CHANGES IN VERSION 1.4.0 ------------------------ o Added importTranscripts() for importing annotation from GFF format o Added plotCoverage() for visualization of per-base read coverage and junction read counts o Added predictVariantEffects() for predicting the effect of splice variants on annotated protein-coding transcripts o findSGVariants() is now able to deal with more complex gene models o SGVariants columns closed5p and closed3p now refer to individual splice variants rather than the splice event they belong to o Bug fixes and other improvements CHANGES IN VERSION 1.2.0 ------------------------ o Renamed class TxVariants to SGVariants o Renamed class TxVariantCounts to SGVariantCounts o Renamed findTxVariants() to findSGVariants() o Renamed getTxVariantCounts() to getSGVariantCounts() o Parallelization is now controlled with a single cores argument o Argument max_complexity for predictTxFeatures() controls skipping of problematic regions o getBamInfo() is no longer run as part of analyzeFeatures() o getSGVariantCounts() now supports obtaining counts from BAM files o Bug fixes and other improvements