Version Release History
=======================

Version 2.3 - May 19, 2023
--------------------------

    
    * BAM QC: include support in region text report
    * Allow 3-column BED file parsing (suggested by Alex Peltzer)
    * BAM QC: report secondary alignments and ignore them from main coverage analysis (reported by Sonia Agrawal)
    * BAM QC: fix Ns collection from RNA-seq alignment (reported by C. Ruckert)
    * BAM QC: fix counts of supplementary alignemnts (reporeted by Alexander Seitz)    
    * Adjust Qualimap non-zero code return (implemented by Valentin Krasontovitsch)
    * BAM QC: fix issue with plotting from OpenJDK (reported by Adrian Garcia Moreno)
    * RNA-seq QC: fix error reports for missing chromosomes
    * Multi BAM QC: fix OpenJDK issue (reported by Marcel Kucharik and Michal Lichvar)
    * BAM QC: fix reverse strand specificity issue (reported by Florian Pflug)
    * BAM QC: add coverage std to text report
    * RNA-seq QC: add settings control for 5'-3' bias comptuation (suggestion from Ryoji Amamoto)
    * BAM QC: allow set maxium coverage size in zoom-in histogram
    * BAM QC: add option to control maximum duplication rate in the plot (suggestion from Xiao Lei)
    * CountsQC: Added header detection ( implemented by Viktor Horvath)
    * BAM QC: add hg38 for GC content inspection


Version 2.2.1 - October 3, 2016
-------------------------------

    * BAM QC: fixed issue with paired-end reads only singletons (reported by Anrold Liao)
    * BAM QC: adapted novel SAM flag for multiple alignment segments ( reported by Alexis Groppi)
    * BAM QC: fixed issue with mapping quality report inside regions (reported by Teresa Requena)
    * BAM QC: added support for counting Ns in read alignments
    * BAM QC: fixed issue with chromosome limit in coverage plot
    * RNA-seq QC: strand-specificity is estimated in case default non-strand-specific protocol stated in the settings  
    * RNA-seq QC: fixed problem with incorrect BAM records    
    * RNA-seq QC: number of correctly marked reads without proper pair reported in a single warning
    * Allowed names with spaces in provided file/folder path for analysis
    * Multi-BAM QC: include strand specificity option for estimation of valid strand reads in each BAM QC report


Version 2.2 - January 29, 2016
------------------------------

    * BAM QC: added a novel option to control the skipping of duplicate alignments (reported by Patrik Smeds and Vlad Saveliev ) The default mode was switched to marked duplicates only.
    * BAM QC: fixed issue with processing alignments (reported by Roberto Spreafico)
    * BAM QC: fixed fail when zero mapped reads inside of region (reported by Jochen Singer)
    * BAM QC: improved the number of windows output (reported by Alexander Peltzer)
    * BAM QC: integrate mm10 support to command line
    * BAM QC: fixed insert size histogram computation
    * Multisample BAM QC: implmeneted support for per sample groups/conditions
    * Multisample BAM QC: added novel statistics report and global coverage plot (suggested by Angela Heck )
    * RNA-seq QC: fixed the numbers of reads computation for paired-end reads (reported by Priyanka Jain )
    * Documentation: updates in BAM QC, Multisample BAM QC, RNA-seq QC
 

Version 2.1.3 - October 29, 2015
----------------------------------

    * Fixed a problem with removal of provided existing output folder in command line mode (reported by Nathan McNeil)
    * BAM QC: added the mm10 GC-content distribution template (suggested by Priyank Shukla )
    * BAM QC: fixed issue with report of duplication rate in regions ( thanks to Christian for report )
    * BAM QC: stabilzed default text output number format (reported by Max Koeppel and Henri-Jean Garchon )
    * Counts QC: fixed issues with single sample adaption ( reported by Yung-Chih Lai )
    * Documentation: update introudction, BAM QC, RNA-seq QC and F.A.Q. blocks
 

