====================================================================
`7MMF'   `7MF'                 db MMP""MM""YMM   db       .M"""bgd
  `MA     ,V                      P'   MM   `7  ;MM:     ,MI    "Y
   VM:   ,V ,6"Yb.  `7Mb,od8 `7MM      MM      ,V^MM.    `MMb.
    MM.  M'8)   MM    MM' "'   MM      MM     ,M  `MM      `YMMNq.
    `MM A'  ,pm9MM    MM       MM      MM     AbmmmqMA   .     `MM
     :MM;  8M   MM    MM       MM      MM    A'     VML  Mb     dM
      VF   `Moo9^Yo..JMML.   .JMML.  .JMML..AMA.   .AMMA.P"Ybmmd"
====================================================================

TODO/ WISHLIST:
- Add more verification for BED file input
- Remove paired percent chart if data is not paired
- Add voting table to report
- Sample IDs with a dash in the name do not work (possibly multiple dashes)

VariTAS 	(2020-11-03)					                        v0.0.2
--------------------------------------------------------------
- Removed names from vignettes

VariTAS 	(2020-08-03)					                        v0.0.2
--------------------------------------------------------------
- Added recommended -B parameter to mpileups for Varscan
- Vardict now filters out germline variants with an awk command
- VarScan now filters out germline variants with an awk command
- read.yaml function now exported
- Added strand bias filtering to MuTect
- Strand bias filtering for MuTect only happens with paired-end data
- Added gnomAD to ANNOVAR databases
- Removed -d parameter from LoFreq without germline samples (it does nothing)
- Added filter that removes duplicated variants from LoFreq output
- Temporarily removed -s and -S parameters from LoFreq (mem limit)
- LoFreq now runs lofreq viterbi on illumina data
- Fixed encoding issue in process.total.coverage.statistics.R in strict latin1 locale

VariTAS 	(2020-02-07)					                        v0.0.1
--------------------------------------------------------------
- Revisions for CRAN submission

VariTAS 	(2019-11-05)					                        v0.8.1
--------------------------------------------------------------
- LoFreq should now call indels
- Added dbSNP filtering to LoFreq
- Added -s (source quality) parameter to LoFreq, should increase accuracy
- Added extra margin to output plots for longer sample names

VariTAS 	(2019-05-06)					                        v0.8.0
--------------------------------------------------------------
- Upgraded to GATK4 throughout pipeline
- targetQC step interacts better with job dependencies
- Fixed text at bottom of report
- Charts now sorted by coverage
- Added more CPUs to VarDict commands
- MuTect and VarDict should run on ontarget.bam rather than source bam (hybrid)
- Fix flagstat with paired normal data
- Fix "empty" normal samples appearing in report

VariTAS 	(2019-03-11)					                        v0.7.3
--------------------------------------------------------------
- Fancy new logo
- Fixed coverage report bugs
- Fixed median coverage plot and adjusted all plot margins
- GATK commands updated to work with GATK4

VariTAS 	(2019-03-01)					                        v0.7.2
--------------------------------------------------------------
- Bugfixes for LoFreq and VarScan
- New helper functions to post-process LoFreq and VarScan output
- New WIP vignette: What Does This Error Mean? to help with learning how to use VariTAS

VariTAS 	(2019-02-07)					                        v0.7.1
--------------------------------------------------------------
- Added support for LoFreq and VarScan, two matched-normal variant callers

VariTAS 	(2018-12-11)					                        v0.7.0
--------------------------------------------------------------
- Rebranded as VariTAS
- New style for plotting coverage by amplicon
- Added requirement for gene/feature ID in panel file
- Improved compatibility for GRCh38

BCN.AmpliSeq.utilities 	(2018-11-14)					          v0.6.3
--------------------------------------------------------------
- Retooled vignettes, now there is only one
- Moved example files to inst/extdata
- Bugfixes for HPC cross-compatibility


BCN.AmpliSeq.utilities 	(2018-11-09)					          v0.6.2
--------------------------------------------------------------
- New function run.all.scripts to handle running the pipeline on a non-HPC system
- Small changes to other scripts to accomodate this
- Added vignette of examples


BCN.AmpliSeq.utilities 	(2018-11-06)					          v0.6.1
--------------------------------------------------------------
- Updated vignette and description details
- Minor bugfix in read.variant.calls
- Added read.yaml to helper.functions to remove lab utils package dependency


BCN.AmpliSeq.utilities 	(2018-10-30)					          v0.6.0
--------------------------------------------------------------
- Added support for single-sample runs in post-processing scripts
- Added config option for different HPC systems (LSF [bsub], PBS [qsub], or none)


BCN.AmpliSeq.utilities 	(2018-08-21)					          v0.5.1
--------------------------------------------------------------
- removed BCN.general.utilities dependency by copying over date.stamp.file.name


BCN.AmpliSeq.utilities 	(2018-08-17)					          v0.5.0
--------------------------------------------------------------
- removed plotting lib dependency


BCN.AmpliSeq.utilities 	(2018-05-11)					          v0.4.3
--------------------------------------------------------------
- debugging after coding standard updates
- include filters for all variant callers in variant specification in variant Excel sheet
- added mean tumour AF column


BCN.AmpliSeq.utilities 	(2018-05-10)					          v0.4.2
--------------------------------------------------------------
- module load R version in post-processing script


BCN.AmpliSeq.utilities 	(2018-04-27)					          v0.4.1
--------------------------------------------------------------
- lots of documentation/ minor code updates to comply with package standards

BCN.AmpliSeq.utilities 	(2018-04-26)					          v0.4.0
--------------------------------------------------------------
- new "mode" option for setting filters
- added support for pan-caller specification of variant filters through the "default" filter

BCN.AmpliSeq.utilities 	(2018-04-24)					          v0.3.4
--------------------------------------------------------------
- added remove_exac filter to remove all ExAC variants at AF>0.01
- new get.gene function to guess gene from panel


BCN.AmpliSeq.utilities 	(2018-04-23)					          v0.3.3
--------------------------------------------------------------
- bugfixes in run.target.qc function
- get.bed.chromosomes: remove header lines starting with "track"
- bugfixed vignette


BCN.AmpliSeq.utilities 	(2018-03-08)					          v0.3.2
--------------------------------------------------------------
- bugfixes to accommodate purely numeric sample IDs


BCN.AmpliSeq.utilities 	(2018-03-08)					          v0.3.1
--------------------------------------------------------------
- added option for email notification when pipeline finishes
- bugfixed reading of MiniSeq sample sheet
- new MiniSeq section in vignette


BCN.AmpliSeq.utilities 	(2018-03-01)					          v0.3.0
--------------------------------------------------------------
- moved all version numbers to config
- restructured output to only send PDF report to collaborators
  by default


BCN.AmpliSeq.utilities 	(2018-02-22)					          v0.2.6
--------------------------------------------------------------
- added plot of median coverage by amplicon


BCN.AmpliSeq.utilities 	(2018-02-20)					          v0.2.5
--------------------------------------------------------------
- more plots, and tweaks to existing ones


BCN.AmpliSeq.utilities 	(2018-02-19)					          v0.2.4
--------------------------------------------------------------
- removed X11 dependency of PDF report


BCN.AmpliSeq.utilities 	(2018-02-16)					          v0.2.3
--------------------------------------------------------------
- incorporated PDF report


BCN.AmpliSeq.utilities 	(2018-01-29)					          v0.2.2
--------------------------------------------------------------
- added per sample scatterplots of coverage per amplicon


BCN.AmpliSeq.utilities 	(2018-01-25)					          v0.2.1
--------------------------------------------------------------
- added prepare.miniseq.specifications to get sample IDs from MiniSeq sample sheet


BCN.AmpliSeq.utilities 	(2018-01-16)					          v0.2.0
--------------------------------------------------------------
- added run.name argument to accommodate simultaneous running
  of different datasets with the same sample IDs
- new diagnostic plot showing proportion of paired reads


BCN.AmpliSeq.utilities 	(2018-01-15)					          v0.1.8
--------------------------------------------------------------
- fixed paired-end reads bug


BCN.AmpliSeq.utilities 	(2017-12-14)					          v0.1.7
--------------------------------------------------------------
- bug fix to accommodate wider range of MiniSeq sample IDs


BCN.AmpliSeq.utilities 	(2017-11-29)					          v0.1.6
--------------------------------------------------------------
- added variant recurrence plots
- changed ontarget percent and mean coverage scatterplots to barplots
- fixed a few bugs


BCN.AmpliSeq.utilities 	(2017-11-29)					          v0.1.5
--------------------------------------------------------------
- more bug fixes
- efforts to accommodate isis variant calls


BCN.AmpliSeq.utilities 	(2017-11-28)					          v0.1.4
--------------------------------------------------------------
- bug fixes
- added isis-specific variant annotation script that does not remove biallelic variants


BCN.AmpliSeq.utilities 	(2017-11-24)					          v0.1.3
--------------------------------------------------------------
- bug fixes and other incremental improvements
- implemented isis filters
- added coverage by sample plots
- added sleep option to post.processing step


BCN.AmpliSeq.utilities 	(2017-11-23)					          v0.1.2
--------------------------------------------------------------
- more bug fixes
- updates to variants per sample barplot to accommodate larger datasets
- incorporated target QC as a stage in main pipeline
- added run.ampliseq.pipeline.hybrid function


BCN.AmpliSeq.utilities 	(2017-11-22)					          v0.1.1
--------------------------------------------------------------
- bug fixes


BCN.AmpliSeq.utilities 	(2017-11-22)					           v0.1.0
--------------------------------------------------------------
- debuting Resources/R version of the package
