[med-svn] r15931 - trunk/packages/flexbar/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-01-31 12:52:32 +0000 (Fri, 31 Jan 2014)
New Revision: 15931

Modified:
   trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch
Log:
Make sure the tests will fail only in case of failure


Modified: trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch
===================================================================
--- trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch	2014-01-31 12:48:24 UTC (rev 15930)
+++ trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch	2014-01-31 12:52:32 UTC (rev 15931)
@@ -5,36 +5,244 @@
 
 --- a/test/flexbar_test_csfasta.sh
 +++ b/test/flexbar_test_csfasta.sh
-@@ -1,4 +1,4 @@
+@@ -1,11 +1,9 @@
 -
 +#!/bin/sh -e
  flexbar --reads test.csfasta --target result_right --format csfasta --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
  a=`diff correct_result_right.csfasta result_right.csfasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfasta, right"
+ echo $a
+ exit -1
+@@ -18,9 +16,7 @@ flexbar --reads test.csfasta --target re
+ 
+ a=`diff correct_result_left.csfasta result_left.csfasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfasta, left"
+ echo $a
+ exit -1
+@@ -33,9 +29,7 @@ flexbar --reads test.csfasta --target re
+ 
+ a=`diff correct_result_any.csfasta result_any.csfasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfasta, any"
+ echo $a
+ exit -1
+@@ -48,9 +42,7 @@ flexbar --reads test.csfasta --target re
+ 
+ a=`diff correct_result_left_tail.csfasta result_left_tail.csfasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfasta, left_tail"
+ echo $a
+ exit -1
+@@ -63,9 +55,7 @@ flexbar --reads test.csfasta --target re
+ 
+ a=`diff correct_result_right_tail.csfasta result_right_tail.csfasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfasta, right_tail"
+ echo $a
+ exit -1
 --- a/test/flexbar_test_csfastq.sh
 +++ b/test/flexbar_test_csfastq.sh
-@@ -1,4 +1,4 @@
+@@ -1,11 +1,9 @@
 -
 +#!/bin/sh -e
  flexbar --reads test.csfastq --target result_right --format csfastq --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
  a=`diff correct_result_right.csfastq result_right.csfastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfastq, right"
+ echo $a
+ exit -1
+@@ -18,9 +16,7 @@ flexbar --reads test.csfastq --target re
+ 
+ a=`diff correct_result_left.csfastq result_left.csfastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfastq, left"
+ echo $a
+ exit -1
+@@ -33,9 +29,7 @@ flexbar --reads test.csfastq --target re
+ 
+ a=`diff correct_result_any.csfastq result_any.csfastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfastq, any"
+ echo $a
+ exit -1
+@@ -48,9 +42,7 @@ flexbar --reads test.csfastq --target re
+ 
+ a=`diff correct_result_left_tail.csfastq result_left_tail.csfastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfastq, left_tail"
+ echo $a
+ exit -1
+@@ -63,9 +55,7 @@ flexbar --reads test.csfastq --target re
+ 
+ a=`diff correct_result_right_tail.csfastq result_right_tail.csfastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode csfastq, right_tail"
+ echo $a
+ exit -1
 --- a/test/flexbar_test_fasta.sh
 +++ b/test/flexbar_test_fasta.sh
-@@ -1,4 +1,4 @@
+@@ -1,11 +1,9 @@
 -
 +#!/bin/sh -e
  flexbar --reads test.fasta --target result_right --format fasta --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
  a=`diff correct_result_right.fasta result_right.fasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, right"
+ echo $a
+ exit -1
+@@ -18,9 +16,7 @@ flexbar --reads test.fasta --target resu
+ 
+ a=`diff correct_result_left.fasta result_left.fasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, left"
+ echo $a
+ exit -1
+@@ -33,9 +29,7 @@ flexbar --reads test.fasta --target resu
+ 
+ a=`diff correct_result_any.fasta result_any.fasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode any, left"
+ echo $a
+ exit -1
+@@ -48,9 +42,7 @@ flexbar --reads test.fasta --target resu
+ 
+ a=`diff correct_result_left_tail.fasta result_left_tail.fasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, left_tail"
+ echo $a
+ exit -1
+@@ -63,9 +55,7 @@ flexbar --reads test.fasta --target resu
+ 
+ a=`diff correct_result_right_tail.fasta result_right_tail.fasta`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, right_tail"
+ echo $a
+ exit -1
 --- a/test/flexbar_test_fastq.sh
 +++ b/test/flexbar_test_fastq.sh
-@@ -1,4 +1,4 @@
+@@ -1,11 +1,9 @@
 -
 +#!/bin/sh -e
  flexbar --reads test.fastq --target result_right --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
  a=`diff correct_result_right.fastq result_right.fastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, right"
+ echo $a
+ exit -1
+@@ -18,9 +16,7 @@ flexbar --reads test.fastq --target resu
+ 
+ a=`diff correct_result_left.fastq result_left.fastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, left"
+ echo $a
+ exit -1
+@@ -33,9 +29,7 @@ flexbar --reads test.fastq --target resu
+ 
+ a=`diff correct_result_any.fastq result_any.fastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode any, left"
+ echo $a
+ exit -1
+@@ -48,9 +42,7 @@ flexbar --reads test.fastq --target resu
+ 
+ a=`diff correct_result_left_tail.fastq result_left_tail.fastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, left_tail"
+ echo $a
+ exit -1
+@@ -63,9 +55,7 @@ flexbar --reads test.fastq --target resu
+ 
+ a=`diff correct_result_right_tail.fastq result_right_tail.fastq`
+ 
+-l1=`expr length "$a"`
+-
+-if [ $l1 != 0 ]; then
++if ! $a ; then
+ echo "error testing mode fasta, right_tail"
+ echo $a
+ exit -1
 --- a/test/flexbar_validate.sh
 +++ b/test/flexbar_validate.sh
 @@ -1,4 +1,4 @@