequencesLoader/SequenceFileDetector.cpp | 380 ++++
code/SequencesLoader/SequenceFileDetector.h | 59 +
.../SequencesLoader.cpp | 185 +-
.../SequencesLoader.h | 41 +-
.../SffLoader.cpp | 35 +-
.../SffLoader.h | 29 +-
.../SpuriousSeedAnnihilator/AnnihilationWorker.cpp | 614 ++++++
code/SpuriousSeedAnnihilator/AnnihilationWorker.h | 141 ++
code/SpuriousSeedAnnihilator/AnnotationFetcher.cpp | 154 ++
code/SpuriousSeedAnnihilator/AnnotationFetcher.h | 70 +
code/SpuriousSeedAnnihilator/AttributeFetcher.cpp | 98 +
code/SpuriousSeedAnnihilator/AttributeFetcher.h | 107 +
.../SpuriousSeedAnnihilator/GossipAssetManager.cpp | 433 +++++
code/SpuriousSeedAnnihilator/GossipAssetManager.h | 73 +
code/SpuriousSeedAnnihilator/GraphExplorer.cpp | 491 +++++
code/SpuriousSeedAnnihilator/GraphExplorer.h | 112 ++
code/SpuriousSeedAnnihilator/GraphSearchResult.cpp | 267 +++
code/SpuriousSeedAnnihilator/GraphSearchResult.h | 89 +
code/SpuriousSeedAnnihilator/Makefile | 13 +
code/SpuriousSeedAnnihilator/NanoMerger.cpp | 167 ++
code/SpuriousSeedAnnihilator/NanoMerger.h | 136 ++
.../SeedFilteringWorkflow.cpp | 138 ++
.../SeedFilteringWorkflow.h | 94 +
code/SpuriousSeedAnnihilator/SeedGossipSolver.cpp | 371 ++++
code/SpuriousSeedAnnihilator/SeedGossipSolver.h | 64 +
.../SeedMergingWorkflow.cpp | 169 ++
code/SpuriousSeedAnnihilator/SeedMergingWorkflow.h | 103 +
.../SpuriousSeedAnnihilator.cpp | 2042 ++++++++++++++++++++
.../SpuriousSeedAnnihilator.h | 363 ++++
code/Surveyor/CoalescenceManager.cpp | 425 ++++
code/Surveyor/CoalescenceManager.h | 82 +
code/Surveyor/ExperimentVertex.cpp | 49 +
code/Surveyor/ExperimentVertex.h | 58 +
code/Surveyor/GenomeGraphReader.cpp | 251 +++
code/Surveyor/GenomeGraphReader.h | 75 +
code/Surveyor/Makefile | 8 +
code/Surveyor/MatrixOwner.cpp | 232 +++
code/Surveyor/MatrixOwner.h | 68 +
code/Surveyor/Mother.cpp | 482 +++++
code/Surveyor/Mother.h | 118 ++
code/Surveyor/StoreKeeper.cpp | 460 +++++
code/Surveyor/StoreKeeper.h | 99 +
.../GenomeToTaxonLoader.cpp | 4 +-
.../GenomeToTaxonLoader.h | 8 +-
code/TaxonomyViewer/Makefile | 6 +
.../TaxonNameLoader.cpp | 4 +-
.../TaxonNameLoader.h | 7 +-
.../TaxonomicTreeLoader.cpp} | 10 +-
.../TaxonomicTreeLoader.h} | 13 +-
.../TaxonomyViewer.cpp} | 117 +-
.../TaxonomyViewer.h} | 52 +-
.../types.h | 0
.../GridTable.cpp | 43 +-
.../GridTable.h | 16 +-
.../GridTableIterator.cpp | 10 +-
.../GridTableIterator.h | 12 +-
code/VerticesExtractor/Makefile | 9 +
.../Vertex.cpp | 128 +-
.../Vertex.h | 97 +-
.../VerticesExtractor.cpp | 94 +-
.../VerticesExtractor.h | 39 +-
code/application_core/Machine.cpp | 444 +++--
code/application_core/Machine.h | 164 +-
code/application_core/Makefile | 5 +-
code/application_core/ray_main.cpp | 16 +-
code/plugin_Amos/Makefile | 7 -
code/plugin_CoverageGatherer/Makefile | 8 -
code/plugin_EdgePurger/Makefile | 8 -
code/plugin_FusionData/Makefile | 5 -
code/plugin_FusionTaskCreator/Makefile | 6 -
code/plugin_GeneOntology/Makefile | 6 -
code/plugin_GenomeNeighbourhood/Makefile | 11 -
code/plugin_JoinerTaskCreator/Makefile | 8 -
code/plugin_KmerAcademyBuilder/Makefile | 8 -
code/plugin_Library/Makefile | 8 -
code/plugin_MachineHelper/Makefile | 7 -
code/plugin_MessageProcessor/Makefile | 7 -
code/plugin_NetworkTest/Makefile | 7 -
code/plugin_Partitioner/Makefile | 6 -
code/plugin_PhylogenyViewer/Makefile | 8 -
code/plugin_Scaffolder/Makefile | 13 -
code/plugin_Searcher/Makefile | 13 -
code/plugin_SeedExtender/Makefile | 14 -
code/plugin_SeedingData/AssemblySeed.cpp | 160 --
code/plugin_SeedingData/AssemblySeed.h | 66 -
code/plugin_SeedingData/Makefile | 8 -
code/plugin_SequencesIndexer/Makefile | 9 -
code/plugin_SequencesLoader/FastqGzLoader.cpp | 81 -
code/plugin_SequencesLoader/FastqLoader.cpp | 76 -
code/plugin_SequencesLoader/Loader.cpp | 207 --
code/plugin_SequencesLoader/Makefile | 13 -
code/plugin_VerticesExtractor/Makefile | 9 -
debian/changelog | 6 +
debian/patches/reorder_args_to_keep_linker_happy | 29 -
debian/patches/series | 1 -
debian/rules | 7 +-
debian/watch | 2 +-
git.txt | 1 -
github.txt | 1 -
