Compatibility for Julia v1.6 bugfixes

This release is compatible with Julia v1.6 (which is a candidate for the next long-term release), but may not work on previous versions of julia. For previous versions use an earlier Whippet release.

Bugfixes for Whippet v1.5.1

Minor bugfixes for Whippet on Julia v1.5.3--

Compatibility for Julia v1.5.3

These updates provide compatibility for Whippet v1.5 on Julia 1.5.3

Compatibility for Julia v1.0 to v1.3

These updates provide compatibility for Whippet v1.0 on Julia 1.1+

v0.11.1 Bugfix

Minor bugfix release for re-buffering empty lines returned by readline function in BufferedStreams.jl v0.4.1 which caused whippet-delta.jl to prematurely terminate when comparing only two samples (though multi-sample comparisons still worked as expected).

This PR increases buffer size beyond expected .psi.gz filesize as a solution for Julia v0.6 and adds additional assertion sanity checks. Note: This bug is already fixed in BufferedStreams.jl v1.0.0, so once the Whippet.jl v1.0.0 update for Julia v1.0 is ready this will be a non-issue.

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.

v0.10.4 Length term bugfix

This release fixes:

• a length error, improving the accuracy of: TPM values, K2+ PSI values, and Tandem UTR values.
• added GTF file sanity checks, that throw errors or warnings as necessary.
• improves test coverage by removing deprecated code

v0.10.3 TE Bugfix Release

This release fixes a few bugs:

1. 0.9+ Bugfix for --sam flag output
2. Removal of an extra dummy psi line before the first node of a TE event.
3. Tandem UTR path length bugfix to produce more stable quantifications.

v0.10.2 Over-enumeration Bugfix

Some very deep-datasets 100M+ (with overlapping chained AS events) and certain indices can over enumerate, causing a hang at the MLE stage. This PR uses down-sampling to enforce an upper bound to path enumeration.

v0.10.1 Minor bugfix version

This is a minor bugfix release for the --circ flag.
It also adds a mouse gencode gtf file to the anno/ directory for convenience.
Add version bounds to StatsBase to avoid unwanted deprecation warnings.