switch from using demuxing and mass parrellel mapping, to extracting UMIs
about to make dedup_umi paired aware
added project pipeline
Two major changes: Include soft-clipped bases when calculateing start position for deduping, and supply list of which libraries used in which lane. Also some tidying and debugging
dedup_umi contains bug with softclipped reads
Add 1kb read ahead buffer to ensure that reads aren't output too early
Tidying up and documentation update for push to new repository
Merge remote branch 'origin/master'