scripts/Build-Link-Time-Optimization.sh | 10 +-
scripts/ShipProduct.sh | 34 +-
scripts/install.sh | 33 -
tag.txt | 1 -
460 files changed, 27912 insertions(+), 6332 deletions(-)
mode change 100755 => 100644 Documentation/454.txt
mode change 100755 => 100644 Documentation/AMAZON_EC2.txt
create mode 100644 Documentation/Blue_Gene_Q.txt
mode change 100755 => 100644 Documentation/COMPILERS.txt
mode change 100755 => 100644 Documentation/Illumina.txt
mode change 100755 => 100644 Documentation/IonTorrent.txt
create mode 100644 Documentation/Migration-to-the-Actor-Model.txt
mode change 100755 => 100644 Documentation/PacBio.txt
create mode 100644 Documentation/Ray-Surveyor.md
mode change 100755 => 100644 Documentation/SOLiD.txt
mode change 100755 => 100644 Documentation/VISUAL_STUDIO.txt
create mode 100644 Documentation/index.markdown
create mode 100644 RayPlatform/Documentation/Actor-Model.txt
create mode 100644 RayPlatform/Documentation/DebugMode.txt
create mode 100644 RayPlatform/Documentation/Gates.txt
create mode 100644 RayPlatform/Documentation/MiniRanks.txt
create mode 100644 RayPlatform/Documentation/Torus.txt
copy LICENSE.txt => RayPlatform/GPL-3.0.txt (100%)
create mode 100644 RayPlatform/LICENSE
rename RayPlatform/{README => README.md} (87%)
create mode 100644 RayPlatform/RayPlatform/actors/Actor.cpp
create mode 100644 RayPlatform/RayPlatform/actors/Actor.h
create mode 100644 RayPlatform/RayPlatform/actors/Playground.cpp
create mode 100644 RayPlatform/RayPlatform/actors/Playground.h
rename RayPlatform/{ => RayPlatform}/communication/BufferedData.cpp (92%)
rename RayPlatform/{ => RayPlatform}/communication/BufferedData.h (90%)
create mode 100644 RayPlatform/RayPlatform/communication/Message.cpp
create mode 100644 RayPlatform/RayPlatform/communication/Message.h
create mode 100644 RayPlatform/RayPlatform/communication/MessageQueue.cpp
create mode 100644 RayPlatform/RayPlatform/communication/MessageQueue.h
rename RayPlatform/{ => RayPlatform}/communication/MessageRouter.cpp (78%)
rename RayPlatform/{ => RayPlatform}/communication/MessageRouter.h (86%)
rename RayPlatform/{ => RayPlatform}/communication/MessagesHandler.cpp (53%)
rename RayPlatform/{ => RayPlatform}/communication/MessagesHandler.h (75%)
rename RayPlatform/{ => RayPlatform}/communication/VirtualCommunicator.cpp (93%)
rename RayPlatform/{ => RayPlatform}/communication/VirtualCommunicator.h (95%)
rename RayPlatform/{ => RayPlatform}/communication/mpi_tags.cpp (84%)
copy RayPlatform/{ => RayPlatform}/communication/mpi_tags.h (77%)
rename RayPlatform/{ => RayPlatform}/core/ComputeCore.cpp (72%)
rename RayPlatform/{ => RayPlatform}/core/ComputeCore.h (74%)
copy RayPlatform/{core/slave_modes.h => RayPlatform/core/MiniRank.cpp} (70%)
copy RayPlatform/{scheduling/Worker.h => RayPlatform/core/MiniRank.h} (55%)
rename RayPlatform/{ => RayPlatform}/core/OperatingSystem.cpp (73%)
rename RayPlatform/{ => RayPlatform}/core/OperatingSystem.h (70%)
create mode 100644 RayPlatform/RayPlatform/core/RankProcess.h
rename RayPlatform/{ => RayPlatform}/core/master_modes.cpp (81%)
rename RayPlatform/{ => RayPlatform}/core/master_modes.h (81%)
rename RayPlatform/{ => RayPlatform}/core/slave_modes.cpp (80%)
rename RayPlatform/{ => RayPlatform}/core/slave_modes.h (81%)
rename RayPlatform/{ => RayPlatform}/core/statistics.cpp (92%)
rename RayPlatform/{ => RayPlatform}/core/statistics.h (87%)
rename RayPlatform/{ => RayPlatform}/core/types.h (78%)
rename RayPlatform/{ => RayPlatform}/cryptography/crypto.cpp (89%)
rename RayPlatform/{communication/mpi_tags.h => RayPlatform/cryptography/crypto.h} (55%)
create mode 100644 RayPlatform/RayPlatform/files/FileReader.cpp
create mode 100644 RayPlatform/RayPlatform/files/FileReader.h
rename RayPlatform/{ => RayPlatform}/handlers/MasterModeExecutor.cpp (64%)
rename RayPlatform/{ => RayPlatform}/handlers/MasterModeExecutor.h (60%)
create mode 100644 RayPlatform/RayPlatform/handlers/MasterModeHandler.h
rename RayPlatform/{ => RayPlatform}/handlers/MessageTagExecutor.cpp (64%)
