FishingCNV Files

===================IMPORTANT INFORMATION=====================

FishingCNV comes in two different releases:
- GUI version (FishingCNV_X.X.X.zip)
- Commandline version (FishingCNV_X.X_Pipeline.tar)


=======Recent release notes for commandline version =========

fishingCNV_2.1_pipeline (2013-10-24):

    - Significant improvement in performance
    - Simplified output, all chromosome plots combined into 
      one file
    - RPKM files halved in size, no more duplicates
    - Added new plots to PDF output
    - The Rsript now takes flag parameters for:
         * Minimum segmentation size (between 2-5)
         * Whether PCA is to be performed
         * If PCA, number of PCs to remove (default 2)
         * Whether to double data for single exon CNV detection
    - Whole exome analyzed at once, no splitting and no 
      generation of temporary files
    - Improved error handling 

fishingCNV_2.0_pipeline (2013-10-18):

    - Significant improvement to the file manipulation code
         * Java program now takes clearly defined flags
         * Improved user interface
         * Improved error handling and logging
         * Combined all relevant file manipulation code
    - Rscript improvement for speed and usability
    - Decoupled file manipulateion code (Java) from statistical
      analysis (Rscript) to reduce linking errors
         * Now you call them separately

=======Recent release notes for GUI version =================

**Note: major improvements pending, to implement new code
from commandline version.

FishingCNV_1.5.2 (2013-07-10): 

    - Fixed some rounding errors -- some integer divisions 
      were changed to floating point divisions

FishingCNV_1.5.2:

    - Multiple file selections are now supported in the Browse function

FishingCNV_1.5.1:

    - Added a new feature under the RPKM tab to convert 
      "coverage.sample_interval_summary" files to RPKM
    - A bug is fixed to allow for different annotations of 
      chromosomes in .bed files
        * now it accepts both "1" and "chr1"

FishingCNV_1.5:

    - Major updates to the program:
        * GATK is bundled into the program so that RPKM files can be generated directly from BAM files
        * Fixed a data-dependent bug in the PCA analysis. Now it will catch all the errors and proceed accordingly.

FishingCNV_1.3:

    - PCA plots are now included in the output