<commit_before># CHANGES IN VERSION 2.8.05 (GitHub version)

## BUG FIXES
- Fix error in `mafSurvGroup` while checking for mutants in `geneSet`. Added `minMut` argument to mitigate. Issue: [741](https://github.com/PoisonAlien/maftools/issues/741)

## ENHANCEMENTS
- Fix the order of features and added colors for the lines in `forestPlot`. Thanks @biosunsci PR: [761](https://github.com/PoisonAlien/maftools/issues/761)
- Added `pwLineCol` and `pwLineWd` for controlling the line color and line width around the pathways in `oncoplot`. Issue: [759](https://github.com/PoisonAlien/maftools/issues/759)
- Added `ORthr` and `featureLvls` arguments to `plotEnrichmentResults`. Issue: [715](https://github.com/PoisonAlien/maftools/issues/715)
- Added `pseudoCount`argument to `MafCompare` for avoiding Inf values in estimated OR. Issue:  [718](https://github.com/PoisonAlien/maftools/issues/718)
- Added `compress`argument to `write.mafSummary` and now the output includes clinical data as well. Issue:  [720](https://github.com/PoisonAlien/maftools/issues/720)

# CHANGES IN VERSION 2.8.0 (Bioconductor release version)

## NEW FUNCTIONS
- `cancerhotspots` Genotype known cancer hotspots from the tumor BAM file
- `bamreadcounts` extract nucleotide counts for targeted variants from the BAM file.
- `maftools` now natively loads TCGA cohorts. `tcgaAvailable` and `tcgaLoad` will display and load the desired cohorts.<commit_msg>update BC version<commit_after># CHANGES IN VERSION 2.8.05

## BUG FIXES
- Fix error in `mafSurvGroup` while checking for mutants in `geneSet`. Added `minMut` argument to mitigate. Issue: [741](https://github.com/PoisonAlien/maftools/issues/741)

## ENHANCEMENTS
- Fix the order of features and added colors for the lines in `forestPlot`. Thanks @biosunsci PR: [761](https://github.com/PoisonAlien/maftools/issues/761)
- Added `pwLineCol` and `pwLineWd` for controlling the line color and line width around the pathways in `oncoplot`. Issue: [759](https://github.com/PoisonAlien/maftools/issues/759)
- Added `ORthr` and `featureLvls` arguments to `plotEnrichmentResults`. Issue: [715](https://github.com/PoisonAlien/maftools/issues/715)
- Added `pseudoCount`argument to `MafCompare` for avoiding Inf values in estimated OR. Issue:  [718](https://github.com/PoisonAlien/maftools/issues/718)
- Added `compress`argument to `write.mafSummary` and now the output includes clinical data as well. Issue:  [720](https://github.com/PoisonAlien/maftools/issues/720)

# CHANGES IN VERSION 2.8.0

## NEW FUNCTIONS
- `cancerhotspots` Genotype known cancer hotspots from the tumor BAM file
- `bamreadcounts` extract nucleotide counts for targeted variants from the BAM file.
- `maftools` now natively loads TCGA cohorts. `tcgaAvailable` and `tcgaLoad` will display and load the desired cohorts.
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