rename RayPlatform/{ => RayPlatform}/handlers/MessageTagExecutor.h (59%)
create mode 100644 RayPlatform/RayPlatform/handlers/MessageTagHandler.h
rename RayPlatform/{ => RayPlatform}/handlers/SlaveModeExecutor.cpp (66%)
rename RayPlatform/{ => RayPlatform}/handlers/SlaveModeExecutor.h (60%)
create mode 100644 RayPlatform/RayPlatform/handlers/SlaveModeHandler.h
rename RayPlatform/{ => RayPlatform}/memory/ChunkAllocatorWithDefragmentation.cpp (97%)
rename RayPlatform/{ => RayPlatform}/memory/ChunkAllocatorWithDefragmentation.h (92%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationGroup.cpp (98%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationGroup.h (96%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationLane.cpp (95%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationLane.h (93%)
create mode 100644 RayPlatform/RayPlatform/memory/DirtyBuffer.cpp
create mode 100644 RayPlatform/RayPlatform/memory/DirtyBuffer.h
rename RayPlatform/{ => RayPlatform}/memory/MyAllocator.cpp (89%)
rename RayPlatform/{ => RayPlatform}/memory/MyAllocator.h (84%)
rename RayPlatform/{ => RayPlatform}/memory/ReusableMemoryStore.cpp (93%)
rename RayPlatform/{ => RayPlatform}/memory/ReusableMemoryStore.h (89%)
create mode 100644 RayPlatform/RayPlatform/memory/RingAllocator.cpp
rename RayPlatform/{ => RayPlatform}/memory/RingAllocator.h (67%)
rename RayPlatform/{ => RayPlatform}/memory/allocator.cpp (87%)
rename RayPlatform/{ => RayPlatform}/memory/allocator.h (84%)
rename RayPlatform/{ => RayPlatform}/plugins/CorePlugin.cpp (82%)
rename RayPlatform/{ => RayPlatform}/plugins/CorePlugin.h (60%)
rename RayPlatform/{ => RayPlatform}/plugins/RegisteredPlugin.cpp (95%)
rename RayPlatform/{ => RayPlatform}/plugins/RegisteredPlugin.h (94%)
rename RayPlatform/{ => RayPlatform}/profiling/Derivative.cpp (86%)
rename RayPlatform/{ => RayPlatform}/profiling/Derivative.h (86%)
create mode 100644 RayPlatform/RayPlatform/profiling/ProcessStatus.cpp
create mode 100644 RayPlatform/RayPlatform/profiling/ProcessStatus.h
rename RayPlatform/{ => RayPlatform}/profiling/Profiler.cpp (93%)
rename RayPlatform/{ => RayPlatform}/profiling/Profiler.h (94%)
rename RayPlatform/{ => RayPlatform}/profiling/TickLogger.cpp (97%)
rename RayPlatform/{ => RayPlatform}/profiling/TickLogger.h (91%)
rename RayPlatform/{ => RayPlatform}/profiling/TimePrinter.cpp (74%)
rename RayPlatform/{ => RayPlatform}/profiling/TimePrinter.h (80%)
rename RayPlatform/{ => RayPlatform}/routing/ConnectionGraph.cpp (88%)
rename RayPlatform/{ => RayPlatform}/routing/ConnectionGraph.h (79%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementation.cpp (98%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementation.h (93%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationComplete.cpp (88%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationComplete.h (85%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationDeBruijn.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationDeBruijn.h (90%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationExperimental.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationExperimental.h (92%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationGroup.cpp (95%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationGroup.h (87%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationKautz.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationKautz.h (91%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationRandom.cpp (93%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationRandom.h (85%)
rename RayPlatform/{routing/Hypercube.cpp => RayPlatform/routing/Polytope.cpp} (87%)
copy RayPlatform/{routing/Hypercube.h => RayPlatform/routing/Polytope.h} (86%)
create mode 100644 RayPlatform/RayPlatform/routing/Torus.cpp
rename RayPlatform/{routing/Hypercube.h => RayPlatform/routing/Torus.h} (58%)
rename RayPlatform/{ => RayPlatform}/scheduling/SwitchMan.cpp (91%)
rename RayPlatform/{ => RayPlatform}/scheduling/SwitchMan.h (86%)
rename RayPlatform/{ => RayPlatform}/scheduling/TaskCreator.cpp (92%)
