[Genabel-commits] r1312 - in pkg/ProbABEL: checks examples

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-08-25 21:18:44 +0200 (Sun, 25 Aug 2013)
New Revision: 1312

Added:
   pkg/ProbABEL/checks/compare_with_old.sh
   pkg/ProbABEL/checks/compare_with_old_short.sh
Removed:
   pkg/ProbABEL/examples/compare_with_old.sh
   pkg/ProbABEL/examples/compare_with_old_short.sh
Log:
Moved Maarten's compare_with_old scripts from the examples directory to the checks directory. These checks are not incorporated in the make check runs yet. I haven't verified them with the recent changes either, although I expect them to fail now that we've added the chi^2 column. 


Copied: pkg/ProbABEL/checks/compare_with_old.sh (from rev 1301, pkg/ProbABEL/examples/compare_with_old.sh)
===================================================================
--- pkg/ProbABEL/checks/compare_with_old.sh	                        (rev 0)
+++ pkg/ProbABEL/checks/compare_with_old.sh	2013-08-25 19:18:44 UTC (rev 1312)
@@ -0,0 +1,64 @@
+echo height_base_add.out.txt && diff height_base_add.out.txt  test_other/height_base_add.out.txt
+echo height_base_fv_add.out.txt && diff height_base_fv_add.out.txt  test_other/height_base_fv_add.out.txt
+echo height_allcov_add.out.txt && diff height_allcov_add.out.txt  test_other/height_allcov_add.out.txt
+echo height_allcov_fv_add.out.txt && diff height_allcov_fv_add.out.txt  test_other/height_allcov_fv_add.out.txt
+echo height_int1_add.out.txt && diff height_int1_add.out.txt  test_other/height_int1_add.out.txt
+echo height_int1_fv_add.out.txt && diff height_int1_fv_add.out.txt  test_other/height_int1_fv_add.out.txt
+echo height_robust_add.out.txt && diff height_robust_add.out.txt  test_other/height_robust_add.out.txt
+echo height_robust_fv_add.out.txt && diff height_robust_fv_add.out.txt  test_other/height_robust_fv_add.out.txt
+echo height_robust_int1_add.out.txt && diff height_robust_int1_add.out.txt  test_other/height_robust_int1_add.out.txt
+echo height_robust_int1_fv_add.out.txt && diff height_robust_int1_fv_add.out.txt  test_other/height_robust_int1_fv_add.out.txt
+echo height_ngp2_add.out.txt && diff height_ngp2_add.out.txt  test_other/height_ngp2_add.out.txt
+echo height_ngp2_fv_add.out.txt && diff height_ngp2_fv_add.out.txt  test_other/height_ngp2_fv_add.out.txt
+echo height_ngp2_domin.out.txt && diff height_ngp2_domin.out.txt  test_other/height_ngp2_domin.out.txt
+echo height_ngp2_fv_domin.out.txt && diff height_ngp2_fv_domin.out.txt  test_other/height_ngp2_fv_domin.out.txt
+echo height_ngp2_over_domin.out.txt && diff height_ngp2_over_domin.out.txt  test_other/height_ngp2_over_domin.out.txt
+echo height_ngp2_fv_over_domin.out.txt && diff height_ngp2_fv_over_domin.out.txt  test_other/height_ngp2_fv_over_domin.out.txt
+echo height_ngp2_recess.out.txt && diff height_ngp2_recess.out.txt  test_other/height_ngp2_recess.out.txt
+echo height_ngp2_fv_recess.out.txt && diff height_ngp2_fv_recess.out.txt  test_other/height_ngp2_fv_recess.out.txt
+echo height_ngp2_2df.out.txt && diff height_ngp2_2df.out.txt  test_other/height_ngp2_2df.out.txt
+echo height_ngp2_fv_2df.out.txt && diff height_ngp2_fv_2df.out.txt  test_other/height_ngp2_fv_2df.out.txt
+echo height_ngp2_allcov_add.out.txt && diff height_ngp2_allcov_add.out.txt  test_other/height_ngp2_allcov_add.out.txt
+echo height_ngp2_allcov_fv_add.out.txt && diff height_ngp2_allcov_fv_add.out.txt  test_other/height_ngp2_allcov_fv_add.out.txt
+echo height_ngp2_allcov_domin.out.txt && diff height_ngp2_allcov_domin.out.txt  test_other/height_ngp2_allcov_domin.out.txt
+echo height_ngp2_allcov_fv_domin.out.txt && diff height_ngp2_allcov_fv_domin.out.txt  test_other/height_ngp2_allcov_fv_domin.out.txt
+echo height_ngp2_allcov_over_domin.out.txt && diff height_ngp2_allcov_over_domin.out.txt  test_other/height_ngp2_allcov_over_domin.out.txt
+echo height_ngp2_allcov_fv_over_domin.out.txt && diff height_ngp2_allcov_fv_over_domin.out.txt  test_other/height_ngp2_allcov_fv_over_domin.out.txt
+echo height_ngp2_allcov_recess.out.txt && diff height_ngp2_allcov_recess.out.txt  test_other/height_ngp2_allcov_recess.out.txt
+echo height_ngp2_allcov_fv_recess.out.txt && diff height_ngp2_allcov_fv_recess.out.txt  test_other/height_ngp2_allcov_fv_recess.out.txt