Version 2.1.2 - September 23, 2015
----------------------------------

    * BAM QC: added an option to analyze overlapping paired-end read alignments (suggested by Eva Koenig) 
    * BAM QC: fixed processing of incorrect alignments (reported by Alexander Peltzer)
    * BAM QC: improved paired reads statistics description (suggested by Jochen Singer)
    * RNA-seq QC: fixed issue with transcript high coverage (reported by Daniel Barrel)
    * RNA-seq QC: added to statistcs number of intronic/intergenic reads overlapping exons
    * RNA-seq QC: minor fix of coverage plot 
    * Counts QC: fixed an issue due to update of NOISeq package 
    * Multisample BAM QC: corrected labels in coverage and GC-content plots (reported by Franziska Singer) 
    * Multisample BAM QC: fixed issue with min X-value in insert size plots (reported by Roland Schmucki) 
    * Improved PDF format output
    * Documentation: update BAM QC, RNA-seq QC descriptions
 

Version 2.1.1 - June 15, 2015 
-----------------------------

    * BAM QC: added chromosome names when drawing chromosome limits
    * BAM QC: fixed fail when no mapped reads; add warning
    * BAM QC: fixed computing coverage standard deviation (reported by Charlotte Peeters)
    * BAM QC: by default duplicates (secondary alignments) are skipped if marked
    * BAM QC: added report for "OutOfMemory" error
    * RNA-seq QC: added support for computing number of read pairs
    * Counts QC: fix fail when sample name starts from number (reported by Alena Dobiasova)
    * Documentation: updated BAM QC, RNA-seq QC
    * Documentation: added special solution regarding DISPLAY issue on Linux server (suggested by Roberto Spreafico)
    

Version 2.1 - March 19, 2015 
----------------------------

    * BAM QC: added percentage of mapped reads with at least one insertion or deletion
    * BAM QC: added an option to skip duplicates when running analysis (suggested by Johan Dalberg)
    * RNA-seq QC: add text report of results (suggested by Lorena Pantano)
    * BAM QC: fixed issue with inRegionReferenceSize outside of regions (reported by Tristan Carland)
    * comp-counts: fixed bug when output file path is wrong (reported by Stephane Plaisance)
    * RNA-seq QC: fixed issue with no-sorting required, improved statistics and input description (thanks to Priyanka Jain for report)
    * RNA-seq QC: fixed issue when num reads equals zero 
    * RNA-seq QC: improved logging (implemented by Lorena Pantano)
    * Feature reader: improved exception processing
    * Fixed an issue with output folder when outformat is PDF
 

Version 2.0.2 - February 10, 2015 
---------------------------------
        
    * Compute counts: fixed issue with GTF file analysis and added support for single-end reads strand specificity (thanks to Roberto Spreafico for reports)
    * BAM QC: added support of mismatches and indels in the text report (thanks to Nils for report)
    * RNA-seq QC: fixed issue with loading GTF files with strange names (thanks to Haroon Kalam for report)
    * RNA-seq QC: fixed crash when there are no junctions detected (thanks to François Lefebvre and Larry Willhelm for reports) 
    * Multi-BamQC: fixed issue with max coverage of BAM file supported


Version 2.0.1 - Januar 6, 2015 
------------------------------
        
    * BAM QC: fixed problem with nucleotide content (thanks to Travis Collier)
    * RNA-seq QC: fixed issue with chromosomes
    * RNA-seq QC: add support for paired-end reads
    * countsQC: fixed bug when population less than sample size
    * Fixed issue with default outdir name