rename RayPlatform/{ => RayPlatform}/scheduling/TaskCreator.h (83%)
rename RayPlatform/{ => RayPlatform}/scheduling/VirtualProcessor.cpp (93%)
rename RayPlatform/{ => RayPlatform}/scheduling/VirtualProcessor.h (91%)
rename RayPlatform/{ => RayPlatform}/scheduling/Worker.h (80%)
create mode 100644 RayPlatform/RayPlatform/store/CarriageableItem.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStore.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStore.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreItem.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreItem.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreRequest.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreRequest.h
rename RayPlatform/{ => RayPlatform}/structures/MyHashTable.h (98%)
rename RayPlatform/{ => RayPlatform}/structures/MyHashTableGroup.h (98%)
rename RayPlatform/{ => RayPlatform}/structures/MyHashTableIterator.h (91%)
rename RayPlatform/{ => RayPlatform}/structures/MyStack.h (89%)
rename RayPlatform/{ => RayPlatform}/structures/SplayNode.h (92%)
rename RayPlatform/{ => RayPlatform}/structures/SplayTree.h (95%)
rename RayPlatform/{ => RayPlatform}/structures/SplayTreeIterator.h (89%)
rename RayPlatform/{ => RayPlatform}/structures/StaticVector.cpp (79%)
rename RayPlatform/{ => RayPlatform}/structures/StaticVector.h (73%)
delete mode 100644 RayPlatform/communication/Message.cpp
delete mode 100644 RayPlatform/communication/Message.h
delete mode 100644 RayPlatform/git.txt
delete mode 100644 RayPlatform/github.txt
delete mode 100644 RayPlatform/handlers/MasterModeHandler.h
delete mode 100644 RayPlatform/handlers/MessageTagHandler.h
delete mode 100644 RayPlatform/handlers/SlaveModeHandler.h
delete mode 100644 RayPlatform/memory/RingAllocator.cpp
delete mode 100644 RayPlatform/tag.txt
rename code/{plugin_Amos => Amos}/Amos.cpp (86%)
rename code/{plugin_Amos => Amos}/Amos.h (77%)
create mode 100644 code/Amos/Makefile
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageDistribution.cpp (93%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageDistribution.h (91%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageGatherer.cpp (82%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageGatherer.h (79%)
create mode 100644 code/CoverageGatherer/Makefile
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurger.cpp (71%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurger.h (76%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurgerWorker.cpp (95%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurgerWorker.h (82%)
create mode 100644 code/EdgePurger/Makefile
create mode 100644 code/Example/Example.cpp
create mode 100644 code/Example/Example.h
create mode 100644 code/Example/Makefile
rename code/{plugin_FusionData => FusionData}/FusionData.cpp (91%)
rename code/{plugin_FusionData => FusionData}/FusionData.h (83%)
create mode 100644 code/FusionData/Makefile
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionTaskCreator.cpp (93%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionTaskCreator.h (70%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionWorker.cpp (92%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionWorker.h (81%)
create mode 100644 code/FusionTaskCreator/Makefile
rename code/{plugin_GeneOntology => GeneOntology}/GeneOntology.cpp (98%)
rename code/{plugin_GeneOntology => GeneOntology}/GeneOntology.h (83%)
rename code/{plugin_GeneOntology => GeneOntology}/KeyEncoder.cpp (96%)
rename code/{plugin_GeneOntology => GeneOntology}/KeyEncoder.h (89%)
create mode 100644 code/GeneOntology/Makefile
rename code/{plugin_GeneOntology => GeneOntology}/types.h (100%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/GenomeNeighbourhood.cpp (96%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/GenomeNeighbourhood.h (81%)
create mode 100644 code/GenomeNeighbourhood/Makefile