+echo height_ngp2_allcov_2df.out.txt && diff height_ngp2_allcov_2df.out.txt  test_other/height_ngp2_allcov_2df.out.txt
+echo height_ngp2_allcov_fv_2df.out.txt && diff height_ngp2_allcov_fv_2df.out.txt  test_other/height_ngp2_allcov_fv_2df.out.txt
+echo height_ngp2_int1_add.out.txt && diff height_ngp2_int1_add.out.txt  test_other/height_ngp2_int1_add.out.txt
+echo height_ngp2_int1_fv_add.out.txt && diff height_ngp2_int1_fv_add.out.txt  test_other/height_ngp2_int1_fv_add.out.txt
+echo height_ngp2_int1_domin.out.txt && diff height_ngp2_int1_domin.out.txt  test_other/height_ngp2_int1_domin.out.txt
+echo height_ngp2_int1_fv_domin.out.txt && diff height_ngp2_int1_fv_domin.out.txt  test_other/height_ngp2_int1_fv_domin.out.txt
+echo height_ngp2_int1_over_domin.out.txt && diff height_ngp2_int1_over_domin.out.txt  test_other/height_ngp2_int1_over_domin.out.txt
+echo height_ngp2_int1_fv_over_domin.out.txt && diff height_ngp2_int1_fv_over_domin.out.txt  test_other/height_ngp2_int1_fv_over_domin.out.txt
+echo height_ngp2_int1_recess.out.txt && diff height_ngp2_int1_recess.out.txt  test_other/height_ngp2_int1_recess.out.txt
+echo height_ngp2_int1_fv_recess.out.txt && diff height_ngp2_int1_fv_recess.out.txt  test_other/height_ngp2_int1_fv_recess.out.txt
+echo height_ngp2_int1_2df.out.txt && diff height_ngp2_int1_2df.out.txt  test_other/height_ngp2_int1_2df.out.txt
+echo height_ngp2_int1_fv_2df.out.txt && diff height_ngp2_int1_fv_2df.out.txt  test_other/height_ngp2_int1_fv_2df.out.txt
+echo height_ngp2_robust_add.out.txt && diff height_ngp2_robust_add.out.txt  test_other/height_ngp2_robust_add.out.txt
+echo height_ngp2_robust_fv_add.out.txt && diff height_ngp2_robust_fv_add.out.txt  test_other/height_ngp2_robust_fv_add.out.txt
+echo height_ngp2_robust_domin.out.txt && diff height_ngp2_robust_domin.out.txt  test_other/height_ngp2_robust_domin.out.txt
+echo height_ngp2_robust_fv_domin.out.txt && diff height_ngp2_robust_fv_domin.out.txt  test_other/height_ngp2_robust_fv_domin.out.txt
+echo height_ngp2_robust_over_domin.out.txt && diff height_ngp2_robust_over_domin.out.txt  test_other/height_ngp2_robust_over_domin.out.txt
+echo height_ngp2_robust_fv_over_domin.out.txt && diff height_ngp2_robust_fv_over_domin.out.txt  test_other/height_ngp2_robust_fv_over_domin.out.txt
+echo height_ngp2_robust_recess.out.txt && diff height_ngp2_robust_recess.out.txt  test_other/height_ngp2_robust_recess.out.txt
+echo height_ngp2_robust_fv_recess.out.txt && diff height_ngp2_robust_fv_recess.out.txt  test_other/height_ngp2_robust_fv_recess.out.txt
+echo height_ngp2_robust_2df.out.txt && diff height_ngp2_robust_2df.out.txt  test_other/height_ngp2_robust_2df.out.txt
+echo height_ngp2_robust_fv_2df.out.txt && diff height_ngp2_robust_fv_2df.out.txt  test_other/height_ngp2_robust_fv_2df.out.txt
+echo height_ngp2_robust_int1_add.out.txt && diff height_ngp2_robust_int1_add.out.txt  test_other/height_ngp2_robust_int1_add.out.txt
+echo height_ngp2_robust_int1_fv_add.out.txt && diff height_ngp2_robust_int1_fv_add.out.txt  test_other/height_ngp2_robust_int1_fv_add.out.txt
+echo height_ngp2_robust_int1_domin.out.txt && diff height_ngp2_robust_int1_domin.out.txt  test_other/height_ngp2_robust_int1_domin.out.txt
+echo height_ngp2_robust_int1_fv_domin.out.txt && diff height_ngp2_robust_int1_fv_domin.out.txt  test_other/height_ngp2_robust_int1_fv_domin.out.txt
+echo height_ngp2_robust_int1_over_domin.out.txt && diff height_ngp2_robust_int1_over_domin.out.txt  test_other/height_ngp2_robust_int1_over_domin.out.txt
+echo height_ngp2_robust_int1_fv_over_domin.out.txt && diff height_ngp2_robust_int1_fv_over_domin.out.txt  test_other/height_ngp2_robust_int1_fv_over_domin.out.txt
+echo height_ngp2_robust_int1_recess.out.txt && diff height_ngp2_robust_int1_recess.out.txt  test_other/height_ngp2_robust_int1_recess.out.txt
+echo height_ngp2_robust_int1_fv_recess.out.txt && diff height_ngp2_robust_int1_fv_recess.out.txt  test_other/height_ngp2_robust_int1_fv_recess.out.txt
+echo height_ngp2_robust_int1_2df.out.txt && diff height_ngp2_robust_int1_2df.out.txt  test_other/height_ngp2_robust_int1_2df.out.txt
