initial import of Trypanosome code base
first commit
removed other non-sense bowtie indexes
added yass scripts
added yass result parser. includes a yassentry object
added Analysis/convertYass2Rdata.py to generate a matrix for Matlab/R of the reads vs ref mapping
added Analysis/convertYass2Rdata.py to generate a matrix for Matlab/R of the reads vs ref mapping
added utility for parallelizing scripts across multiple inputs
more debugging
neat new script to speed up the yass alignment
added more stats
intersects reads against trinity assembled contigs
added next() method as a wrapper to the iterator
added yass direction label to the output dir
performs intersection between the contigs and the blast results performed using contigs
performs intersection between assembled contigs and their raw reads
fixed to handle assembly of stage 2 (against RNA databases) mapped reads
run blast on trinity assembled contigs and perform intersection
made more generic
renamed since this is only for aligning adaptors in the preprocessing step