[med-svn] r15934 - trunk/packages/flexbar/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-01-31 13:55:38 +0000 (Fri, 31 Jan 2014)
New Revision: 15934

Modified:
   trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch
Log:
Adapt option names used inside tests to the new version


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 12:59:35 UTC (rev 15933)
+++ trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch	2014-01-31 13:55:38 UTC (rev 15934)
@@ -1,7 +1,8 @@
 Author: Andreas Tille <tille at debian.org>
 Date: Fri, 31 Jan 2014 12:55:18 +0100
 Description: Add shebang line for shell scripts and make
- scripts fail in case of errors
+ scripts fail in case of errors;
+ Adapt option names used inside tests to the new version
 
 --- a/test/flexbar_test_csfasta.sh
 +++ b/test/flexbar_test_csfasta.sh
@@ -187,8 +188,9 @@
 +++ b/test/flexbar_test_fastq.sh
 @@ -1,11 +1,9 @@
 -
+-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
 +#!/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
++flexbar --reads test.fastq --target result_right --format 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`
  
@@ -199,8 +201,13 @@
  echo "error testing mode fasta, right"
  echo $a
  exit -1
-@@ -18,9 +16,7 @@ flexbar --reads test.fastq --target resu
+@@ -14,13 +12,11 @@ echo "Test 1 OK"
+ fi
  
+ 
+-flexbar --reads test.fastq --target result_left --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end LEFT > /dev/null
++flexbar --reads test.fastq --target result_left --format i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end LEFT > /dev/null
+ 
  a=`diff correct_result_left.fastq result_left.fastq`
  
 -l1=`expr length "$a"`
@@ -210,8 +217,13 @@
  echo "error testing mode fasta, left"
  echo $a
  exit -1
-@@ -33,9 +29,7 @@ flexbar --reads test.fastq --target resu
+@@ -29,13 +25,11 @@ echo "Test 2 OK"
+ fi
  
+ 
+-flexbar --reads test.fastq --target result_any --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end ANY > /dev/null
++flexbar --reads test.fastq --target result_any --format i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end ANY > /dev/null
+ 
  a=`diff correct_result_any.fastq result_any.fastq`
  
 -l1=`expr length "$a"`
@@ -221,8 +233,13 @@
  echo "error testing mode any, left"
  echo $a
  exit -1
-@@ -48,9 +42,7 @@ flexbar --reads test.fastq --target resu
+@@ -44,13 +38,11 @@ echo "Test 3 OK"
+ fi
  
+ 
+-flexbar --reads test.fastq --target result_left_tail --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end LEFT_TAIL > /dev/null
++flexbar --reads test.fastq --target result_left_tail --format i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end LEFT_TAIL > /dev/null
+ 
  a=`diff correct_result_left_tail.fastq result_left_tail.fastq`
  
 -l1=`expr length "$a"`
@@ -232,8 +249,13 @@
  echo "error testing mode fasta, left_tail"
  echo $a
  exit -1
-@@ -63,9 +55,7 @@ flexbar --reads test.fastq --target resu
+@@ -59,13 +51,11 @@ echo "Test 4 OK"
+ fi
  
+ 
+-flexbar --reads test.fastq --target result_right_tail --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT_TAIL > /dev/null
++flexbar --reads test.fastq --target result_right_tail --format i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT_TAIL > /dev/null
+ 
  a=`diff correct_result_right_tail.fastq result_right_tail.fastq`
  
 -l1=`expr length "$a"`