[med-svn] [gwama] 02/03: Cleaned test files

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository gwama.

commit 2cf869b03f9de89501d0b378aaf30132282f7077
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Thu Dec 18 19:08:38 2014 +0100

    Cleaned test files
---
 debian/tests/run-sample-analysis                           | 10 ++--------
 debian/upstream.docs/samples/{output/README => README.out} |  0
 debian/upstream.docs/samples/{output => }/fixed.out        |  0
 debian/upstream.docs/samples/output/fixed.err.out          |  3 ---
 debian/upstream.docs/samples/output/fixed.gc.out           |  1 -
 debian/upstream.docs/samples/output/fixed.log.out          | 13 -------------
 debian/upstream.docs/samples/output/random.err.out         |  3 ---
 debian/upstream.docs/samples/output/random.gc.out          |  1 -
 debian/upstream.docs/samples/output/random.log.out         | 13 -------------
 debian/upstream.docs/samples/{output => }/random.out       |  0
 10 files changed, 2 insertions(+), 42 deletions(-)

diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
index 4cc1015..a725334 100644
--- a/debian/tests/run-sample-analysis
+++ b/debian/tests/run-sample-analysis
@@ -15,17 +15,11 @@ GWAMA_TEST='GWAMA --filelist "gwama.in" --quantitative'
 
 # Fixed analysis
 $GWAMA_TEST --output "test_fixed" 
-diff test_fixed.out output/fixed.out
-diff test_fixed.log.out output/fixed.log.out
-diff test_fixed.gc.out output/fixed.gc.out
-diff test_fixed.err.out output/fixed.err.out
+diff test_fixed.out fixed.out
 
 # Random analysis
 $GWAMA_TEST --output "test_random" --random
-diff test_random.out output/random.out
-diff test_random.log.out output/random.log.out
-diff test_random.gc.out output/random.gc.out
-diff test_random.err.out output/random.err.out
+diff test_random.out random.out
 
 rm -f $ADTTMP/*
 
diff --git a/debian/upstream.docs/samples/output/README b/debian/upstream.docs/samples/README.out
similarity index 100%
rename from debian/upstream.docs/samples/output/README
rename to debian/upstream.docs/samples/README.out
diff --git a/debian/upstream.docs/samples/output/fixed.out b/debian/upstream.docs/samples/fixed.out
similarity index 100%
rename from debian/upstream.docs/samples/output/fixed.out
rename to debian/upstream.docs/samples/fixed.out
diff --git a/debian/upstream.docs/samples/output/fixed.err.out b/debian/upstream.docs/samples/output/fixed.err.out
deleted file mode 100644
index b257341..0000000
--- a/debian/upstream.docs/samples/output/fixed.err.out
+++ /dev/null
@@ -1,3 +0,0 @@
-E000000001 pop1.txt has problem with odds ratio or its CI of rs2905035!
-E000000001 pop1.txt Given values: BETA=-0.0435863 SE=NA. Marker not used!
-E000000002 pop3.txt error: Marker rs12138618 has wrong alleles. Marker dropped.
diff --git a/debian/upstream.docs/samples/output/fixed.gc.out b/debian/upstream.docs/samples/output/fixed.gc.out
deleted file mode 100644
index 1d5b754..0000000
--- a/debian/upstream.docs/samples/output/fixed.gc.out
+++ /dev/null
@@ -1 +0,0 @@
-Cohort	directly_genotyped_markers_lambda		directly_genotyped_markers_count	imputed_markers_lambda	imputed_markers_count
diff --git a/debian/upstream.docs/samples/output/fixed.log.out b/debian/upstream.docs/samples/output/fixed.log.out
deleted file mode 100644
index cab0776..0000000
--- a/debian/upstream.docs/samples/output/fixed.log.out
+++ /dev/null
@@ -1,13 +0,0 @@
-Running GWAMA 2.1
-Reading input file list:
-	pop1.txt
-	pop2.txt
-	pop3.txt
-END-OF-FILE
-Study count: 3
- [1] Reading file: pop1.txt
-pop1.txt has problem with beta and se for marker rs2905035!(E000000001)
- [2] Reading file: pop2.txt
- [3] Reading file: pop3.txt
-Error: Marker rs12138618 has wrong alleles. (E000000002)
-Analysis finished.
diff --git a/debian/upstream.docs/samples/output/random.err.out b/debian/upstream.docs/samples/output/random.err.out
deleted file mode 100644
index b257341..0000000
--- a/debian/upstream.docs/samples/output/random.err.out
+++ /dev/null
@@ -1,3 +0,0 @@
-E000000001 pop1.txt has problem with odds ratio or its CI of rs2905035!
-E000000001 pop1.txt Given values: BETA=-0.0435863 SE=NA. Marker not used!
-E000000002 pop3.txt error: Marker rs12138618 has wrong alleles. Marker dropped.
diff --git a/debian/upstream.docs/samples/output/random.gc.out b/debian/upstream.docs/samples/output/random.gc.out
deleted file mode 100644
index 1d5b754..0000000
--- a/debian/upstream.docs/samples/output/random.gc.out
+++ /dev/null
@@ -1 +0,0 @@
-Cohort	directly_genotyped_markers_lambda		directly_genotyped_markers_count	imputed_markers_lambda	imputed_markers_count
diff --git a/debian/upstream.docs/samples/output/random.log.out b/debian/upstream.docs/samples/output/random.log.out
deleted file mode 100644
index cab0776..0000000
--- a/debian/upstream.docs/samples/output/random.log.out
+++ /dev/null
@@ -1,13 +0,0 @@
-Running GWAMA 2.1
-Reading input file list:
-	pop1.txt
-	pop2.txt
-	pop3.txt
-END-OF-FILE
-Study count: 3
- [1] Reading file: pop1.txt
-pop1.txt has problem with beta and se for marker rs2905035!(E000000001)
- [2] Reading file: pop2.txt
- [3] Reading file: pop3.txt
-Error: Marker rs12138618 has wrong alleles. (E000000002)
-Analysis finished.
diff --git a/debian/upstream.docs/samples/output/random.out b/debian/upstream.docs/samples/random.out
similarity index 100%
rename from debian/upstream.docs/samples/output/random.out
rename to debian/upstream.docs/samples/random.out

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