add qsignature feature

add qsignature to standard pipeline

add qsignatures functions

add downsampling
Provide Delly specific filtering on paired end and split read evidence. Prepare Delly specific exclude file
Move datadict lookups, set globals instead of using a class.

It is safe to do this with globals. locals has this warning in the
python docs:

'The contents of this dictionary should not be modified; changes
may not affect the values of local and free variables.'
globals does not have the same warning so it should be safe to modify
Add dexseq_gff, rRNA and the refFlat file to the genome resources.
Run dexseq from a bcbio-dict with unit test.
Fix for new downsample function signature.
Remove skip of dexseq unit test cleanup.
Add optional global defaults to the datadict.
Add DEXseq to rnaseq pipeline.
Expose algorithm keys we avoid processing on to use from bcbio_vm data preparation code
Add support for fastqc 0.11+ with combined single HTML file output (Fixes chapmanb/bcbio-nextgen#512)
fix qsignature function at second step

add qsignature_summary as multitask step

add qsignature file to datadict

add xml.tree parser for qsignature

add chromosome selection to reduce file

remove qsignature as option

add qsignature file to datadict

add slice option to select chr22

add qsignature resources
Extra annotations to transcriptome-assembly.

1) use the main reference as a scaffold for newly assembled transcripts,
this keeps known gene_ids and transcript_ids and places novel transcripts
of a known gene_id on the known gene_id
2) broadly classify as lincRNA, ncRNA and protein_coding by training
a logistic model to classify non_coding and coding transcripts in
the known reference.
3) remove some Cufflinks specific garbage transcripts such as single exon
novel genes
Updated with work over the last month.
Throw error if fastq1 == fastq2 in the configuration file.
Remove cpat requirement until conda install has chance to propagate (heads up @roryk). Utility function to retrieve data dictionary from argument list
vardict development started
Vardict integrated into bcbio-nextgen
Vardict changes to accommodate empty files containing no variants
vardict development started