[med-svn] [SCM] ray annotated tag, 1.2.4, created. 1.2.4
Sébastien Boisvert
seb at boisvert.info
Sat Nov 3 20:44:30 UTC 2012
The annotated tag, 1.2.4 has been created
at 85ff3a0ffe48ca3f4a8c3279fbfc5d786ac71e5a (tag)
tagging b6a668371070b8cc219878531014b3c782f8eaa5 (commit)
tagged by Sébastien Boisvert
on Wed Feb 23 16:03:55 2011 +0000
- Shortlog ------------------------------------------------------------
Ray version 1.2.4
Sébastien Boisvert (933):
(null)
Moving stuff around
Loading a parameter: the directory name
added a message limit
Changes, test1, test2, and test3 are working properly
MPI_Waitall is better
* possibly proceed separatly for direct and reverse for edges.
* possibly proceed separatly for direct and reverse for edges.
* possibly proceed separatly for direct and reverse for edges.
test1, test2, and SRA001125 file 1 load
* free message memory
commit 7938e7a2edaabf8ee0f55eb1b34e30f76e53c015
test1 and test2 ok with coverage calculation
Works ok.
Sending code
Added command for MPICH2
commit 6686b74dbe4d2e6ad6577bd1d978602b5d4b77cc
commit 72db23dd80245fe0706462eda62e138ff2ce94b4
commit 3c9cb7ae8bcba1e7c0df4a136cdb90536bf11065
commit 1e3ad1ba3bcb24442b441740b1d42d290fb88c0c
commit 639ecd60b249491e3523c7d596aa72461297a887
commit 107f7de8cc18564fe23e7332dd799451e10f067e
commit 800b776a78e2fa752914917fb5174dfa4381fdc6
* the seeds are now computed correctly. (need to test stuff in TODO.txt)
* Fixed problem with Finalize and MPI_Barrier.
* Fixed a bug in building seeds.
* will fix these later or never (they are not that important.):
Seems ok to me:
* Reads get attached now.
* Ray returns immediatly if given an invalid configuration file.
* added version in stdout
commit 370f620230c9676e0ca8d5dce77ae8f1b33d4cda
* Show progress when attaching reads.
* show progress for vertex seeding.
No message, just commiting stuff.
Done: now I have 2*n seeds! yay.
Reduced communication:
* Fixed a SEG FAULT when sending large sequences.
Updated TODO .
This behavior is correct:
* The coverage of a vertex is now stored as a 'char', with a maximum of 255.
* Edges are stored as a 'char'.
* fixed compilation warnings.
* removed cout's
The memory usage is lowered, now each vertex is a (uint64_t,char,char,bool)
Summary of today's work:
commit ae3f25682210aca70f34272ce21ddeccd18152b9
Fixed:
* The extension is now done in both direction.
fixed compilation warnings
* I added constants for allocator's chunk sizes.
* only keep seeds with at least 100 nucleotides.
* removed commented code lines in the code.
* FIXED: random mismatches plague seeding?
* remove Edge class (it was replaced by ReadAnnotation)
FIXED:
Added this feature:
Updated TODO.
Updating TODOs
Directions are copied.
* Restored extension.
Implemented:
Fixed misassembly.
Setting the PERIOD for MPI_Barrier back to 100
Removed paired-end Class.
Added the direction class.
* removed the line break before the Minimum Coverage
The fusion has begun.
WORKS-FOR-ME:
Fixed:
Fixed:
Fixed compilation errors.
Fixed:
Fix in README.
The next milestone:
Updated TODO.
working on a bug
good .
* Removed the DUMMY message.
Currently investigating the hang.
The hang is caused by the btl sm.
Removing ther Makefile for colosse.
Testing speed limitation.
Speed regulator works on Llactis with 8 MPI processes.
* Removed all MPI_Barrier calls from the program (they are broken with shared memory for
Implemented:
* added progress when attaching reads.
SRA001125 preliminary results:
* Remove calls to Get_processor_name in code.
* Removed time.h and sys/time.h from includes.
Debuging on colosse.
Removed TODO.txt
Removed the qsub SGE submission script. It does not belong there.
Removing all Barriers.
Added a detection of MPICH2
Fixed the detection of MPICH2.
Use shortcut when sending message to self.
Fixed ticket http://genome.ulaval.ca/seb-trac/trac/ticket/30.
Detection of MPICH2 and Open-MPI is done.
Documented the code for MPI implementations.
Adding progression in fusion steps.
* Implemented Ticket #22 (new enhancement) -- possibly use a map<,> to hold information on path lengths.
Partial fix for #15 (when complete coverage of a contig invalids it)
Removed cout's
Work in progress.
Debugging stuff.
Added a script to analyse assemblies.
Added segments.
Fixed #47
Added the content of the website.
Moved the content of the site in README.txt
Updated the README.
Changed http to https.
Implemented #45: add a compilation flag for writing things in stdout.
Implemented ticket #16.
Added endl.
Updated the README
Small changes in the README.txt
Added message for SeqAnswers.com
Added URI.
Updated the text for Seq Answers.com
commit e67047e5f60a440f6891bc96185c2b5f413bfc87
Implemented ticket #52.
Corrected the text.
Corrected the README.
Cleaned the code.
Added an error message.
Fixed #54: SEGFAULT on SRA001125 unpaired.
Work in progress.
Fixed the duplication of the first contig.
I only have to make them go together now.
Fixed ticket #53 (Ray produces too much thing for SpPaired)
Updated year in copyright.
Fixed possible infinite loop.
* disabling cycling for now...
Making some tests.
Removed a false assert (it can be false, but it is not a problem..)
Making some comments.
Fixed compilation error.
Added some comments.
* Added comments
Fixed #69 (check if maximum cycling is reached.)
Removed test.
* Fixed typo in documentation
Work in progress.
Sending stuff.
Working hard on color space!
Implemented Distant Segments Graph.
Testing on SOLiD data, but they seem to be rich in errors...
Fixed several SEGFAULTS caused by reads shorter than wordSize
Fixed ticket #80. (stop if no peak coverage is observed.)
Implementation of a tip detector.
Adjusted the maximum coverage using COVERAGE_TYPE.
Some patchwork on tip detection!
Adding mummer validate script.
Fixed SEGFAULT (ticket #84).
Added CoverageDistribution.txt and Parameters.txt to outputs.
Implemented BubbleTool. (for tickets #18 and #19)
Updated RP
Fixed a SEGFAULT by reducing the number of members in Machine.
Bubble detection tool is online.
Some work done.
I think I found a good algorithm for homopolymers.
Removed alignment of addresses.
Switching to ls30
The algorithm is working out now.
Almost done with the bubble detector.
Sending work.
Possibly fixed a SEGFAULT. (ticket #86)
Fixed bug #86. (SEG FAULT.)
Avoid bubble detection unless the maximum vertices to visit is not reached.
Created a framework for bubble detection.
Fix of the day for ticket #88 (SpPaired @ k=21 fails).
Changes.
I misassembled contig now.
Added another test.
I think this fixed the problem.
Fixed two situations.
Implemented another thing to avoid misassemblies.
Close to version 0.0.4
Updated procedure.
Updated wiki.
Cleared some things written on-screen.
Ticket #92 fixed.
Done with ticket #93.
Started to work on AMOS output (ticket #58)
* added AMOS support (ticket #58)
Ticket #94 -- allows on to provide arguments -- is implemented.
Unified the documentation.
Support for AMOS is finished.
Fixed a bug.
Updated Release Procedure.
Corrected a bug for coverage distribution.
Added a read trimmer to remove letters that are not nucleotides from both ends.
Fixed crash when one read is provided. (ticket #99)
Working on bubbles.
Fixed a bug in amos output.
Working on ticket #100.
Sending code.
Adding new scripts.
This might be a fix for #103.
Changes for today.
Updated scripts.
Adding scripts.
Updated the wiki.
added identifiers. in tests.
Updating the script.
adding scripts directory.
adding scripts.
removing script.
Move things around.
Updated scripts.
added log files.
adding new scripts.
adding scripts.
adding scripts.
Adding scripts.
adding scripts.
modified scripts.
Adding scripts.
Fix to ticket #105.
adding scripts again.