+echo height_ngp2_robust_int1_fv_2df.out.txt && diff height_ngp2_robust_int1_fv_2df.out.txt  test_other/height_ngp2_robust_int1_fv_2df.out.txt
+echo mmscore_add.out.txt && diff mmscore_add.out.txt  test_other/mmscore_add.out.txt
+echo mmscore_fv_add.out.txt && diff mmscore_fv_add.out.txt test_other/mmscore_fv_add.out.txt
+echo mmscore_prob_add.out.txt && diff mmscore_prob_add.out.txt test_other/mmscore_prob_add.out.txt 
+echo mmscore_prob_fv_add.out.txt && diff mmscore_prob_fv_add.out.txt test_other/mmscore_prob_fv_add.out.txt

Copied: pkg/ProbABEL/checks/compare_with_old_short.sh (from rev 1301, pkg/ProbABEL/examples/compare_with_old_short.sh)
===================================================================
--- pkg/ProbABEL/checks/compare_with_old_short.sh	                        (rev 0)
+++ pkg/ProbABEL/checks/compare_with_old_short.sh	2013-08-25 19:18:44 UTC (rev 1312)
@@ -0,0 +1,60 @@
+echo height_base_add.out.txt && diff height_base_add.out.txt  test_other/height_base_add.out.txt |wc -l
+echo height_base_fv_add.out.txt && diff height_base_fv_add.out.txt  test_other/height_base_fv_add.out.txt |wc -l
+echo height_allcov_add.out.txt && diff height_allcov_add.out.txt  test_other/height_allcov_add.out.txt |wc -l
+echo height_allcov_fv_add.out.txt && diff height_allcov_fv_add.out.txt  test_other/height_allcov_fv_add.out.txt |wc -l
+echo height_int1_add.out.txt && diff height_int1_add.out.txt  test_other/height_int1_add.out.txt |wc -l
+echo height_int1_fv_add.out.txt && diff height_int1_fv_add.out.txt  test_other/height_int1_fv_add.out.txt |wc -l
+echo height_robust_add.out.txt && diff height_robust_add.out.txt  test_other/height_robust_add.out.txt |wc -l
+echo height_robust_fv_add.out.txt && diff height_robust_fv_add.out.txt  test_other/height_robust_fv_add.out.txt |wc -l
+echo height_robust_int1_add.out.txt && diff height_robust_int1_add.out.txt  test_other/height_robust_int1_add.out.txt |wc -l
+echo height_robust_int1_fv_add.out.txt && diff height_robust_int1_fv_add.out.txt  test_other/height_robust_int1_fv_add.out.txt |wc -l
+echo height_ngp2_add.out.txt && diff height_ngp2_add.out.txt  test_other/height_ngp2_add.out.txt |wc -l
+echo height_ngp2_fv_add.out.txt && diff height_ngp2_fv_add.out.txt  test_other/height_ngp2_fv_add.out.txt |wc -l
+echo height_ngp2_domin.out.txt && diff height_ngp2_domin.out.txt  test_other/height_ngp2_domin.out.txt |wc -l
+echo height_ngp2_fv_domin.out.txt && diff height_ngp2_fv_domin.out.txt  test_other/height_ngp2_fv_domin.out.txt |wc -l
+echo height_ngp2_over_domin.out.txt && diff height_ngp2_over_domin.out.txt  test_other/height_ngp2_over_domin.out.txt |wc -l
+echo height_ngp2_fv_over_domin.out.txt && diff height_ngp2_fv_over_domin.out.txt  test_other/height_ngp2_fv_over_domin.out.txt |wc -l
+echo height_ngp2_recess.out.txt && diff height_ngp2_recess.out.txt  test_other/height_ngp2_recess.out.txt |wc -l
+echo height_ngp2_fv_recess.out.txt && diff height_ngp2_fv_recess.out.txt  test_other/height_ngp2_fv_recess.out.txt |wc -l
+echo height_ngp2_2df.out.txt && diff height_ngp2_2df.out.txt  test_other/height_ngp2_2df.out.txt |wc -l
+echo height_ngp2_fv_2df.out.txt && diff height_ngp2_fv_2df.out.txt  test_other/height_ngp2_fv_2df.out.txt |wc -l
+echo height_ngp2_allcov_add.out.txt && diff height_ngp2_allcov_add.out.txt  test_other/height_ngp2_allcov_add.out.txt |wc -l
+echo height_ngp2_allcov_fv_add.out.txt && diff height_ngp2_allcov_fv_add.out.txt  test_other/height_ngp2_allcov_fv_add.out.txt |wc -l
+echo height_ngp2_allcov_domin.out.txt && diff height_ngp2_allcov_domin.out.txt  test_other/height_ngp2_allcov_domin.out.txt |wc -l
+echo height_ngp2_allcov_fv_domin.out.txt && diff height_ngp2_allcov_fv_domin.out.txt  test_other/height_ngp2_allcov_fv_domin.out.txt |wc -l
+echo height_ngp2_allcov_over_domin.out.txt && diff height_ngp2_allcov_over_domin.out.txt  test_other/height_ngp2_allcov_over_domin.out.txt |wc -l
+echo height_ngp2_allcov_fv_over_domin.out.txt && diff height_ngp2_allcov_fv_over_domin.out.txt  test_other/height_ngp2_allcov_fv_over_domin.out.txt |wc -l
+echo height_ngp2_allcov_recess.out.txt && diff height_ngp2_allcov_recess.out.txt  test_other/height_ngp2_allcov_recess.out.txt |wc -l
