Added bam->sam conversion using samtools.

bam<->sam using sambamba removed, samtools will be
fine for simple conversion (via @lomereiter)

Using this instead of Picard's SortSam fixes the
out-of-memory errors post-alignment and during
transcript counting.
Ensure discordant grading CSV output is sorted consistently. Fixes #208.
Remove unnecessary bam->sam conversion during htseq-count.

Thanks to @lomereiter.
Improve detection of fastq pairs: Avoid extraneous matches in file path that lead to non-correct pairings. Provide warnings when samples are missing metadata when metadata supplied. Fixes #224