Corrected scripts.
Added additional scripts.
Modified script.
Corrected scripts.
adding scripts.
Adding scripts.
Modified scripts.
Corrected scripts.
Corrected scripts.
Corrected scripts.
corrected scripts.
Only open Amos file once.
Skip the first base AND the first color in SOLiD reads.
Fixed ticket #103.
Fixed ticket #113.
Corrected scripts.
Corrected scripts.
Implementation for vertices, ticket #114.
Flushing arcs in groups (ticket #114).
Started to work on grouping indexing communications.
Added a comment.
Added a constant.
This patch is for sequence distribution grouping of communications.
Grouping communications for pairing of sequences. (ticket #114)
Investigate the number of elements.
Implemented Ticket #115 -- early skipping of 1-coverage vertices in extension
Created a component VerticesExtractor (ticket #116)
Added two constants.
ticket #117 done.
Ticket #116 (new enhancement)
Added a watchdog on the coverage to assess when a maximum coverage is attained.
Implemented Ticket #120 (move computation of sums, counts, and maxs in mapping of reads onto arcs.)
Fixed a SEG FAULT brought by -ticket #120.
Corrected serious bugs.
Added a component.
Investigating ticket #123.
#123 (-DSHOW_CHOICE removal tricks things)
#116 (create components to reduce the number of C++ lines in a single file.)
Added the 'Tron' algorithm, which can replace the 'OpenAssembler' algorithm.
Changes
Added a watchdog for repeated vertices.
added a repeated-region watchdog.
Fixing Makefile.
Changed parameters.
#83 (fix compilation errors for 'make test')
#48 (Fix compilation errors for Simulation tools.)
* Fixed basename when the file is in the current directory.
Corrected scripts.
Updated a script.
Added codes for SOLID.
adding scripts
Optimizer
Prototype for #126 (new coverage detection based on linear algebra)
#126 (new coverage detection based on linear algebra)
Fixed bugs in the new algorithm for coverage detection.
Added documentation on how to use this script.
added code for circular genomes.
Updated README.txt
Sending updated scripts.
Corrected the Makefile
Restored the good old coverage detector.
Changed alarm.
Restored threshold.
Fixed SEGFAULTS
Ok now.
Updated release procedure.
Updated Released procedure.
added a change log.
removed line
Updated version to 0.0.7
Corrected typos.
Multiplicators set to 1.3 are good.
Some work for ticket #55.
ticket #55.
Working on ticket #55.
Added MPIOPTS in scripts.
Improved speed.
#135 (change multiplicator depending on coverage.)
Working on 0mix14.
#136 (add running time in scripts.)
Corrected a bug.
Changed name.
Send script.
#116 (create components to reduce the number of C++ lines in a single file.)
Probably a fix for #132 (fix 0mix14-ray)
#21 (speed hack: when extending reverse-complement paths, only thread reads at the ~1000 last vertices.)
Fixed bugs.
Single change, but not much.
1 is not good, remember?
Updated the Makefile.
Adding a script.
Updated scripts and Makefile.
added a watchdog for decision on tips.
Introducing watchdogs:
Soft watchdog.
Sending data.
I am ready to run everything.
#129 (robustness for arguments parsing)
#116 (create components to reduce the number of C++ lines in a single file.)
Fixed compilation errors.
Sending modifications.
Removed hard-coded thing.
sending changes.
pre-release of 0.0.7
Changes in scripts.
Some work on Splay
#150 (pass the allocator to SplayTree when creating them.)
#151 (freeze splay tree after vertice distribution)
#149 (create an array of splay tree, and hash vertices to place them in)
Small fix.
Small changes.
some changes.
#131 (automatic detection of fragment length and standard deviation)
#131 (automatic detection of fragment length and standard deviation)
Working on distances,
Sending code.
#131 (automatic detection of fragment length and standard deviation)
Updated scripts.
#156 (Group communications for library distances)
Some small changes.
Added an option to dump libraries.
This will fix #162 (find why Ray crashes on mix21 and mix23)
Fixed cabog script.
Added a script to analyze the quality.
#162 (find why Ray crashes on mix21 and mix23)
Fixed Makefile.
