Name-sort the transcriptome BAM file.
Name-sort the transcriptome BAM file.

This works around having to stick eXpress in the multithreaded
quantitation, since it is not multithreaded. Thanks to
@schelhorn for the fix.

Addresses part of #1028.

a113n/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lpantano/bcbio-nextgen,lpantano/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,brainstorm/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,biocyberman/bcbio-nextgen,lbeltrame/bcbio-nextgen,vladsaveliev/bcbio-nextgen,brainstorm/bcbio-nextgen,chapmanb/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,mjafin/bcbio-nextgen,lbeltrame/bcbio-nextgen,mjafin/bcbio-nextgen,biocyberman/bcbio-nextgen,biocyberman/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lpantano/bcbio-nextgen,chapmanb/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,lbeltrame/bcbio-nextgen,mjafin/bcbio-nextgen,brainstorm/bcbio-nextgen,chapmanb/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen