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I've added this patch to the bug-tracker system, but it may be worth to post it here instead...
Basically adds a new predicate (ill2sanger) to convert illumina fastq to sanger fastq.
2009-08-20 15:35:24 UTC in Mapping and Assembly with Qualities
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As new Illumina software (GA 1.3+) has changed quality score encoding, I've written a small patch which adds 'ill2sanger' function, to convert new illumina fastq files into sanger fastq.
It applies to maq-0.7.1. Essentially it takes the illumina score and adds 2. The function to read fastq files (defined in seq.c) removes 33 to this score, so that the overall operation is removal of 31 from...
2009-07-20 15:31:37 UTC in Mapping and Assembly with Qualities
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Hi all, I've installed R 2.7.1 on FreeBSD 6.3.
After that I've installed rpy1.0.3 with python 2.5.
I have this error and it seems I'm not the only one.
I don't ask for a ready solution, although it would be great, I just want somebody to help me to figure out what this error means:
>>> from rpy import *
*** caught segfault ***
address 0x54d8, cause 'unknown'
Traceback:
1...
2008-09-05 15:50:50 UTC in RPy (R from Python)
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daweonline registered the mipfe project.
2008-07-29 10:17:30 UTC in mipfe
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Hi all,
I've noticed that there's an error in autoconf files that prevents to configure openms properly:
checking Checking for CGAL support... enabled
checking for CGAL header files... (/Users/dawe/Downloads/OpenMS-1.1.1/contrib/include)
checking for libCGAL.so... (/Users/dawe/Downloads/OpenMS-1.1.1/contrib/lib)
checking linking against CGAL... no
Cannot link against libCGAL . Please...
2008-07-24 09:09:29 UTC in OpenMS
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Hi there, I've been trying to build OpenMS but make fails:
Entering directory DATASTRUCTURES ...
/usr/bin/g++ -W -fPIC -O3 -Wall -Wno-long-long -Wno-deprecated -Wno-non-virtual-dtor -pedantic -I/Users/dawe/Downloads/OpenMS-1.1.1/include -I/Users/dawe/Downloads/OpenMS-1.1.1/contrib/include -c SuffixArraySeqan.C -o SuffixArraySeqan.o
SuffixArraySeqan.C: In member function 'virtual void...
2008-07-24 09:04:39 UTC in OpenMS
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Hi all, I'm very sorry but the last month and half has been full of other tasks... I even couldn't open the directory where I started everything! I promise that the new year will have some code released, also because I need something working for my alpha machines!
2006-12-14 22:39:32 UTC in GNU SRS
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daweonline registered the GNU SRS project.
2006-09-21 21:05:16 UTC in GNU SRS
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This is the patchset that adds type long handling on 64
bit platforms, as reported in bug #1438189
(https://sourceforge.net/tracker/?func=detail&atid=714418&aid=1438189&group_id=129302)
I hope this can help.
Beware: I haven't tested it thoroughly, especially for
full MPI functionality but, in principle, it should work.
dawe.
2006-08-08 14:41:27 UTC in MrBayes
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Logged In: YES
user_id=1570539
Hi guys, I've apparently fixed it on my 64bit platforms.
The problem is that in sumt (and all over the source code)
there are several variables defined as 'long' or 'long int'.
on 32bit sizeof(long)=4 bytes, whereas on 64bit
sizeof(long)=8 bytes, therefore there are memory management
(mallocs and who knows what else) that can fail. I've put this:
[code]...
2006-08-08 14:10:51 UTC in MrBayes