#163 (add an option to for prefix output)
Now it seems to be ok.
Removed a blank space.
Sending small changes.
Ready for 0.0.7
Sending README
Updating wiki.txt
Moving wiki.
Ajout d'un Define.
# 446
Enabled -v is default.
Verbose mode.
make k a tunable parameter
add reference in Ray
Write the coverage distribution.
[boiseb01 at ls28 trunk]$ svn merge -r 3680:3683 http://genome.ulaval.ca/svn/boisvert/Ray/branches/Ray-0.1.0_vector
check the code for
Adding files.
Removed some line breaks.
#164 working on it
#164
Added exception when out of memory or requested memory exceeds CHUNK SIZE
Added the number of k-mer for a given size.
Updated the release procedure.
Removed a loop.
COrrected a bug in MPI count
Removed a print
Sending diff.
SYncing
the error was in MessageProcessor
cache paired end queries in seed extension
only do the silly DFS
Moved wiki file.
Now I am ready to face the trials
Updated the Makefile.
Some fixes.
Add/Change #491 (remove messages that use TAG_HAS_PAIRED_READ)
Add/Change #153 (Use only a int to represent a Read index in PairedRead)
Add/Change #154 (Use only a int to represent a Read index in ReadAnnotation)
Add/Change #494 (implement a TimePrinter with cool features)
Added indicator of temporal advancement
Corrected keys, changed them to u64
Sending a small change
Adding examples.
Updating scripts.
Corrected the Makefile.
Moved script.
Corrected the script.
Add/Change #495 (group TAG_GET_PAIRED_READ with TAG_REQUEST_READ_SEQUENCE)
Simplified extension of seeds.
Changed period to 10 for fusion reporting
Corrected a critical flaw
Remove codename
Changed LICENSE file
Changed readme file name
Updated files.
The AMOS FILE name is now based on -o option.
Updated options.
Removing a file
Using 1.4.3 in examples.
Corrected INSTALL
Updated NEWS
Add/Change #498 (Do a test by ordering the seeds by the length before processing them.)
Sending information.
Updating Makefile
Moved code in code.
Removing useless files.
The Makefile is awesome now.
Updated the Makefile.
Updating README
Updated released procedure
Updated the Makefile.
Removed a debug message.
Removing sort, it is useless.
Added an example
Sending commands.
sending modifications.
corrected TimePrinter
Sending small changes
Added dates in output of elapsed times.
Updated scripts.
removing stuff.
Adding a script.
Moved scripts.
Added a script.
Adding a script.
Sending news
Updated the NEWS.
Updated NEWS.
Sending stuff
Corrected an output for library computations.
Corrected a bug .
Version is 0.1.1
Added gnuplot scripts.
Added a script to prepare for gnuplot
Adding another script.
Add/Change #521 (Do a test with a paired library of 1000 on E. coli.)
Sending configure stuff.
Removing makefile.
commit 32508bf3aeeb946fe88e66ecaf22d390083ea045
commit 91a43c375aeea1aa3cc07e8a99429cf1851dabc4
Adding files.
Sending stuff.
sending data.
Adding a new loader.
sending new file.
Sending code.
Sending new code.
AAdd/Change #512 (add support for .gz files)
Add/Change #525 (add support for .fasta.gz)
Add/Change #526 (left reads are not linked with the right one... this is a bug.)
APossibly a fix for:
Adding a file.
Removed memcpy for sending messages to self.
Sending code with modifications for regulation.
sending new files
the tribe is regulated with a scale of 5 micro-seconds
Changed it to 15 us.
Removed the regulator.
sending diffs.
Add/Change #23 (add an early-stop technology (To speed up the process.))
Add/Change #529 (why is there no message near 'Rank 0: fusion is done.')
ASending diff.
Debuggng messages.
Add/Change #537 (do an assertion with message size under 4096 in MPI_Send-utilizing function)
Add/Change #538 (in Ray, if message is more than 4096 for TAG_REQUEST_READS, send it in chunks)
Add/Change #540 (use sentinel to remove two messages coupled with TAG_REQUEST_READS)
Fixed an infinite loop
Corrected an error, bug
Optimized messages.
added a comment
Fixed another pesky bug.
sending stuff.
