CHANGELOG

CHANGELOG
v1.1.1:
Bugfix: SNPs VCF file wasn't being preserved.  This fixes that issue.  

v1.1.0: 
Bugfixes:
    Add testConfig.csv file, which was accidentally omitted in the 1.0.0 release
    Fix bug with depth plots where zero-depth positions could accidentally be labeled as having non-zero depth
    Fix crashes from running samples that produce no DCS data
    Change the default recovery script to avoid synlinks
New Features: 
    Additional output options for the bamToCountmuts program
        Allow summing total and genes by gene or by block
        Allow outputting all, overall + genes, overall + blocks, or just overall
    Add VERSION file, and specify pipeline version in the report output.
    Get mutation counts from the VCF file, instead of directly from the BAM file
    Add ability to set maximum number of cores to use during setup.
Internal changes:
    Simplify bed file column naming in depth plotting script
    Separate mutanal steps into different snakemake rules
    General code cleanup
    
V1.0.0:
New release of the Duplex Sequencing Bioinformatics Pipeline, based on Snakemake instead of Bash.