added gra option to subtraction
added environment variables for running gra
added gra to subtraction and fixed the bug when reading the xeno file
added a file for calculating gra using third party software readscan that needs to be installed (see the /etc directory)
changed the filtering approach / no collapsing of FASTQ files only filtering (single, pair-end)
allow mapped reads to be inserted into the database
news
Initial work on testing. I’m trying to get TDD to a point where I can actually develop
Added exit status for errors
More testing added to detect duplicate samples, along with integrate the sample identifier references needed by the new web application schema
Added index fixes needed to make samples unique within projects
Added a first alignment test
Fixed the alignment schema indexing
Added test data
Added Genbank file for testing
Added tests for gbloader
Added small performance fix to speed up some of the very large string searches, when strings consist entirely of N
Testing now handles the basic subtraction process too.
Added more complete subtraction tests
Initial integration of the modified readscan.pl script. Now calls this OK, and generates data.