reverted a wrong hunk from commit 7c361f1530d084c6f99

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
FusionTaskCreator: don't lose genomic regions during merging

FusionTaskCreator is a plugin that eliminates genome paths that
are more or less included in other paths. The code allows some extra
objects that don't match, but no upper bound is given. This patch
adds an upper bound on these rare events.

Resolves-bug: https://github.com/sebhtml/ray/issues/101
Reviewed-by: Maxime Déraspe <maxime.deraspe.1@ulaval.ca>
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
SeedExtender: properly format extension file name

The name for a extension file is Rank9.RayExtensions.fasta, not
Rank9RayExtensions.fasta.

Resolves-bug: https://github.com/sebhtml/ray/issues/102
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
Scaffolder: only put one new line after scaffold sequence

When a scaffold has a number of nucleotides that is a multiple
of the number of columns, there is an extra new line. This patch
fixes that.

Resolves-bug: https://github.com/sebhtml/ray/issues/103
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
KmerAcademyBuilder: use vertexRank() to find who owns an object

In order to have more concise code, vertexRank() should be the only
way to obtain ownership information of objects.

Resolves-bug: https://github.com/sebhtml/ray/issues/107
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
new file GraphPartition.txt shows the distribution of objects

The GraphDistribution.txt file shows how good is the balancing
of objects.

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
the line that shows the process identifier was moved

The line that shows the process identifier is visible
when calling Ray -version, which should not be the case.

Resolves-bug: https://github.com/sebhtml/ray/issues/104
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
CoverageGatherer: kmers.txt should have 1 header only

Resolves-bug: https://github.com/sebhtml/ray/issues/105
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
recursive make was improved

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
readahead operations are used for reading gz files

Instead of calling fgets, the readahead code call gzread with
a large byte count.

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
SequencesLoader: added the rank number when loading files

The rank number was added when loading a file. The printed information
is now more relevant.

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
core: the partitioner needs the correct rank number

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
core: fixed a race condition occurring with -route-messages

The routing subsystem must be enabled if -route-messages is
provided regardless of anything else.

Resolves-bug: https://github.com/sebhtml/ray/issues/99
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
SeedExtender: display the number of traversed nucleotide symbols

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
Seeds: new runtime metrics for seeding algorithms

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
new header for SeedLengthDistribution.txt

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
new header for any paired read file LibraryN.txt

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
SequencesLoader: added a few assertions for read partitions

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
new header for CoverageDistribution.txt

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
Merge branch 'master' of github.com:sebhtml/ray