0.3.0: Improved data generation, metrics bug fix

* This commit updates the blastdbcmd to use the -outfmt
  flag which outputs only the fields of interest and doesn't
  require any FASTA parsing
* This commit also fixes a bug in the calculation of
  sensitivity and specificity

CMakeLists.txt

@@ -1,8 +1,8 @@
 cmake_minimum_required(VERSION 2.6)
 project(chipper)
 set (CHIPPER_VERSION_MAJOR 0)
-set (CHIPPER_VERSION_MINOR 2)
-set (CHIPPER_VERSION_PATCH 1)
+set (CHIPPER_VERSION_MINOR 3)
+set (CHIPPER_VERSION_PATCH 0)
 set (CHIPPER_VERSION "${CHIPPER_VERSION_MAJOR}.${CHIPPER_VERSION_MINOR}.${CHIPPER_VERSION_PATCH}")
 enable_testing()
 

README.md

@@ -303,8 +303,8 @@ Chipper compares favorably against other proteasomal cleavage detection systems.
 |[FragPredict](http://www.mpiib-berlin.mpg.de/MAPPP/fragpredict.html) | 72.1 | 41.4 | 0.12 |
 |[NetChop](http://www.cbs.dtu.dk/services/NetChop/) 1.0 |34.4 |91.4 |0.31 |
 |[NetChop](http://www.cbs.dtu.dk/services/NetChop/) 2.0 |57.4 |76.4 |0.32 |
-|chipper (LR) | **77.6** | **84.8** | **0.620** |
-|chipper (SVC) | **78.2** | **79.0** | **0.572** |
+|chipper (LR) | **87.0** | **74.5** | **0.620** |
+|chipper (SVC) | **79.3** | **77.9** | **0.572** |
 
 The SVC model uses a linear kernel which makes interpreting the effect of the hydrophobic, steric, and electronic properties possible, while the performance of the logistic regression model has better specificity.