Closes #422.
Uses the warning API properly rather than directly to stderr
Merge pull request #424 from Garonenur/travis

Travis changes
Merge pull request #423 from standage/cairo

Closes #422.
clearer fix for double free bug

Closes #340
simplify a disabled AddIDsStream

If the AddIDsStream is disabled we don't have to do anything here.
Merge pull request #425 from gordon/doublefree

Doublefree
fix steps incement over step size if filters are combined
Merge pull request #426 from Garonenur/seqfilter

fix steps incement over step size if filters are combined
fix blast call for protein input
Merge pull request #427 from Garonenur/blast_process_call

fix blast call for protein input
pre-select features tab in HTML template
Merge pull request #432 from satta/html_template

pre-select features tab in HTML template
Store attributes from GTF
Adds ID, Parent, gene_id, and transcript_id attributes to gene and transcript features
gtlua: add genome_node:change_seqid()
Merge pull request #434 from satta/luaseqid

gtlua: add genome_node:change_seqid()
Merge pull request #433 from standage/gtf-attr

More complete parsing of GTF attributes
do not output cji/cjo/jnc if not required
Merge pull request #435 from ggonnella/fix_readjoiner

do not output cji/cjo/jnc if not required