Started to implement the function arrays
Started to work on this.
some work
Changed the CXXFLAGS to -g
updated the makefile
Add/Change #539 (optimize the big if/else if/else if in MessageProcessor.cpp, using an array of pointers probably)
Add/Change #539 (optimize the big if/else if/else if in MessageProcessor.cpp, using an array of pointers probably)
Add/Change #545 (create MASTER_MODE and SLAVE_MODE in Machine::processData)
sending data
Checkpoint
Almost done.
Checkpoint, almost done with ticket 545
m_master_mode is completed.
ticket done
Add/Change #546 (use an array of method pointers for MASTER_MODE & SLAVE_MODE)
Add/Change #165 ("-i" / "LoadInterleavedPairedEndReads")
Sending a small change
Maybe fixed:
Add/Change #549 (in updateDistances, left sequences don't get their sequence updated.)
Sending diffs.
envoi des données
Sending code back to the home so I can work on another place.
Sending a preliminary diff.
Maybe this will fix the problem.
Corrected visual flaws.
Fixed a bug.
fixed compilation errors with MPICH2
adding two classes
Sending Makefile.in
Now it works with MPICH2 and OpenMPI
Small changes.
sending
Add/Change #558 (make Ray compliant with MPI 2.2, regardless of implementation)
Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
Add/Change #559 (for message allocation of outgoing messages, I must implement a custom allocator)
C'est tout pour aujourd'hui.
Envoyer un patch de code.
Replaced vector<Message> for inbox * outbox with a StaticAllocator.
Implemented a RingAllocator for inbox and outbox allocations.
Added regulation for RingAllocator .
Small changes.
Add/Change #558 (make Ray compliant with MPI 2.2, regardless of implementation)
* Removed messages replies for send_sequence
Working on Add/Change #497 (add a file for detectDistances and updateDistances)
Add/Change #497 (add a file for detectDistances and updateDistances)
New code is ready.
Moved a script
Sending code.
Add/Change #568 (Dont' load files when indexing reads...)
Changed the intervals.
Sending diff.
Sending stuff.
Now, the verticesExtractor and the EdgeExtractors wait for a reply before continuing.
Changed the period for seeding from 30000 to 100000
Add/Change #569 (glue sequences together in the distribution of them.)
Add/Change #570 (flush a destination instead of looping them all)
Fixed the bug.
Add/Change #571 (send paired information after sending sequences)
More beautiful output in stdout.
Add/Change #572 (test on ls30 with MPICH2)
Add/Change #572 (test on ls30 with MPICH2)
Now busy-waiting when flushing paired information.
There is a residual bug.
Finally fixed the bug.
Corrected the TimePrinter so it can print a message every hour.
Management of invalid files.
Fixed the bug:
Fixed another bug.
Changed two periods.
Adding diff.
Added two example scripts.
Sending a BzReader.
Add/Change #576 (support bz Files (fastq and fasta))
Add/Change #576 (support bz Files (fastq and fasta))
Sending new scripts.
COrrected a bug for library distribution (size updates)
Added some files for distribution.
Sending a file.
Renaming file.
ggA Add/Change #578 (add installation of scripts with 'make install')
Sending test
Updated the configure script.
Sending packages.
Added printing of MPI implementation.
Changed slightly the output.
Printing the number of messages received.
Added printing of updating distances.
added +1
Changed the period.
Changed stuff.
Adding a file.
Sending changes.
Renamed ChangeLog.
Sending change of license name
Sending DESIGNs.
Sending stuff.
Changed the place where showStats is called.
Added busy-waiting for distance updating.
Au revoir message moved.
Sending correction.
Adding a script.
Adding a script.
Add/Change #575 (run Ray with -i on ls30 with MPICH2 & SRA001125)
Small fix.
Corrected scripts.
Sending scripts.
Add/Change #575 (run Ray with -i on ls30 with MPICH2 & SRA001125)
Added sequences in output.
ggA Add/Change #581 (run Ray on Pseudomonas -p)
Add/Change #581 (run Ray on Pseudomonas -p)
Added a script for pseudomonas -p
ADded the full path for the reference.