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/Neighbour.cpp (95%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/Neighbour.h (93%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/NeighbourPair.cpp (93%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/NeighbourPair.h (94%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerTaskCreator.cpp (92%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerTaskCreator.h (72%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerWorker.cpp (83%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerWorker.h (84%)
create mode 100644 code/JoinerTaskCreator/Makefile
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/BloomFilter.cpp (93%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/BloomFilter.h (94%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/Kmer.cpp (67%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/Kmer.h (57%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/KmerAcademyBuilder.cpp (91%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/KmerAcademyBuilder.h (77%)
create mode 100644 code/KmerAcademyBuilder/Makefile
rename code/{plugin_Library => Library}/Library.cpp (83%)
rename code/{plugin_Library => Library}/Library.h (73%)
rename code/{plugin_Library => Library}/LibraryPeakFinder.cpp (97%)
rename code/{plugin_Library => Library}/LibraryPeakFinder.h (95%)
rename code/{plugin_Library => Library}/LibraryWorker.cpp (92%)
rename code/{plugin_Library => Library}/LibraryWorker.h (84%)
create mode 100644 code/Library/Makefile
rename code/{plugin_MachineHelper => MachineHelper}/MachineHelper.cpp (78%)
rename code/{plugin_MachineHelper => MachineHelper}/MachineHelper.h (61%)
create mode 100644 code/MachineHelper/Makefile
delete mode 100644 code/Makefile
create mode 100644 code/MessageProcessor/Makefile
rename code/{plugin_MessageProcessor => MessageProcessor}/MessageProcessor.cpp (88%)
rename code/{plugin_MessageProcessor => MessageProcessor}/MessageProcessor.h (51%)
create mode 100644 code/Mock/Makefile
create mode 100644 code/Mock/Mock.cpp
rename RayPlatform/cryptography/crypto.h => code/Mock/Mock.h (66%)
rename code/{application_core => Mock}/Parameters.cpp (86%)
rename code/{application_core => Mock}/Parameters.h (91%)
rename code/{application_core => Mock}/common_functions.cpp (71%)
rename code/{application_core => Mock}/common_functions.h (73%)
rename code/{application_core => Mock}/constants.h (62%)
create mode 100644 code/NetworkTest/Makefile
rename code/{plugin_NetworkTest => NetworkTest}/NetworkTest.cpp (86%)
rename code/{plugin_NetworkTest => NetworkTest}/NetworkTest.h (79%)
create mode 100644 code/Partitioner/Makefile
rename code/{plugin_Partitioner => Partitioner}/Partitioner.cpp (84%)
rename code/{plugin_Partitioner => Partitioner}/Partitioner.h (77%)
create mode 100644 code/PathEvaluator/Makefile
create mode 100644 code/PathEvaluator/PathEvaluator.cpp
create mode 100644 code/PathEvaluator/PathEvaluator.h
create mode 100644 code/Scaffolder/Makefile
rename code/{plugin_Scaffolder => Scaffolder}/Scaffolder.cpp (75%)
rename code/{plugin_Scaffolder => Scaffolder}/Scaffolder.h (71%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingAlgorithm.cpp (94%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingAlgorithm.h (86%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingEdge.cpp (97%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingEdge.h (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingLink.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingLink.h (95%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingVertex.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingVertex.h (85%)
rename code/{plugin_Scaffolder => Scaffolder}/SummarizedLink.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/SummarizedLink.h (89%)
rename code/{plugin_Searcher => Searcher}/ColorSet.cpp (99%)
rename code/{plugin_Searcher => Searcher}/ColorSet.h (99%)
rename code/{plugin_Searcher => Searcher}/ColoredPeakFinder.cpp (97%)
rename code/{plugin_Searcher => Searcher}/ColoredPeakFinder.h (96%)
rename code/{plugin_Searcher => Searcher}/ContigHit.cpp (96%)
rename code/{plugin_Searcher => Searcher}/ContigHit.h (90%)