+echo height_ngp2_allcov_fv_recess.out.txt && diff height_ngp2_allcov_fv_recess.out.txt  test_other/height_ngp2_allcov_fv_recess.out.txt |wc -l
+echo height_ngp2_allcov_2df.out.txt && diff height_ngp2_allcov_2df.out.txt  test_other/height_ngp2_allcov_2df.out.txt |wc -l
+echo height_ngp2_allcov_fv_2df.out.txt && diff height_ngp2_allcov_fv_2df.out.txt  test_other/height_ngp2_allcov_fv_2df.out.txt |wc -l
+echo height_ngp2_int1_add.out.txt && diff height_ngp2_int1_add.out.txt  test_other/height_ngp2_int1_add.out.txt |wc -l
+echo height_ngp2_int1_fv_add.out.txt && diff height_ngp2_int1_fv_add.out.txt  test_other/height_ngp2_int1_fv_add.out.txt |wc -l
+echo height_ngp2_int1_domin.out.txt && diff height_ngp2_int1_domin.out.txt  test_other/height_ngp2_int1_domin.out.txt |wc -l
+echo height_ngp2_int1_fv_domin.out.txt && diff height_ngp2_int1_fv_domin.out.txt  test_other/height_ngp2_int1_fv_domin.out.txt |wc -l
+echo height_ngp2_int1_over_domin.out.txt && diff height_ngp2_int1_over_domin.out.txt  test_other/height_ngp2_int1_over_domin.out.txt |wc -l
+echo height_ngp2_int1_fv_over_domin.out.txt && diff height_ngp2_int1_fv_over_domin.out.txt  test_other/height_ngp2_int1_fv_over_domin.out.txt |wc -l
+echo height_ngp2_int1_recess.out.txt && diff height_ngp2_int1_recess.out.txt  test_other/height_ngp2_int1_recess.out.txt |wc -l
+echo height_ngp2_int1_fv_recess.out.txt && diff height_ngp2_int1_fv_recess.out.txt  test_other/height_ngp2_int1_fv_recess.out.txt |wc -l
+echo height_ngp2_int1_2df.out.txt && diff height_ngp2_int1_2df.out.txt  test_other/height_ngp2_int1_2df.out.txt |wc -l
+echo height_ngp2_int1_fv_2df.out.txt && diff height_ngp2_int1_fv_2df.out.txt  test_other/height_ngp2_int1_fv_2df.out.txt |wc -l
+echo height_ngp2_robust_add.out.txt && diff height_ngp2_robust_add.out.txt  test_other/height_ngp2_robust_add.out.txt |wc -l
+echo height_ngp2_robust_fv_add.out.txt && diff height_ngp2_robust_fv_add.out.txt  test_other/height_ngp2_robust_fv_add.out.txt |wc -l
+echo height_ngp2_robust_domin.out.txt && diff height_ngp2_robust_domin.out.txt  test_other/height_ngp2_robust_domin.out.txt |wc -l
+echo height_ngp2_robust_fv_domin.out.txt && diff height_ngp2_robust_fv_domin.out.txt  test_other/height_ngp2_robust_fv_domin.out.txt |wc -l
+echo height_ngp2_robust_over_domin.out.txt && diff height_ngp2_robust_over_domin.out.txt  test_other/height_ngp2_robust_over_domin.out.txt |wc -l
+echo height_ngp2_robust_fv_over_domin.out.txt && diff height_ngp2_robust_fv_over_domin.out.txt  test_other/height_ngp2_robust_fv_over_domin.out.txt |wc -l
+echo height_ngp2_robust_recess.out.txt && diff height_ngp2_robust_recess.out.txt  test_other/height_ngp2_robust_recess.out.txt |wc -l
+echo height_ngp2_robust_fv_recess.out.txt && diff height_ngp2_robust_fv_recess.out.txt  test_other/height_ngp2_robust_fv_recess.out.txt |wc -l
+echo height_ngp2_robust_2df.out.txt && diff height_ngp2_robust_2df.out.txt  test_other/height_ngp2_robust_2df.out.txt |wc -l
+echo height_ngp2_robust_fv_2df.out.txt && diff height_ngp2_robust_fv_2df.out.txt  test_other/height_ngp2_robust_fv_2df.out.txt |wc -l
+echo height_ngp2_robust_int1_add.out.txt && diff height_ngp2_robust_int1_add.out.txt  test_other/height_ngp2_robust_int1_add.out.txt |wc -l
+echo height_ngp2_robust_int1_fv_add.out.txt && diff height_ngp2_robust_int1_fv_add.out.txt  test_other/height_ngp2_robust_int1_fv_add.out.txt |wc -l
+echo height_ngp2_robust_int1_domin.out.txt && diff height_ngp2_robust_int1_domin.out.txt  test_other/height_ngp2_robust_int1_domin.out.txt |wc -l
+echo height_ngp2_robust_int1_fv_domin.out.txt && diff height_ngp2_robust_int1_fv_domin.out.txt  test_other/height_ngp2_robust_int1_fv_domin.out.txt |wc -l
+echo height_ngp2_robust_int1_over_domin.out.txt && diff height_ngp2_robust_int1_over_domin.out.txt  test_other/height_ngp2_robust_int1_over_domin.out.txt |wc -l
+echo height_ngp2_robust_int1_fv_over_domin.out.txt && diff height_ngp2_robust_int1_fv_over_domin.out.txt  test_other/height_ngp2_robust_int1_fv_over_domin.out.txt |wc -l
+echo height_ngp2_robust_int1_recess.out.txt && diff height_ngp2_robust_int1_recess.out.txt  test_other/height_ngp2_robust_int1_recess.out.txt |wc -l
+echo height_ngp2_robust_int1_fv_recess.out.txt && diff height_ngp2_robust_int1_fv_recess.out.txt  test_other/height_ngp2_robust_int1_fv_recess.out.txt |wc -l