Updated the citation
Added two directories: one for each implementations.
Moved scripts in directories.
added a file for the sun grid engine.
Add/Change #581 (run Ray on Pseudomonas -p)
Sending changes
Add/Change #582 (output a message matrix)
No trimming when the sequence does not come from a file.
Add/Change #582 (output a message matrix)
Add/Change #582 (output a message matrix)
Add/Change #582 (output a message matrix)
Add/Change #582 (output a message matrix)
Removed a useless output.
Changed the method name in Parameters for the prefix setting.
Updated scripts.
Modified scripts.
Add/Change #581 (run Ray on Pseudomonas -p)
Add/Change #584 (Index both read of the pair for paired information)
Add/Change #590 (enumc for mpi tags)
Add/Change #588 (ENUM FOR master modes)
Add/Change #589 (enum for slave modes)
ggA Add/Change #585 (Write the distribution of the libraries too)
adding a script.
Moved scripts.
Add/Change #585 (Write the distribution of the libraries too)
modified a script.
MOved a line in the output.
Add/Change #591 (optimize finishFusions (currently O(N^2) LOL)
added the logo.
Modified scripts.
Moved an output string.
Removed writting of temporary sequences.
added a file for paired pseudomonas.
Fixed
Only update paired read is they need it.
«Fixed a compile error.
Add/Change #598 (pseudomonas-p.sh has 1 error with HEAD, but 0 with r3846)
Add/Change #598 (pseudomonas-p.sh has 1 error with HEAD, but 0 with r3846)
Changed the maximum size of messages to 4000, as suggested by Open-MPI folks.
Removed a field.
added regression script.
Almost ready for release.
Corrected the release data in the ChangeLog.
Changed the change log
sending changes
Modified scripts.
Sending new release procedure.
Sending regression.
Updating regressions scripts.
Sending diff: changed 4096 for maxToProcess.
Sending patch for Library.cpp
Fixed (at least I think I did) the evil bug.
Now it is fixed (?)
adding regression.
Modified the regression runner.
Problem apparently fixed:
merged the branch.
Updated the ChangeLog.
commit 0d0a0eb6261206f4a61103a54a477bd39eb6b75a
Corrected the comments.
Add/Change #73 (coli-mpich2-interleaved-bz2.sh has many contigs, but coli-mpich2-interleaved.sh is OK)
Corrected a major flaw.
Renamed test.
fixed a compilation warning on Sparc V9
sending tested architectures
Adding simple test
sending x86 as a tested architecture
Added architectures.
Final commit before release.
Add/Change #75 (fix compilation warning on SPARC)
Add/Change #78 (test with PowerPC)
Corrected the file.
Add/Change #67 (add an early-stop technology (To speed up the process.))
sending a file.
Updated the CHangeLog
Removed simple test.
Implemented Early-stopping.
Worked a little on the early-stopping.
Add/Change #76 (add thanks to René in AUTHORS + Add colosse folks too+ add René for SPARC)
Add/Change #82 (Alert the user if the extension is unknown.)
changelog changed.
removed comparison scripts.
sending old version of script.
aclocal is correct.
Au revoir !
Add/Change #84 (use printf to make output beautiful with MPICH2)
Add/Change #79 (Load only 10000 sequence at one instant,)
Fixed a bug
Corrected ifdef.
Fixed configure script.
changed cout for printf.
Fixed an coding error.
new files.
Add/Change #88 (code a special arrays for myReads)
Now the Loader frees its memory.
Add/Change #89 (misassembly poped back)
Corrected the makefile.
Sending changes.
Sending optimization for finishing fusions and
Updated finishFusions.
Sending code.
Add/Change #91 (too many contigs for SRA001125)
Sending code, almost done fixing #91
Working on several tickets, but this commit is to allow code to be in scratch.
Add/Change #96 (Problem with reproducibility of paired distance approximation,)
Removed couts
Add/Change #50 (Use only a int to represent a library in PairedRead)
Add/Change #93 (remove half seeds, but not before the approximation)
Added a script.