rename code/{plugin_Searcher => Searcher}/ContigSearchEntry.cpp (97%)
rename code/{plugin_Searcher => Searcher}/ContigSearchEntry.h (91%)
rename code/{plugin_Searcher => Searcher}/DistributionWriter.cpp (96%)
rename code/{plugin_Searcher => Searcher}/DistributionWriter.h (94%)
create mode 100644 code/Searcher/Makefile
rename code/{plugin_Searcher => Searcher}/QualityCaller.cpp (97%)
rename code/{plugin_Searcher => Searcher}/QualityCaller.h (94%)
rename code/{plugin_Searcher => Searcher}/SearchDirectory.cpp (96%)
rename code/{plugin_Searcher => Searcher}/SearchDirectory.h (93%)
rename code/{plugin_Searcher => Searcher}/Searcher.cpp (98%)
rename code/{plugin_Searcher => Searcher}/Searcher.h (76%)
rename code/{plugin_Searcher => Searcher}/VirtualKmerColor.cpp (97%)
rename code/{plugin_Searcher => Searcher}/VirtualKmerColor.h (95%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleData.h (86%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleTool.cpp (97%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleTool.h (87%)
rename code/{plugin_SeedExtender => SeedExtender}/Chooser.cpp (94%)
rename code/{plugin_SeedExtender => SeedExtender}/Chooser.h (88%)
rename code/{plugin_SeedExtender => SeedExtender}/DepthFirstSearchData.cpp (95%)
rename code/{plugin_SeedExtender => SeedExtender}/DepthFirstSearchData.h (88%)
rename code/{plugin_SeedExtender => SeedExtender}/Direction.cpp (85%)
rename code/{plugin_SeedExtender => SeedExtender}/Direction.h (87%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionData.cpp (82%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionData.h (81%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionElement.cpp (78%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionElement.h (79%)
create mode 100644 code/SeedExtender/Makefile
rename code/{plugin_SeedExtender => SeedExtender}/NovaEngine.cpp (98%)
rename code/{plugin_SeedExtender => SeedExtender}/NovaEngine.h (92%)
rename code/{plugin_SeedExtender => SeedExtender}/OpenAssemblerChooser.cpp (98%)
rename code/{plugin_SeedExtender => SeedExtender}/OpenAssemblerChooser.h (91%)
rename code/{plugin_SeedExtender => SeedExtender}/ReadFetcher.cpp (93%)
rename code/{plugin_SeedExtender => SeedExtender}/ReadFetcher.h (85%)
rename code/{plugin_SeedExtender => SeedExtender}/SeedExtender.cpp (90%)
rename code/{plugin_SeedExtender => SeedExtender}/SeedExtender.h (73%)
rename code/{plugin_SeedExtender => SeedExtender}/TipWatchdog.cpp (96%)
rename code/{plugin_SeedExtender => SeedExtender}/TipWatchdog.h (82%)
rename code/{plugin_SeedExtender => SeedExtender}/VertexMessenger.cpp (92%)
rename code/{plugin_SeedExtender => SeedExtender}/VertexMessenger.h (88%)
create mode 100644 code/SeedingData/GraphPath.cpp
create mode 100644 code/SeedingData/GraphPath.h
create mode 100644 code/SeedingData/Makefile
create mode 100644 code/SeedingData/PathHandle.cpp
create mode 100644 code/SeedingData/PathHandle.h
rename code/{plugin_SeedingData => SeedingData}/SeedWorker.cpp (65%)
rename code/{plugin_SeedingData => SeedingData}/SeedWorker.h (70%)
rename code/{plugin_SeedingData => SeedingData}/SeedingData.cpp (60%)
rename code/{plugin_SeedingData => SeedingData}/SeedingData.h (74%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/DynamicVector.h (93%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/IndexerWorker.cpp (97%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/IndexerWorker.h (86%)
create mode 100644 code/SequencesIndexer/Makefile
rename code/{plugin_SequencesIndexer => SequencesIndexer}/PairedRead.cpp (81%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/PairedRead.h (85%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/ReadAnnotation.cpp (85%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/ReadAnnotation.h (87%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/SequencesIndexer.cpp (95%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/SequencesIndexer.h (75%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ArrayOfReads.cpp (96%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ArrayOfReads.h (90%)
