chaining bwa, samtools and annotation commands
edited annote to make name of feature N or C or misc
edited directory making steps
code up to end of both assembly steps
code up to assemble steps, split bwa index and mem
split bwa and samtools commands, working to assemble step
move contigs out of velvet assembly folders and rename
making contigHit files complete
finished final annotate steps
corrected blast step, made blast against single fasta database
relaxed annotation paramters
changed annotation script to annotateBlastHits_IS.py
fixed bug so N terminus appears as feature type
added delete dir step
Merge branch 'ismapping'