[med-svn] [SCM] ray annotated tag, 0.0.7, created. 0.0.7
Sébastien Boisvert
seb at boisvert.info
Sat Nov 3 20:44:27 UTC 2012
The annotated tag, 0.0.7 has been created
at 502234f1012d120824fe953dec5c4146fa9d2ce5 (tag)
tagging 54eeaf0032e903cd62eeacb02b0d2184ec43f83e (commit)
tagged by Sébastien Boisvert
on Sat Apr 24 12:17:54 2010 +0000
- Shortlog ------------------------------------------------------------
Version 0.0.7
Sébastien Boisvert (354):
(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
Version 0.0.7
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