create mode 100644 code/SequencesLoader/BufferedReader.cpp
create mode 100644 code/SequencesLoader/BufferedReader.h
rename code/{plugin_SequencesLoader => SequencesLoader}/BzReader.cpp (93%)
rename code/{plugin_SequencesLoader => SequencesLoader}/BzReader.h (88%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceDecoder.cpp (76%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceDecoder.h (81%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceLoader.cpp (79%)
copy code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceLoader.h (71%)
create mode 100644 code/SequencesLoader/ExportLoader.cpp
rename code/{plugin_SequencesLoader/FastqLoader.h => SequencesLoader/ExportLoader.h} (55%)
create mode 100644 code/SequencesLoader/FastaBz2Loader.cpp
rename code/{plugin_SequencesLoader/FastqGzLoader.h => SequencesLoader/FastaBz2Loader.h} (60%)
create mode 100644 code/SequencesLoader/FastaGzLoader.cpp
copy code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastaGzLoader.h} (59%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastaLoader.cpp (89%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastaLoader.h (69%)
create mode 100644 code/SequencesLoader/FastaLoaderForReads.cpp
copy code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastaLoaderForReads.h} (63%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastqBz2Loader.cpp (62%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastqBz2Loader.h (58%)
create mode 100644 code/SequencesLoader/FastqGzLoader.cpp
create mode 100644 code/SequencesLoader/FastqGzLoader.h
create mode 100644 code/SequencesLoader/FastqLoader.cpp
rename code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastqLoader.h} (59%)
create mode 100644 code/SequencesLoader/Loader.cpp
rename code/{plugin_SequencesLoader => SequencesLoader}/Loader.h (55%)
create mode 100644 code/SequencesLoader/LoaderFactory.cpp
create mode 100644 code/SequencesLoader/LoaderFactory.h
create mode 100644 code/SequencesLoader/LoaderInterface.cpp
copy code/{plugin_PhylogenyViewer/GenomeToTaxonLoader.h => SequencesLoader/LoaderInterface.h} (50%)
create mode 100644 code/SequencesLoader/Makefile
rename code/{plugin_SequencesLoader => SequencesLoader}/Read.cpp (85%)
rename code/{plugin_SequencesLoader => SequencesLoader}/Read.h (85%)
create mode 100644 code/SequencesLoader/ReadHandle.cpp
create mode 100644 code/SequencesLoader/ReadHandle.h
create mode 100644 code/SequencesLoader/SequenceFileDetector.cpp
create mode 100644 code/SequencesLoader/SequenceFileDetector.h
rename code/{plugin_SequencesLoader => SequencesLoader}/SequencesLoader.cpp (70%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SequencesLoader.h (62%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SffLoader.cpp (88%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SffLoader.h (70%)
create mode 100644 code/SpuriousSeedAnnihilator/AnnihilationWorker.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AnnihilationWorker.h
create mode 100644 code/SpuriousSeedAnnihilator/AnnotationFetcher.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AnnotationFetcher.h
create mode 100644 code/SpuriousSeedAnnihilator/AttributeFetcher.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AttributeFetcher.h
create mode 100644 code/SpuriousSeedAnnihilator/GossipAssetManager.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GossipAssetManager.h
create mode 100644 code/SpuriousSeedAnnihilator/GraphExplorer.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GraphExplorer.h
create mode 100644 code/SpuriousSeedAnnihilator/GraphSearchResult.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GraphSearchResult.h
create mode 100644 code/SpuriousSeedAnnihilator/Makefile
create mode 100644 code/SpuriousSeedAnnihilator/NanoMerger.cpp
create mode 100644 code/SpuriousSeedAnnihilator/NanoMerger.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedGossipSolver.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedGossipSolver.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedMergingWorkflow.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedMergingWorkflow.h
