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- Create "group" object to sub-cluster sequences/contigs/scaffolds/etc
- Remove iid concept - keep bid and let message files use eids for cross-referencing. this will allow the merging of files
- Remove the layout objects - equivalent with contig without a sequence
- New way to store sequence data targeted at short sequences for which it's too verbose to store names and such
- figure out a way to handle 454 mate-pairs, esp. in hawkeye
- build a better 'toAmos'
Note: some progress in these directions has been made but the changes need to be cleaned up.
- integrate other aligners - Daniela has a preliminary pipeline that works with SOAP but why not Bowtie? A solution would be to allow inputs in BAM format.
- Handle scaffolds better than currently done (now the code uses "contigs" instead of scaffolds)
- Write good documentation and put together pipelines for various types of data and underlying assemblers