[t.lawson@utah rDiff-master]$ make example
echo Entering ./examples
Entering ./examples
cd examples ; make example
make[1]: Entering directory `/NGS/Software/rDiff-master/examples'
./run_example.sh param

: This program is part of the rDiff version .

rDiff performs differential expression testing from RNA-Seq measurements.

%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

Writting results to: results
1a. load the genome annotation in GFF3 format, create an annotation object
warning: X11 DISPLAY environment variable not set

Compute index for the bam files
Indexing data/example_condition_A_replicate_1.bam
data/example_condition_A_replicate_1.bam already indexed
Indexing data/example_condition_A_replicate_2.bam
data/example_condition_A_replicate_2.bam already indexed
Indexing data/example_condition_B_replicate_1.bam
data/example_condition_B_replicate_1.bam already indexed
Indexing data/example_condition_B_replicate_2.bam
data/example_condition_B_replicate_2.bam already indexed

%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2. Differential testing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%

warning: X11 DISPLAY environment variable not set
Set the paths
Load configuration
Compute regions common to multiple genes
Compute alternative regions
Measure gene expression
Getting gene expression for: data//example_condition_A_replicate_1.bam
Finished 100 out of 100 genes
Elapsed time is 52.5777 seconds.
Getting gene expression for: data//example_condition_A_replicate_2.bam
Finished 100 out of 100 genes
Elapsed time is 53.0777 seconds.
Getting gene expression for: data//example_condition_B_replicate_1.bam
Finished 100 out of 100 genes
Elapsed time is 52.1038 seconds.
Getting gene expression for: data//example_condition_B_replicate_2.bam
Finished 100 out of 100 genes
Elapsed time is 51.8088 seconds.
ans = 0
Estimating variance function for rDiff.parametric
Loading gene expression
Loading alternative region counts
estimating variance function for sample 1
estimating variance function for sample 2
Loading gene expression
Loading alternative region counts
Performing parametric testing
Current gene: Gene:AT1G02960
Reading temporary results
Writing output files

make[1]: Leaving directory `/NGS/Software/rDiff-master/examples'
