SequencesLoader: fix bad automatic pairing of sequence files

test:

[boisver1@ip03-mp2 NIH_Human_Microbiome_Project-Phase-1-shotgun]$ Ray -detect-sequence-files SRS014613 -output SRS014613-z
^C
[boisver1@ip03-mp2 NIH_Human_Microbiome_Project-Phase-1-shotgun]$ cat SRS014613-z/RaySmartCommand.txt
mpiexec -n 1 Ray \
 -detect-sequence-files \
 SRS014613 \
 -output \
 SRS014613-z \
 LoadPairedEndReads \
 SRS014613/SRR061226_1.fastq.gz \
 SRS014613/SRR061226_2.fastq.gz \
 LoadPairedEndReads \
 SRS014613/SRR061229_1.fastq.gz \
 SRS014613/SRR061229_2.fastq.gz \
 LoadSingleEndReads \
 SRS014613/SRR045715.fastq.gz \
 LoadSingleEndReads \
 SRS014613/SRR047386.fastq.gz

Link: https://github.com/sebhtml/ray/issues/214
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>