create mode 100644 code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.h
create mode 100644 code/Surveyor/CoalescenceManager.cpp
create mode 100644 code/Surveyor/CoalescenceManager.h
create mode 100644 code/Surveyor/ExperimentVertex.cpp
create mode 100644 code/Surveyor/ExperimentVertex.h
create mode 100644 code/Surveyor/GenomeGraphReader.cpp
create mode 100644 code/Surveyor/GenomeGraphReader.h
create mode 100644 code/Surveyor/Makefile
create mode 100644 code/Surveyor/MatrixOwner.cpp
create mode 100644 code/Surveyor/MatrixOwner.h
create mode 100644 code/Surveyor/Mother.cpp
create mode 100644 code/Surveyor/Mother.h
create mode 100644 code/Surveyor/StoreKeeper.cpp
create mode 100644 code/Surveyor/StoreKeeper.h
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/GenomeToTaxonLoader.cpp (94%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/GenomeToTaxonLoader.h (91%)
create mode 100644 code/TaxonomyViewer/Makefile
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/TaxonNameLoader.cpp (95%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/TaxonNameLoader.h (91%)
rename code/{plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp => TaxonomyViewer/TaxonomicTreeLoader.cpp} (83%)
rename code/{plugin_PhylogenyViewer/PhylogeneticTreeLoader.h => TaxonomyViewer/TaxonomicTreeLoader.h} (83%)
rename code/{plugin_PhylogenyViewer/PhylogenyViewer.cpp => TaxonomyViewer/TaxonomyViewer.cpp} (91%)
rename code/{plugin_PhylogenyViewer/PhylogenyViewer.h => TaxonomyViewer/TaxonomyViewer.h} (83%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/types.h (100%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTable.cpp (83%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTable.h (86%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTableIterator.cpp (88%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTableIterator.h (82%)
create mode 100644 code/VerticesExtractor/Makefile
rename code/{plugin_VerticesExtractor => VerticesExtractor}/Vertex.cpp (74%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/Vertex.h (73%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/VerticesExtractor.cpp (86%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/VerticesExtractor.h (76%)
delete mode 100644 code/plugin_Amos/Makefile
delete mode 100644 code/plugin_CoverageGatherer/Makefile
delete mode 100644 code/plugin_EdgePurger/Makefile
delete mode 100644 code/plugin_FusionData/Makefile
delete mode 100644 code/plugin_FusionTaskCreator/Makefile
delete mode 100644 code/plugin_GeneOntology/Makefile
delete mode 100644 code/plugin_GenomeNeighbourhood/Makefile
delete mode 100644 code/plugin_JoinerTaskCreator/Makefile
delete mode 100644 code/plugin_KmerAcademyBuilder/Makefile
delete mode 100644 code/plugin_Library/Makefile
delete mode 100644 code/plugin_MachineHelper/Makefile
delete mode 100644 code/plugin_MessageProcessor/Makefile
delete mode 100644 code/plugin_NetworkTest/Makefile
delete mode 100644 code/plugin_Partitioner/Makefile
delete mode 100644 code/plugin_PhylogenyViewer/Makefile
delete mode 100644 code/plugin_Scaffolder/Makefile
delete mode 100644 code/plugin_Searcher/Makefile
delete mode 100644 code/plugin_SeedExtender/Makefile
delete mode 100644 code/plugin_SeedingData/AssemblySeed.cpp
delete mode 100644 code/plugin_SeedingData/AssemblySeed.h
delete mode 100644 code/plugin_SeedingData/Makefile
delete mode 100644 code/plugin_SequencesIndexer/Makefile
delete mode 100644 code/plugin_SequencesLoader/FastqGzLoader.cpp
delete mode 100644 code/plugin_SequencesLoader/FastqLoader.cpp
delete mode 100644 code/plugin_SequencesLoader/Loader.cpp
delete mode 100644 code/plugin_SequencesLoader/Makefile
delete mode 100644 code/plugin_VerticesExtractor/Makefile
delete mode 100644 debian/patches/reorder_args_to_keep_linker_happy
delete mode 100644 git.txt
delete mode 100644 github.txt
delete mode 100755 scripts/install.sh
delete mode 100644 tag.txt
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