Version 2.2.0 just released

[Nathan Clement]

GNUMAP version 2.2.0 has just been released. It can be downloaded from http://dna.cs.byu.edu/gnumap/gnumap-2.2.0.tgz

Notable fixes to this release:

* SAM format is now completely in concordance with the specifications, and can be used with samtools.
* Several of the alignment matrices have been updated to be more biologically relevant. Significant improvements in accuracy on real data have been achieved using these new matrices (used by default).
* Small bug fixes: Segmentation Fault on 454 reads has been fixed.

Cheers,
Nathan Clement

[Daniel Standage]

Nathan,

I just tried building 2.2.0 on Ubuntu 10.04 and got the following message.

In file included from /usr/include/features.h:378,
                 from /usr/include/signal.h:29,
                 from src/Driver.cpp:9:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
src/Driver.cpp: In function ‘int main(int, const char**)’:
src/Driver.cpp:1002: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1005: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1024: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1026: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1060: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1071: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1082: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp:1121: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp: In function ‘int set_arg(const char*, const char*, int&)’:
src/Driver.cpp:2350: warning: deprecated conversion from string constant to ‘char*’
src/Driver.cpp: In function ‘int set_arg_ext(const char*, const char*, int&)’:
src/Driver.cpp:2554: warning: deprecated conversion from string constant to ‘char*’
make: *** [obj/Driver.o] Error 1

Any ideas? Thanks.

Daniel

[Nathan Clement]

Are you in a 32-bit or 64-bit environment?  We're using 64-bit flags to compile.  

Nathan

[Daniel Standage]

Interesting. It's definitely a 64-bit capable machine (24GB RAM, 8 procs), but it looks like they installed the 32-bit version of Ubuntu! Thanks for the pointer!

Daniel

[Nathan Clement]

You can try compiling without the 64-bit flags, and it should still perform the same.  Of course, you'd be limited to a smaller genome (less than 1G bases long, probably), but that goes without saying.  You'd need to modify the Makefile for GNUMAP (remove the -m64 from the OPT_FLAGS variable), and might need to modify the compilation for the gsl library (it would complain if it couldn't link).  Alternatively, you could just install the 64-bit version...

Nathan

[Natacha P. Leitão]

Hello,

I'm trying to install the latest version of GNUMAP and at the end I get the same error (make: *** [obj/Driver.o] Error 1), despite the fact I'm in a 64-bit version of Ubuntu 12.04.

Thanks for the attention,
Natacha

[Nathan Clement]

Can you check and see if your machine has the file:
/usr/include/gnu/stubs-64.h

Or if there is any file of the format 

/usr/include/gnu/stubs-*.h

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