
----------------------------------------------------------
0.5.3 | Thu January 11 2018

  * new parameter to set random seed; results using the same seed should be identical
  * Contributed by Gilad Mishne: https://gist.github.com/giladmishne/5fe49bcda9b2dac1a652fc125c612832
  
----------------------------------------------------------
0.5.3 | Mon January 25 2016

  * faster graph traversal for finding repeats; 20% to 30% speedup
  * fixed missing sample name in VCF header when no variants to export
  * fixed error when providing empty BED file
  
----------------------------------------------------------
0.5.2 | Wed August 12 2015

  * new user interface for the discovery tool (scalpel-discovery)
  * new user interface for the export tool (scalpel-export)
  * new options for exporting in each mode of operation (single, somatic, denovo)
  * sample name extracted from BAM SM field
  * fisher exact score for somatic variants (via the Text-NSP-1.27 perl module)
  * multiple new filters (e.g.,LowFisherScore,LowAltCntTumor,etc.)
  * multi-sample VCF output for somatic and denovo calls
  * fix compilation issues for Mac OSX
  
----------------------------------------------------------
0.4.1 | Wed April 15 2015

  * improved core algorithm of graph traversal
  * select min number of (src-to-sink) paths covering every edge of the graph
  * process each connected component separately
  * source and sink are selected within each component (increased sensitivity)
  * parallelization of alignments analysis (for "somatic" and "denovo" modes)
  * several C++ code optimization
  * changed option --validate to --two-pass. Updated manual and usage info
  * callbacks to get child exit codes
  * better detection of .bai index files
  
----------------------------------------------------------
0.3.2 | Tue Jan 14 2015
 
  * speed up thansk to g++ compilation with -O3 optimization flag 
  * pass along pathlimit and reference arguments to sub commands
  * pass reference argument to exportVariants for VCF generation

----------------------------------------------------------
0.3.1 | Tue Nov 11 2014

  * increased specificity for somatic and denovo calls
  * call indel directly from alignment using samtools (validation mode)
  * added samtool/bcftools source to the distribution
  * added support for region analysis (e.g., 2:132465-235435)
  * use samtools faidx to extract sequences < 10Kb (faster)
  * set maximum coverage per region using --maxregcov parameter

----------------------------------------------------------
0.2.2 | Tue Aug 22 2014

  * by default delete log files (to save disk space for WGS)
  * added --log option to keep them if needed
  * fix bug when export intarget mutations

----------------------------------------------------------
0.2.1 | Fri Aug 15 2014

  * new export tool to extract mutations from DB file
  * improved speed for whole-genome studies
  * fixed DB lock file issue for NFS file system
  * added support for VCF output format

----------------------------------------------------------
0.2.1 | Wed Dec 11 2013

  * first public (beta) release
