New RNASeq pipeline. Removing old one
Add IVA assembler as option to assmebly pipeline
use inner join instead of left join when looking for lanes to map
Merge pull request #263 from andrewjpage/speedup_searching_for_mapping_lanes

use inner join instead of left join when looking for lanes to map
Pipeline now calling new Bio-RNASeq application
Merge pull request #264 from js21/no_rna_seq

No rna seq
Move identical map_and_generate_stats functions into Assembly.pm
Use system() instead of backticks and check return codes
Remove smalt and faidx index files after filtering reads
Merge pull request #265 from martinghunt/add_iva_assembler

Add iva assembler
Fix typo so that adapter trimming gets run
Merge pull request #266 from martinghunt/pipeline

Fix typo so that adapter trimming gets run
Remove debugging print
Pass trimming info to iva in dynamic perl script
Merge pull request #267 from martinghunt/pipeline

Fix so adapter trimming happens with IVA
Corrected the file names

This should fix th behaviour described on the RT ticket 390430
Corrected the filenames specified on RT ticket 390430
Merge branch 'no_rna_seq' of https://github.com/js21/vr-codebase into no_rna_seq
Merge pull request #268 from js21/no_rna_seq

Corected filenames for db update and clean up
Filenames now changed properly