Version 2.0 - August 27, 2014
-----------------------------

    * New mode: multi-sample BAM QC
    * Counts QC: completely redesigned, add support for multi-sample input
    * RNA-seq QC: add new plots (coverage across genebody, reads genomic origin, junction analysis)
    * Command line interface improved
    * BAM QC: changed order of plots
    * BAM QC: fix insert size overflow
    * BAM QC: add insert size info to plain text report
    * BAM QC: fix bug with stats inside of regions
    * BAM QC: performance improved for long genomes
    * RNA-seq QC: fix default protocol 
    * Add utility script to create species annotations for Counts QC
    * Add condtion to exit on error in main script (suggestion from Johan Dahlberg)
    * Fix coverage quota in plain text report (bugfix from John Budde)
    * Major documentation update

A number of renamings in command line interface were introduced.

common:
    -rscriptpath => -R or --rscriptpath
bamqc:
    -outcov => -oc or --output-genome-coverage
rnaseq:
    -counts => -oc
    -algorithm => -a or --algorithm
    -protocol => -p or --sequencing-protocol
comp-counts
    -sorted => -s or --sorted
    -paired => -pe or --paired
    -algorithm => -a or --algorithm
    -protocol => -p or --sequencing-protocol


Version 1.0 - May 29, 2014
--------------------------

    * BAM QC: add computation of mismatches and error rate
    * BAM QC: add new metrics for insert size
    * BAM QC: contig coverage added to text report (patch from Johan Dahlberg)
    * BAM QC: add option to output per-base coverage
    * Compute counts: add full support for paired-end reads
    * RNA-seq QC: add new plots and statistics
    * Updated documentation


Version 0.8.1 - May 5, 2014 
---------------------------
        
    * Fixed bug with CountsQC and R version 3
    * Fixed bug with double reference size computation

Version 0.8 - March 5, 2014 
------------------------------
        
    * Added new analysis mode "RNA-seq QC"
    * Added PDF output path
    * Fixed bug with R-version recognition
    * Fixed bug with per-chromosome standard deviation calculation
    * Fixed integer overflow in number of reads
    * Fixed crash with insert size 
    * Fixed bug with empty SAMRecord

Version 0.7.1 - April 19, 2013 
------------------------------
        
    * Fixed bug with "Coverage Across Reference" plot
    * Fixed bug in BAM QC when regions don't have any coverage 


Version 0.7 - April 10, 2013 
----------------------------

    * Fixed bug in per chromosome coverage report (https://groups.google.com/d/msg/qualimap/AO_6111Gg1E/21SdvEWeAfUJ)
    * Deletions are now properly computed when calculating coverage
    * Fixed bug in renaming of tabs
    * Added global parameter to set Rscript path 
    * Minor fixes in command line tools argument parsing
    * Improved handling of discordant regions between the BED/GFF and BAM files in BAM QC
    * Updated documentation 

Version 0.6 - October 30, 2012 
--------------------------

    * Fixed bug with small homopolymer indels estimation 
    * Fixed bug with EQ and X SAM format tags in BAM QC
    * BAM QC: added option to set minimum homopolymer size
    * BAM QC: added option to open SAM files along with BAM files from GUI

Version 0.5 - July 25, 2012 
--------------------------

    * BED format is now supported throughout application 
    * Raw data from BAM QC and Counts QC plots can be exported
    * BAM QC: Added homopolymer indels estimation
    * BAM QC: Added strand specificity calculation
    * BAM QC: Added clipping profile and number of clipped reads statistics 
    * Compute counts: Added 5' to 3' prime bias calculation 
    * Allow to set java memory size from launching script 
    * Fixed problem with upperCoverageBound in Coverage Across Reference chart 
    * Fixed issue with insert size limits 
    * Added missing qualimap.bat to launch application on MS Windows

Version 0.4 - June 4, 2012 
--------------------------

    * Fixed problem with chromsome limits in Insert Size chart
    * Fixed issue with "compute counts" when regions are having several 
    intersecting reads
    * Fixed crash with Coverage Histogram 0-50X for high coverage samples
    * Fixed Coverage Histogram when minimal coverage is more than zero
    * Fixed issue with GFF files, containing empty lines  


Version 0.3 - May 18,2012
-------------------------

    First public release.


