Set quality flag properly for Tophat alignment.

Thanks to @mjafin.
Merge branch 'tophat-quality-fix'
Update Tophat fix.
Keep original compressed fastq files.
Save original compressed FASTQ files.

Also write uncompressed FASTQ files to the work directory so
they can be cleaned up easily.

Swapped the explant integration testing data to use gzipped files.
Also added another replicate, just because.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Use standard exist instead of checking file size when transferring directories to final location. Touch final copied directories to avoid multiple transfers with time preserving copytree. Fixes #198
Fixed transcriptome-index not being located correctly.

Thanks to @mjafin.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added .ver to the end of the transcriptome_index files.
Tophat and FASTQ fixes.
Bumped version numbers on resources files so they get tagged as new.
Annotate NA12878 example datasets as females so variant calling will treat sex chromosomes correctly
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen