## [4.7] - 2021-08-23

## Added
- Added multiqc to summarize reports
- Added tiled plot which containes PCA,RPCA,RPCAscore and Pearson plots
- Added RPCAScore (RPKM based) plots in addtion to RPCA (RPKM based)

## Updated
- removed deprecated code that incorrectly identified R1, R2 reads 
 
## [4.6] - 2021-07-14

### Added
- Added RPCA plots in addition to PCA and TSNE
- Added additional report (step 14) about FASTQ headers
- Added experiment number for SEGEX output (step 14)

### Changed
- changed FPKM to TPM for SEGEX output (step 14)


## [4.5.1] - 2021-06-04

### Updated
- for SEGEX output files for values less than 1e-300 automatically set 0
- added FPKM for SEGEX output names
- for Fam205_GL name was reduced to 18 characters
- fixing SVD behavior after refactoring
- Updated TACO documentation
- added info about FC and FDR for Venn diagrams


## [4.5] - 2021-04-23

### Added
- option KEEP_BAM_AFTER_RUN which allows user to keep/delete BAM
  files after pipeline execution (BAMs are required only for steps 06,
  08,10,11)
- TSNE plots in the same way as PCA/correlation plots

### Changed
- set intersection for non-significant and union for significant merged
  outputs (PCA/TSNE/Correlation). Output file names represent info
  about intersection/union
- running StringTie / TACO / TACOREFCOMP conveyer with/without
  reference GTF file:
  -- two sets of output tracks with RefOn/RefOff suffixes
  -- bigBed file names and corresponding UCSC captions represent
     RefOn/RefOff suffixes

### Multiple minor changes:
 - Reformatting / combining / renaming output pdfs for steps 12-14


## [4.4.1] - 2021-04-06

### Updated
- updated 10_TACO step, added taco_refcomp script to conduct
  comparisons between reference GTF and combined by groups GTFs. Added
  new variables to the 00/Setup_Pipeline.conf which allow user to
  change behavior of this step.
- added notes to 00/Sample_Labels.txt with preferable colors for UCSC
  browser

## [4.4] - 2021-03-31

### Added
- added step 10_TACO, which allows the pipeline to calculate isoforms
  for different groups and represent them as tracks for UCSC browser.
  Please read README.txt in 10_TACO for details.

### Changed
- Step 11 do not need anymore run Combined.qsub script to check if
  combined files exist. This checking moved to Run_Jobs.sh

## [4.3] - 2021-03-24

### Changed
- fixed README.txt
- refactored step 13 (PCA/correlation plots)
  for plots with multiple comparisons set intersection of genes
  instead of union
- added Combined track which contains all combined tracks
- added file consistency check for Venn config and Comparisons config,
  throws an error if not consistent
- added log.txt in 00 directory which contained whole stdout/stderr
  output
- added XS tag for STAR output
- fixed option which allows overwrite CRAM file for owner

## [4.2] - 2021-03-17

### Added
- support of commentaries in config files using # character
- ACL rw permissions
- new documentation in README.txt

### Changed
- default directory for FASTQC now is PROJECT_DIR
- pipeline inform if user try to rewrite existed bw/cram file without
  permissions
- improved error messages if format of config file is not correct

## [4.1] - 2021-03-10

### Added
- script make_cleanup.sh for removing BAM files
- script make_archive.sh for making archive of Scripts directory
- support of index files which contain information about project and
  fastq files for each sample (users can provide their own files and
  place them in 00 directory. The file name should have name ended
  with '*index.csv' suffix)
- option START for ./02_Run_Pipeline.sh which allows to reuse
  precalculated results
- automatic creation of sample directories

### Changed
- by default all samples temporary files will be located in SAMPLES
  subdirectory
- Sample_DIR column was removed from Sample_Labels.txt file
- default directory for all new bigwig files is
  waxmanlabvm.bu.edu/TRACKS/INDEXED_PROJECTS/PROJECT_NAME/
- CRAM files will be created on mapping step (Step 04)
- fixing small bugs in all steps

