DROP 1.4.0

• FRASER counting is done using the strand of each sample instead of the strand of the whole cohort
• FRASER results no longer contain sample annotation info
• If a subset of genes to test were provided, the FRASER results are now tidy -> one row per event with multiple columns containing all the p-values and adjusted p-values
• Sample annotation file now must always contain STRAND for all samples, including external ones

DROP 1.3.4

• fixes the FRASER version to 1.99.3 commit d6a422c to ensure reproducibility
• fixes the OUTRIDER version to 1.20.1
• fixes certain scripts affected by a snakemake update

DROP 1.3.3

Fixes a bug when compiling the aberrant splicing results.

DROP 1.3.2

Fixes issues with having only 1 internal sample. Simplifies the counting Summary html in the aberrant splicing module.

DROP 1.3.1

• small bugfix in the Aberrant Splicing Counting Summary Script when providing only 1 external sample

DROP 1.3.0

• Supports FRASER 2.0, an improved version that uses the Intron Jaccard Index as its single splice metric
• Allows to provide lists of genes to test during FDR correction in addition to the transcriptome-wide FDR across all expressed genes

DROP 1.2.4

What's Changed

• Bug Fixes in MAE
• yieldSize and dnaRnaMatchCutoff config values
  • yieldSize: allows for memory consideration in VCF and BAM file processing
  • dnaRnaMatchCutoff: sets the threshold for MAE sample matching
• Summary edits to aberrantSplicing

Full Changelog: 1.2.3...1.2.4

DROP 1.2.3

• Fix AE Export #353
• Multiple bug fixes #350, #364, #378
• Simplified QC reporting #361, #390
• Improve Reporting/Summaries #376, #384
• Match documentation and defaults in config: 45075c4

Full Changelog: 1.2.2...1.2.3

DROP 1.2.2

Fixes a bug in the aberrant expression module when external counts are not provided.

Full Changelog: 1.2.1...1.2.2

DROP 1.2.1

Full Changelog: 1.2.0...1.2.1

fix for Bioconda test

What's Changed

• Dev by @nickhsmith in #336

Full Changelog: 1.2.0...1.2.1