v0.11 de novo Release

This is a major release with changes affecting Whippet's indexing capabilities. This branch enables a user to supplement standard-annotation files with more sources of splice-sites for Whippet to utilize when indexing/building CSG nodes. These changes allow Whippet to produce more comprehensive CSGs in poorly annotated species, utilizing unannotated splice-sites (and therefore also unannotated exons) from read alignments in a pre-existing BAM file created by another program with novel spliced-read alignment abilities.

Specific changes are:

• Unannotated splice site support:
  • Sorted/indexed BAM files may now be supplied using the --bam parameter (whippet-index.jl)
  • Splice sites are extracted from BAM file in strand-specific manner. (refset.jl)
  • By default at least one splice-site in each spliced read must match a splice site from the annotation set: turn off this requirement with --bam-both-novel flag.
• CSG building improvements, which now utilizes both the annotated and unannotated splice sites from BAM. (graph.jl)
  • New nodes (can be either AA/AD/CE) can be built within sequence annotated as intronic for regions on the "match operation" side of each spliced-read. eg. upstream of novel 5' splice site, and regions downstream of novel 3' splice sites from spliced-alignments.
• Documentation README.md changes to guide building of indexes with --bam parameter.
• Alignment and CSG building bugfixes:
  • No short overhangs past ->LS/SR<- edges.
  • SAM output always matches inferred strand from CSGA regardless of sequence orientation.
  • Splice-sites always override internal TxStart/TxEnd in CSG-building
• Deprecated: refflat format no longer supported--refflat flag (whippet-index.jl).
• New warnings for GTF files whose sequence names aren't found in the fasta file.
• New output: an .exons.gz file from whippet-index.jl that maps all putative exons in the Whippet index to the corresponding Whippet nodes and their annotation status.