+echo height_ngp2_robust_int1_2df.out.txt && diff height_ngp2_robust_int1_2df.out.txt  test_other/height_ngp2_robust_int1_2df.out.txt |wc -l
+echo height_ngp2_robust_int1_fv_2df.out.txt && diff height_ngp2_robust_int1_fv_2df.out.txt  test_other/height_ngp2_robust_int1_fv_2df.out.txt |wc -l
\ No newline at end of file

Deleted: pkg/ProbABEL/examples/compare_with_old.sh
===================================================================
--- pkg/ProbABEL/examples/compare_with_old.sh	2013-08-25 19:15:56 UTC (rev 1311)
+++ pkg/ProbABEL/examples/compare_with_old.sh	2013-08-25 19:18:44 UTC (rev 1312)
@@ -1,64 +0,0 @@
-echo height_base_add.out.txt && diff height_base_add.out.txt  test_other/height_base_add.out.txt
-echo height_base_fv_add.out.txt && diff height_base_fv_add.out.txt  test_other/height_base_fv_add.out.txt
-echo height_allcov_add.out.txt && diff height_allcov_add.out.txt  test_other/height_allcov_add.out.txt
-echo height_allcov_fv_add.out.txt && diff height_allcov_fv_add.out.txt  test_other/height_allcov_fv_add.out.txt
-echo height_int1_add.out.txt && diff height_int1_add.out.txt  test_other/height_int1_add.out.txt
-echo height_int1_fv_add.out.txt && diff height_int1_fv_add.out.txt  test_other/height_int1_fv_add.out.txt
-echo height_robust_add.out.txt && diff height_robust_add.out.txt  test_other/height_robust_add.out.txt
-echo height_robust_fv_add.out.txt && diff height_robust_fv_add.out.txt  test_other/height_robust_fv_add.out.txt
-echo height_robust_int1_add.out.txt && diff height_robust_int1_add.out.txt  test_other/height_robust_int1_add.out.txt
-echo height_robust_int1_fv_add.out.txt && diff height_robust_int1_fv_add.out.txt  test_other/height_robust_int1_fv_add.out.txt
-echo height_ngp2_add.out.txt && diff height_ngp2_add.out.txt  test_other/height_ngp2_add.out.txt
-echo height_ngp2_fv_add.out.txt && diff height_ngp2_fv_add.out.txt  test_other/height_ngp2_fv_add.out.txt
-echo height_ngp2_domin.out.txt && diff height_ngp2_domin.out.txt  test_other/height_ngp2_domin.out.txt
-echo height_ngp2_fv_domin.out.txt && diff height_ngp2_fv_domin.out.txt  test_other/height_ngp2_fv_domin.out.txt
-echo height_ngp2_over_domin.out.txt && diff height_ngp2_over_domin.out.txt  test_other/height_ngp2_over_domin.out.txt
-echo height_ngp2_fv_over_domin.out.txt && diff height_ngp2_fv_over_domin.out.txt  test_other/height_ngp2_fv_over_domin.out.txt
-echo height_ngp2_recess.out.txt && diff height_ngp2_recess.out.txt  test_other/height_ngp2_recess.out.txt
-echo height_ngp2_fv_recess.out.txt && diff height_ngp2_fv_recess.out.txt  test_other/height_ngp2_fv_recess.out.txt
-echo height_ngp2_2df.out.txt && diff height_ngp2_2df.out.txt  test_other/height_ngp2_2df.out.txt
-echo height_ngp2_fv_2df.out.txt && diff height_ngp2_fv_2df.out.txt  test_other/height_ngp2_fv_2df.out.txt
-echo height_ngp2_allcov_add.out.txt && diff height_ngp2_allcov_add.out.txt  test_other/height_ngp2_allcov_add.out.txt
-echo height_ngp2_allcov_fv_add.out.txt && diff height_ngp2_allcov_fv_add.out.txt  test_other/height_ngp2_allcov_fv_add.out.txt
-echo height_ngp2_allcov_domin.out.txt && diff height_ngp2_allcov_domin.out.txt  test_other/height_ngp2_allcov_domin.out.txt
-echo height_ngp2_allcov_fv_domin.out.txt && diff height_ngp2_allcov_fv_domin.out.txt  test_other/height_ngp2_allcov_fv_domin.out.txt
-echo height_ngp2_allcov_over_domin.out.txt && diff height_ngp2_allcov_over_domin.out.txt  test_other/height_ngp2_allcov_over_domin.out.txt
-echo height_ngp2_allcov_fv_over_domin.out.txt && diff height_ngp2_allcov_fv_over_domin.out.txt  test_other/height_ngp2_allcov_fv_over_domin.out.txt
-echo height_ngp2_allcov_recess.out.txt && diff height_ngp2_allcov_recess.out.txt  test_other/height_ngp2_allcov_recess.out.txt
-echo height_ngp2_allcov_fv_recess.out.txt && diff height_ngp2_allcov_fv_recess.out.txt  test_other/height_ngp2_allcov_fv_recess.out.txt
-echo height_ngp2_allcov_2df.out.txt && diff height_ngp2_allcov_2df.out.txt  test_other/height_ngp2_allcov_2df.out.txt
-echo height_ngp2_allcov_fv_2df.out.txt && diff height_ngp2_allcov_fv_2df.out.txt  test_other/height_ngp2_allcov_fv_2df.out.txt