Add/Change #84 (use printf to make output beautiful with MPICH2)
Add/Change #79 (Load only 10000 sequence at one instant,)
Add/Change #79 (Load only 10000 sequence at one instant,)
Add/Change #79 (Load only 10000 sequence at one instant,)
Add/Change #79 (Load only 10000 sequence at one instant,)
Sending new configure script.
Sending old configure.ac.
Changed the ring size.
Sending configure.
Sending configure that works.
Adding config.h.in
Fixed a bug in loaders:
added foreign directive.
Sending stuff.
Changed batch size to 1 000 000
Sending documentation.
Add/Change #57 (merge all instances of BufferedData)
Add/Change #50 (Use only a int to represent a library in PairedRead)
Fixed a printing problem.
Sending code,
I need to fix the code on SRA001125.
I think the problem is fixed.
Removed text.
Now the mismatches are calculated by mummer too.
Add/Change #69 (add installation of scripts with 'make install')
Add/Change #55 (add a file for finishFusions( and makeFusions)
Updated changelog.
Sending information.
Add/Change #56 (puts seeding routines in SeedingData)
Fixed a bug in the print-latex.sh script.
Sending scripts.
Sending updates for scripts.
Sending code for ls30
Fixed http://genome.ulaval.ca/trac/ticket/113#comment:1
Now it is faster !!!
sending change.
SOme code for A
Almost done with this.
Add/Change #66 (support polymorphic genomes (which data to use, simulated data?))
Removed the number of k-mers in the output.
Fixed some problems for polymorphic genomes.
Removed CHI-Square tests.
Updated change log.
Fixed compilation warnings.
Sending debug messages.
Sending dummy changes.
Envois des changements:
Corrected the bug in libraries.
Updated CHangeLog
Added a crypto file
changed the crypto-function
Changed VERTEX_TYPE to uint64_t
Sending patch to detect the source of the bug.
added code for removing node in splay trees.
Added an iterator over forests.
Add/Change #123 (Implémenter l'algorithme de Jacques: poussin v. pouzin)
Add/Change #126 (change MODE_ variables for RAY_SLAVE_MODE_)
Add/Change #127 (change TAG_ for RAY_MPI_TAG_)
Add/Change #128 (change MASTER_MODE_ for RAY_MASTER_MODE_)
Add/Change #130 (change m_mode for slave_mode)
Add/Change #131 (add code not to index a read on a vertex that is not in the graph)
Add/Change #132 (add code for not adding an edge if any vertex of the pair does not exist)
Add/Change #132 (add code for not adding an edge if any vertex of the pair does not exist)
Fixed bugs
Au revoir !
Add/Change #123 (Implémenter l'algorithme de Jacques: poussin v. pouzin)
Almost done.
sending code
Almost done.
From: Sébastien Boisvert <Sebastien.Boisvert.3 at ulaval.ca>
sending stuff.
Good job.
Sending stuff.
Deleted EdgesExtractor
Sending code.
Envoi du code
Fixed the bug.
Sending changes.
The bug is that here exists a seed with no reverse-complement seed.
Add/Change #134 (seg fault in trunk while implementing memory usage reduction)
Sending some changes.
Memory usage reduction is working a little.
Sending data
Only one message in the inbox.
Possibly fixed a bug.
the assertion was wrong.
With memory reducer:
Doing a test.
Code is operational.
Seems to work well.
On SRA001125:
Left to do:
Fixed
Some changes
Fixed a compilation warning.
Adding scripts + modified errors simulator.
Fixed -r option.
Changed the threshold + swapped a cout for a printf.
Modified change log.
Updated the change log.
Updated RELEASE procedure.
Updated the changelog.
Sending new Makefile.
Added assertions to track down the bug http://genome.ulaval.ca/trac/ticket/140
Add/Change #135 (implement <flushRemainingBuffers>)
The number of sent messages is below or equal to the number of MPI ranks.
Fixed the limit for vertices
Add/Change #140 (Fatal error in PMPI_Isend: Invalid rank, error stack:)
Fixed a compilation warning.
Sending chunk allocator, removed realloc in ArrayOfReads.
Working on
Fixed this:
Fixed:
Removed useless print
Updated the ChangeLog.
Now the paired information is packed.
The memory reducer is now run at the end of vertices distribution too.
