First attempt at a hiseqx pipeline (without filtering)
First attempt at an improved viewer / editor
move bam12auxmerge into bwa_post_proc, and other minor changes
Changed names of bed files
improved viewer - work in progress
Handle vtf files as well as json and cfg files
Work in progress on the hiseqx pipeline
Work in progress for pipeline progress viewer. Animations and python cgi script working
Added -p flag to bwa mwm. Now runs to completion without errors.
Clear intervals before resetting them
Display job status (running, waiting, completed)
Clear intervalArray array
viv.pl - enhanced error message
vtfp.pl - added ability to link one output to several inouts in a subgraph (VTFILE node)
added refactored templates for stage 2 alignment and realignment
corrected execute bit on viv.pl
pre_alignment_realign.json - corrected "bamreset resetaux=0..." to "bamreset resetaux=1...", and "bamadapterclip" to "bamadapterfind clip=1"
added auxfilter list to bamreset in auxmerge_prep_realign.json
corrected bamadapterclip to bamadapterfind clip=1
some amendment of subst_param names in template
changed potentially problematic duplicate subst_param name: final_output_prep to final_output_prep_target_name and final_output_prep_phix_name
Tidying and minor UI improvements