-echo height_ngp2_int1_add.out.txt && diff height_ngp2_int1_add.out.txt  test_other/height_ngp2_int1_add.out.txt
-echo height_ngp2_int1_fv_add.out.txt && diff height_ngp2_int1_fv_add.out.txt  test_other/height_ngp2_int1_fv_add.out.txt
-echo height_ngp2_int1_domin.out.txt && diff height_ngp2_int1_domin.out.txt  test_other/height_ngp2_int1_domin.out.txt
-echo height_ngp2_int1_fv_domin.out.txt && diff height_ngp2_int1_fv_domin.out.txt  test_other/height_ngp2_int1_fv_domin.out.txt
-echo height_ngp2_int1_over_domin.out.txt && diff height_ngp2_int1_over_domin.out.txt  test_other/height_ngp2_int1_over_domin.out.txt
-echo height_ngp2_int1_fv_over_domin.out.txt && diff height_ngp2_int1_fv_over_domin.out.txt  test_other/height_ngp2_int1_fv_over_domin.out.txt
-echo height_ngp2_int1_recess.out.txt && diff height_ngp2_int1_recess.out.txt  test_other/height_ngp2_int1_recess.out.txt
-echo height_ngp2_int1_fv_recess.out.txt && diff height_ngp2_int1_fv_recess.out.txt  test_other/height_ngp2_int1_fv_recess.out.txt
-echo height_ngp2_int1_2df.out.txt && diff height_ngp2_int1_2df.out.txt  test_other/height_ngp2_int1_2df.out.txt
-echo height_ngp2_int1_fv_2df.out.txt && diff height_ngp2_int1_fv_2df.out.txt  test_other/height_ngp2_int1_fv_2df.out.txt
-echo height_ngp2_robust_add.out.txt && diff height_ngp2_robust_add.out.txt  test_other/height_ngp2_robust_add.out.txt
-echo height_ngp2_robust_fv_add.out.txt && diff height_ngp2_robust_fv_add.out.txt  test_other/height_ngp2_robust_fv_add.out.txt
-echo height_ngp2_robust_domin.out.txt && diff height_ngp2_robust_domin.out.txt  test_other/height_ngp2_robust_domin.out.txt
-echo height_ngp2_robust_fv_domin.out.txt && diff height_ngp2_robust_fv_domin.out.txt  test_other/height_ngp2_robust_fv_domin.out.txt
-echo height_ngp2_robust_over_domin.out.txt && diff height_ngp2_robust_over_domin.out.txt  test_other/height_ngp2_robust_over_domin.out.txt
-echo height_ngp2_robust_fv_over_domin.out.txt && diff height_ngp2_robust_fv_over_domin.out.txt  test_other/height_ngp2_robust_fv_over_domin.out.txt
-echo height_ngp2_robust_recess.out.txt && diff height_ngp2_robust_recess.out.txt  test_other/height_ngp2_robust_recess.out.txt
-echo height_ngp2_robust_fv_recess.out.txt && diff height_ngp2_robust_fv_recess.out.txt  test_other/height_ngp2_robust_fv_recess.out.txt
-echo height_ngp2_robust_2df.out.txt && diff height_ngp2_robust_2df.out.txt  test_other/height_ngp2_robust_2df.out.txt
-echo height_ngp2_robust_fv_2df.out.txt && diff height_ngp2_robust_fv_2df.out.txt  test_other/height_ngp2_robust_fv_2df.out.txt
-echo height_ngp2_robust_int1_add.out.txt && diff height_ngp2_robust_int1_add.out.txt  test_other/height_ngp2_robust_int1_add.out.txt
-echo height_ngp2_robust_int1_fv_add.out.txt && diff height_ngp2_robust_int1_fv_add.out.txt  test_other/height_ngp2_robust_int1_fv_add.out.txt
-echo height_ngp2_robust_int1_domin.out.txt && diff height_ngp2_robust_int1_domin.out.txt  test_other/height_ngp2_robust_int1_domin.out.txt
-echo height_ngp2_robust_int1_fv_domin.out.txt && diff height_ngp2_robust_int1_fv_domin.out.txt  test_other/height_ngp2_robust_int1_fv_domin.out.txt
-echo height_ngp2_robust_int1_over_domin.out.txt && diff height_ngp2_robust_int1_over_domin.out.txt  test_other/height_ngp2_robust_int1_over_domin.out.txt
-echo height_ngp2_robust_int1_fv_over_domin.out.txt && diff height_ngp2_robust_int1_fv_over_domin.out.txt  test_other/height_ngp2_robust_int1_fv_over_domin.out.txt
-echo height_ngp2_robust_int1_recess.out.txt && diff height_ngp2_robust_int1_recess.out.txt  test_other/height_ngp2_robust_int1_recess.out.txt
-echo height_ngp2_robust_int1_fv_recess.out.txt && diff height_ngp2_robust_int1_fv_recess.out.txt  test_other/height_ngp2_robust_int1_fv_recess.out.txt
-echo height_ngp2_robust_int1_2df.out.txt && diff height_ngp2_robust_int1_2df.out.txt  test_other/height_ngp2_robust_int1_2df.out.txt
-echo height_ngp2_robust_int1_fv_2df.out.txt && diff height_ngp2_robust_int1_fv_2df.out.txt  test_other/height_ngp2_robust_int1_fv_2df.out.txt
-echo mmscore_add.out.txt && diff mmscore_add.out.txt  test_other/mmscore_add.out.txt
-echo mmscore_fv_add.out.txt && diff mmscore_fv_add.out.txt test_other/mmscore_fv_add.out.txt
-echo mmscore_prob_add.out.txt && diff mmscore_prob_add.out.txt test_other/mmscore_prob_add.out.txt 
