BFAST-0.6.0 released

[nilshomer]

BFAST 0.6.0 represents a major release.

BFAST is a fast and accurate short read aligner. Specifically, BFAST was designed to facilitate whole-genome re-sequencing, where mapping billions of short reads with variants is of utmost importance.

We have changed a lot in this version (read carefully below) and we welcome any feedback (positive or negative). Send help or questions to
[email protected]

Summary of changes:
- an index can be efficiently split to fit in any amount of memory (RAM).
- local alignment now up to 10 times faster using seed-constrained local
alignment.
- newly designed and unified command line interface.
- ability to automate and parallelize large alignments on a
cluster.
- supports a pipe-and-filter model

Hopefully, you find BFAST easier to use as well as faster than ever!

Nils Homer

[dakl]

Hi,

I'm trying to compile it on Fedora10/x86_64 and get the following error:

$./configure
...
$make
gcc -DHAVE_CONFIG_H -I. -I..     -Wall -g -O2 -pthread -m64 -D_FILE_OFFSET_BITS=64 -MT BfastBAFConvert.o -MD -MP -MF .deps/BfastBAFConvert.Tpo -c -o BfastBAFConvert.o BfastBAFConvert.c
BfastBAFConvert.c: In function ‘BfastBAFConvert’:
BfastBAFConvert.c:55: warning: implicit declaration of function ‘getopt’
BfastBAFConvert.c:57: error: ‘optarg’ undeclared (first use in this function)
BfastBAFConvert.c:57: error: (Each undeclared identifier is reported only once
BfastBAFConvert.c:57: error: for each function it appears in.)
BfastBAFConvert.c:66: error: ‘optind’ undeclared (first use in this function)
make[2]: *** [BfastBAFConvert.o] Error 1
make[2]: Leaving directory `/home/daniel.klevebring/Illumina_data/bfast-0.6.0d/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/daniel.klevebring/Illumina_data/bfast-0.6.0d'
make: *** [all] Error 2
$

Any ideas on this?

Thanks
/Daniel

[nilshomer]

Hi,

I'm trying to compile it on Fedora10/x86_64 and get the following error:

$./configure
...
$make
gcc -DHAVE_CONFIG_H -I. -I..     -Wall -g -O2 -pthread -m64 -D_FILE_OFFSET_BITS=64 -MT BfastBAFConvert.o -MD -MP -MF .deps/BfastBAFConvert.Tpo -c -o BfastBAFConvert.o BfastBAFConvert.c
BfastBAFConvert.c: In function ‘BfastBAFConvert’:
BfastBAFConvert.c:55: warning: implicit declaration of function ‘getopt’
BfastBAFConvert.c:57: error: ‘optarg’ undeclared (first use in this function)
BfastBAFConvert.c:57: error: (Each undeclared identifier is reported only once
BfastBAFConvert.c:57: error: for each function it appears in.)
BfastBAFConvert.c:66: error: ‘optind’ undeclared (first use in this function)
make[2]: *** [BfastBAFConvert.o] Error 1
make[2]: Leaving directory `/home/daniel.klevebring/Illumina_data/bfast-0.6.0d/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/daniel.klevebring/Illumina_data/bfast-0.6.0d'
make: *** [all] Error 2
$

Any ideas on this?

Thanks
/Daniel

Good catch. I have fixed this in the latest source code but you will need to add the following define to the beginning of each source file where it complains it is missing "getopt":

#define <unistd.h>

Add them to:

 bfast/BfastBAFConvert.c
 bfast/BfastBMFConvert.c
 bfast/BfastBRG2Fasta.c
 bfast/BfastHeader.c

I wil silently update the latest release (0.6.0d) to include this fix (md5sum: e41ad3ce033f450400238c07b823ab6a). Thanks again!