Update readme.md

readme.md

@@ -1,8 +1,8 @@
 [1 Image patch extraction](#1-image-patch-extraction)  
-[1.3 Retreiving wall-clock time statistics for extraction and grouping](#1.3-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)  
 [2 Prediction](#2-prediction)  
 [3 Heatmap stitching](#3-heatmap-stitching)  
 [4 Retreiving run-time statistics for prediction](#4-Retreiving-run-time-statistics-for-prediction)  
+[5 Retreiving wall-clock time statistics for extraction and grouping](#5-Retreiving-wall-clock-time-statistics-for-extraction-and-grouping)  
 
 
 # 1 Image patch extraction
@@ -21,13 +21,6 @@
 
 The lookup tables are created only once and used at [Prediction](#2-prediction) stage for launching array job tasks. These tasks are run in parallel and scalable manner - if there are not enough resourcs for running all tasks then they are queued up automatically and started as resources become available. Each task processes only one group. 
 
-## 1.3 Retreiving wall-clock time statistics for extraction and grouping
-Run *time_stats_sg_V2.sh* Linux scrip with two arguments: a) type of slides (test, normal or tumor) and b) the root directory of the results:
-- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR  
-
-An example run:  
-- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440  
-
 # 2 Prediction
 - Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
 - Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
@@ -60,4 +53,10 @@ In *wall_clock_time_stats_pred.sh* file adjust job results root directory, DIR a
 Then run:  
 - time bash ./wall_clock_time_stats_pred.sh  
 
+# 5 Retreiving wall-clock time statistics for extraction and grouping
+Run *time_stats_sg_V2.sh* Linux scrip with two arguments: a) type of slides (test, normal or tumor) and b) the root directory of the results:
+- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR  
+
+An example run:  
+- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440