-echo mmscore_prob_fv_add.out.txt && diff mmscore_prob_fv_add.out.txt test_other/mmscore_prob_fv_add.out.txt

Deleted: pkg/ProbABEL/examples/compare_with_old_short.sh
===================================================================
--- pkg/ProbABEL/examples/compare_with_old_short.sh	2013-08-25 19:15:56 UTC (rev 1311)
+++ pkg/ProbABEL/examples/compare_with_old_short.sh	2013-08-25 19:18:44 UTC (rev 1312)
@@ -1,60 +0,0 @@
-echo height_base_add.out.txt && diff height_base_add.out.txt  test_other/height_base_add.out.txt |wc -l
-echo height_base_fv_add.out.txt && diff height_base_fv_add.out.txt  test_other/height_base_fv_add.out.txt |wc -l
-echo height_allcov_add.out.txt && diff height_allcov_add.out.txt  test_other/height_allcov_add.out.txt |wc -l
-echo height_allcov_fv_add.out.txt && diff height_allcov_fv_add.out.txt  test_other/height_allcov_fv_add.out.txt |wc -l
-echo height_int1_add.out.txt && diff height_int1_add.out.txt  test_other/height_int1_add.out.txt |wc -l
-echo height_int1_fv_add.out.txt && diff height_int1_fv_add.out.txt  test_other/height_int1_fv_add.out.txt |wc -l
-echo height_robust_add.out.txt && diff height_robust_add.out.txt  test_other/height_robust_add.out.txt |wc -l
-echo height_robust_fv_add.out.txt && diff height_robust_fv_add.out.txt  test_other/height_robust_fv_add.out.txt |wc -l
-echo height_robust_int1_add.out.txt && diff height_robust_int1_add.out.txt  test_other/height_robust_int1_add.out.txt |wc -l
-echo height_robust_int1_fv_add.out.txt && diff height_robust_int1_fv_add.out.txt  test_other/height_robust_int1_fv_add.out.txt |wc -l
-echo height_ngp2_add.out.txt && diff height_ngp2_add.out.txt  test_other/height_ngp2_add.out.txt |wc -l
-echo height_ngp2_fv_add.out.txt && diff height_ngp2_fv_add.out.txt  test_other/height_ngp2_fv_add.out.txt |wc -l
-echo height_ngp2_domin.out.txt && diff height_ngp2_domin.out.txt  test_other/height_ngp2_domin.out.txt |wc -l
-echo height_ngp2_fv_domin.out.txt && diff height_ngp2_fv_domin.out.txt  test_other/height_ngp2_fv_domin.out.txt |wc -l
-echo height_ngp2_over_domin.out.txt && diff height_ngp2_over_domin.out.txt  test_other/height_ngp2_over_domin.out.txt |wc -l
-echo height_ngp2_fv_over_domin.out.txt && diff height_ngp2_fv_over_domin.out.txt  test_other/height_ngp2_fv_over_domin.out.txt |wc -l
-echo height_ngp2_recess.out.txt && diff height_ngp2_recess.out.txt  test_other/height_ngp2_recess.out.txt |wc -l
-echo height_ngp2_fv_recess.out.txt && diff height_ngp2_fv_recess.out.txt  test_other/height_ngp2_fv_recess.out.txt |wc -l
-echo height_ngp2_2df.out.txt && diff height_ngp2_2df.out.txt  test_other/height_ngp2_2df.out.txt |wc -l
-echo height_ngp2_fv_2df.out.txt && diff height_ngp2_fv_2df.out.txt  test_other/height_ngp2_fv_2df.out.txt |wc -l
-echo height_ngp2_allcov_add.out.txt && diff height_ngp2_allcov_add.out.txt  test_other/height_ngp2_allcov_add.out.txt |wc -l
-echo height_ngp2_allcov_fv_add.out.txt && diff height_ngp2_allcov_fv_add.out.txt  test_other/height_ngp2_allcov_fv_add.out.txt |wc -l
-echo height_ngp2_allcov_domin.out.txt && diff height_ngp2_allcov_domin.out.txt  test_other/height_ngp2_allcov_domin.out.txt |wc -l
-echo height_ngp2_allcov_fv_domin.out.txt && diff height_ngp2_allcov_fv_domin.out.txt  test_other/height_ngp2_allcov_fv_domin.out.txt |wc -l
-echo height_ngp2_allcov_over_domin.out.txt && diff height_ngp2_allcov_over_domin.out.txt  test_other/height_ngp2_allcov_over_domin.out.txt |wc -l
-echo height_ngp2_allcov_fv_over_domin.out.txt && diff height_ngp2_allcov_fv_over_domin.out.txt  test_other/height_ngp2_allcov_fv_over_domin.out.txt |wc -l
-echo height_ngp2_allcov_recess.out.txt && diff height_ngp2_allcov_recess.out.txt  test_other/height_ngp2_allcov_recess.out.txt |wc -l
-echo height_ngp2_allcov_fv_recess.out.txt && diff height_ngp2_allcov_fv_recess.out.txt  test_other/height_ngp2_allcov_fv_recess.out.txt |wc -l
-echo height_ngp2_allcov_2df.out.txt && diff height_ngp2_allcov_2df.out.txt  test_other/height_ngp2_allcov_2df.out.txt |wc -l
-echo height_ngp2_allcov_fv_2df.out.txt && diff height_ngp2_allcov_fv_2df.out.txt  test_other/height_ngp2_allcov_fv_2df.out.txt |wc -l