Updated reducer to 10 M
Sending data to root
Fixed:
sending diffs.
Add/Change #151 (Reproduce and fix the bug wherein the number of sent messages overflow the ring buffer.)
Problem:
Add/Change #150 (change RAY_MASTER_RAY_SLAVE_ for RAY_MASTER_)
Add/Change #149 (Group communication (2 instead of 4) for INDEX PAIRED)
Fixed a compilation warning.
Fixed error in compilation.
I did some work on the internal buffers.
Debug messages
Fixed a bug.
Restored message size.
Add/Change #157 (parallel read for input files)
Removed pending request
Fixed a bug in Library.cpp
Reads are now encoded in 2-bits.
SImulators are not compiled now.
Fixed a bug for maximum number of sequences.
Fixed a critical bug: I had removed a line that should not.
Cleaned the code.
Updating regressions script.
Add/Change #167 (hangs without parameters or with -s or -p with insuficient operands)
Add/Change #167 (hangs without parameters or with -s or -p with insuficient operands)
Added a script to dump commands.
Added memory usage dump too.
Sending sequences.
Removed simulators.
Changes
== UPDATE ChangeLog ==
Add/Change #178 (move scripts in
Add/Change #177 (in FusionData::finishFusions(), only fetch paths for -1 up to -1-minimumOverlap)
Fusions.
Disabled SHOW_CHOICE.
Now reporting the memory usage for sequences and vertices.
ggAChanges
Forgot this file.
Fixed compilation errors.
added some outputs.
Added VirtualCommunicator
Add/Change #171 (group messages in SeedingData to make it faster)
Add/Change #188 (add Doxygen file)
Some work on an event-driven thing.
Some updates on virtual stuff.
Some work
Add/Change #171 (group messages in SeedingData to make it faster)
works on Strept. but not on E. coli.
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
Virtualization of communicators works like a charm.
Add/Change #184 (MessageProcessor::call_RAY_MPI_TAG_GET_PATH_LENGTH(Message*): Assertion `m_fusionData->m_FUSION_identifier_map.count(id)>0' failed.)
Updated the change log
Add/Change #185 (Rank 0 must not gather fusions. Instead, each rank must write them to disk.)
Add/Change #186 (adapt the AMOS writer to the parallel writting of contigs.)
Adding missing pieces.
Updated the INSTALL script.
Sending fix.
AFlat profile:
Flat profile:
kmerAtPosition is no longer among the slowest functions
Add/Change #193
Fixed a bug with caching.
200, 1000, 10000
M trunk/scripts/mummer-validate.rb
4 libraries
With SRA001125
Sending stuff.
Completion of the assembly: 8 minutes, 17 seconds
Add/Change #153 (Reducer increases memory usage ?? (probably STL, it sucks so much LOL))
Removed some leaks.
commit f87e4fafd35f0883900df29c02903b90a35b0069
Add/Change #195 (remove the inner loop for doChoice)
Fixed the assembly errors.
Adding file numbers.
added a manual
commit 3b8f74f3acab7e218c6e0526714778a580f1a986
Sending stuff.
Fixed a bug.
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
Senidng changes.
Updated scripts.
Version 1.2.3
Added a grid allocator.
Reduced memory fragmentation in the extension of seeds.
Fixed compilation error.
Missing coverage.
* Force the packing of structures and classes if using gcc
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
Fixed makefile.alternate
Added the option to pack things up.
Sending patch.
Changements dans le code.
Added current vertex in output.
Grouped messages in finishing fusions.
Fixed:
commit 936ae8f2f47399254a85696a638e9b380dba18a1
Now ready for another run on the human genome.
L1
adding a simulator that uses boost
The maximumum allowed coverage is now 65535.
Work is under way to index reads on the good vertex.
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
The place where to index a read is carefully choosed now.
% & numberOfContigs & bases & meanSize & n50 & max & coverage & misassembled & mismatches & indels
Ok ready for paper submission.
Updated makefile.
Added some verbosity
commit 9dea8bb06f98ed3b3559040dc58606fdde974ee1
Fixed stuff.
Updated scripts; manual and CHangelog
Sending stuff.
Ray version 1.2.4
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