-echo height_ngp2_int1_add.out.txt && diff height_ngp2_int1_add.out.txt  test_other/height_ngp2_int1_add.out.txt |wc -l
-echo height_ngp2_int1_fv_add.out.txt && diff height_ngp2_int1_fv_add.out.txt  test_other/height_ngp2_int1_fv_add.out.txt |wc -l
-echo height_ngp2_int1_domin.out.txt && diff height_ngp2_int1_domin.out.txt  test_other/height_ngp2_int1_domin.out.txt |wc -l
-echo height_ngp2_int1_fv_domin.out.txt && diff height_ngp2_int1_fv_domin.out.txt  test_other/height_ngp2_int1_fv_domin.out.txt |wc -l
-echo height_ngp2_int1_over_domin.out.txt && diff height_ngp2_int1_over_domin.out.txt  test_other/height_ngp2_int1_over_domin.out.txt |wc -l
-echo height_ngp2_int1_fv_over_domin.out.txt && diff height_ngp2_int1_fv_over_domin.out.txt  test_other/height_ngp2_int1_fv_over_domin.out.txt |wc -l
-echo height_ngp2_int1_recess.out.txt && diff height_ngp2_int1_recess.out.txt  test_other/height_ngp2_int1_recess.out.txt |wc -l
-echo height_ngp2_int1_fv_recess.out.txt && diff height_ngp2_int1_fv_recess.out.txt  test_other/height_ngp2_int1_fv_recess.out.txt |wc -l
-echo height_ngp2_int1_2df.out.txt && diff height_ngp2_int1_2df.out.txt  test_other/height_ngp2_int1_2df.out.txt |wc -l
-echo height_ngp2_int1_fv_2df.out.txt && diff height_ngp2_int1_fv_2df.out.txt  test_other/height_ngp2_int1_fv_2df.out.txt |wc -l
-echo height_ngp2_robust_add.out.txt && diff height_ngp2_robust_add.out.txt  test_other/height_ngp2_robust_add.out.txt |wc -l
-echo height_ngp2_robust_fv_add.out.txt && diff height_ngp2_robust_fv_add.out.txt  test_other/height_ngp2_robust_fv_add.out.txt |wc -l
-echo height_ngp2_robust_domin.out.txt && diff height_ngp2_robust_domin.out.txt  test_other/height_ngp2_robust_domin.out.txt |wc -l
-echo height_ngp2_robust_fv_domin.out.txt && diff height_ngp2_robust_fv_domin.out.txt  test_other/height_ngp2_robust_fv_domin.out.txt |wc -l
-echo height_ngp2_robust_over_domin.out.txt && diff height_ngp2_robust_over_domin.out.txt  test_other/height_ngp2_robust_over_domin.out.txt |wc -l
-echo height_ngp2_robust_fv_over_domin.out.txt && diff height_ngp2_robust_fv_over_domin.out.txt  test_other/height_ngp2_robust_fv_over_domin.out.txt |wc -l
-echo height_ngp2_robust_recess.out.txt && diff height_ngp2_robust_recess.out.txt  test_other/height_ngp2_robust_recess.out.txt |wc -l
-echo height_ngp2_robust_fv_recess.out.txt && diff height_ngp2_robust_fv_recess.out.txt  test_other/height_ngp2_robust_fv_recess.out.txt |wc -l
-echo height_ngp2_robust_2df.out.txt && diff height_ngp2_robust_2df.out.txt  test_other/height_ngp2_robust_2df.out.txt |wc -l
-echo height_ngp2_robust_fv_2df.out.txt && diff height_ngp2_robust_fv_2df.out.txt  test_other/height_ngp2_robust_fv_2df.out.txt |wc -l
-echo height_ngp2_robust_int1_add.out.txt && diff height_ngp2_robust_int1_add.out.txt  test_other/height_ngp2_robust_int1_add.out.txt |wc -l
-echo height_ngp2_robust_int1_fv_add.out.txt && diff height_ngp2_robust_int1_fv_add.out.txt  test_other/height_ngp2_robust_int1_fv_add.out.txt |wc -l
-echo height_ngp2_robust_int1_domin.out.txt && diff height_ngp2_robust_int1_domin.out.txt  test_other/height_ngp2_robust_int1_domin.out.txt |wc -l
-echo height_ngp2_robust_int1_fv_domin.out.txt && diff height_ngp2_robust_int1_fv_domin.out.txt  test_other/height_ngp2_robust_int1_fv_domin.out.txt |wc -l
-echo height_ngp2_robust_int1_over_domin.out.txt && diff height_ngp2_robust_int1_over_domin.out.txt  test_other/height_ngp2_robust_int1_over_domin.out.txt |wc -l
-echo height_ngp2_robust_int1_fv_over_domin.out.txt && diff height_ngp2_robust_int1_fv_over_domin.out.txt  test_other/height_ngp2_robust_int1_fv_over_domin.out.txt |wc -l
-echo height_ngp2_robust_int1_recess.out.txt && diff height_ngp2_robust_int1_recess.out.txt  test_other/height_ngp2_robust_int1_recess.out.txt |wc -l
-echo height_ngp2_robust_int1_fv_recess.out.txt && diff height_ngp2_robust_int1_fv_recess.out.txt  test_other/height_ngp2_robust_int1_fv_recess.out.txt |wc -l
-echo height_ngp2_robust_int1_2df.out.txt && diff height_ngp2_robust_int1_2df.out.txt  test_other/height_ngp2_robust_int1_2df.out.txt |wc -l
-echo height_ngp2_robust_int1_fv_2df.out.txt && diff height_ngp2_robust_int1_fv_2df.out.txt  test_other/height_ngp2_robust_int1_fv_2df.out.txt |wc -l
\ No newline at end of file