[med-svn] [subread] 01/14: Remove trailing white spaces

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit 8f897789c79440e6e8b28e266ffc71232c750181
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Mar 23 14:47:25 2016 +0100

    Remove trailing white spaces
---
 debian/README.source       |  2 +-
 debian/README.test         |  2 +-
 debian/filter.pl           |  2 +-
 debian/rules               |  4 ++--
 debian/tests/subread-tests | 14 +++++++-------
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/debian/README.source b/debian/README.source
index 85060e8..b3dfd84 100644
--- a/debian/README.source
+++ b/debian/README.source
@@ -8,7 +8,7 @@
 
  arm64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 mipsel ppc64elo
 
- It is possible to built subread also on powerpc, mips and s390x, 
+ It is possible to built subread also on powerpc, mips and s390x,
  but a few core tools of subread suite fail on these architectures.
  exactSNP can't read the input BAM file and subjunc segfaults.
 
diff --git a/debian/README.test b/debian/README.test
index 0bfcd5e..0fc4f7e 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -1,5 +1,5 @@
 Subread provides "test" directory with various tests.
-Some of the tests are performed during package build process and can 
+Some of the tests are performed during package build process and can
 be found in debian/test directory.
 
 To see the original tests one needs to install subread-data package
diff --git a/debian/filter.pl b/debian/filter.pl
index d87d3ec..a7a9fac 100755
--- a/debian/filter.pl
+++ b/debian/filter.pl
@@ -32,7 +32,7 @@ while ( <STDIN> ) {
     # tidy up help2man removeDuP output:
     s/Repeated\sRead\sRemoval.*accessible:\s\'\'//xms;
     s/(.SH\sNAME\n[\w\d-]*):/$1/gxms;
-    # remove "./" from examples 
+    # remove "./" from examples
     s/(\\\&\.\/)([\w\d-]*)/$2/gxms;
     # remove indent and "boldify" the name
     s/(\.SH\sUSAGE\n*)(\.IP\n|\s|\.TP\n)([\w\d\\-]*)/$1\\fB$3\\fR/xms;
diff --git a/debian/rules b/debian/rules
index 30e07a6..0a972b2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,7 +14,7 @@ BIBDOC := SubreadUsersGuide.aux
 DOCDIR := doc
 
 DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
-EXTRA_CC_FLAGS = 
+EXTRA_CC_FLAGS =
 ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),amd64 i386))
         EXTRA_CC_FLAGS = -mtune=generic -msse3
 endif
@@ -77,7 +77,7 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
 
 override_dh_installexamples-indep:
 	tar -cJf $(CURDIR)/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz  test/
-	
+
 override_dh_compress:
 # do not compress pdfs
 	dh_compress -X.pdf -Xtest.tar.xz
diff --git a/debian/tests/subread-tests b/debian/tests/subread-tests
index ddddcd2..da23b0c 100755
--- a/debian/tests/subread-tests
+++ b/debian/tests/subread-tests
@@ -1,8 +1,8 @@
 #!/bin/sh
 
-#use test.tar.xz from /usr/share/doc/subread/examples/ if executed with 
+#use test.tar.xz from /usr/share/doc/subread/examples/ if executed with
 #autpkgtest
-#use binaries and test dir from the source package if executed 
+#use binaries and test dir from the source package if executed
 #by override_dh_auto_test:
 
 set -e
@@ -13,7 +13,7 @@ then
     TMPDIR=$(mktemp -d)
     tar -xf ${examplesdir}/test.tar.xz -C $TMPDIR
     WORKDIR=${TMPDIR}/test
-else 
+else
     #run tests in the source package if executed during building process
     TMPDIR=$1
     cp -r ${TMPDIR}/test ${TMPDIR}/adt_test
@@ -26,7 +26,7 @@ featureCounts -a data/test-minimum.GTF -o test-minimum.FC data/test-minimum.sam
 
 cd $WORKDIR/subjunc
 mkdir tmp
-subread-buildindex -o tmp/small1 ../chr901.fa 
+subread-buildindex -o tmp/small1 ../chr901.fa
 subjunc --SAMoutput -i tmp/small1 -o junctions.sam -r data/junction-reads-A.fq \
 -R data/junction-reads-B.fq
 subjunc -i tmp/small1 -o junctionsNfusions.bam \
@@ -34,7 +34,7 @@ subjunc -i tmp/small1 -o junctionsNfusions.bam \
 
 cd $WORKDIR/subread-align
 mkdir tmp
-subread-buildindex -B -F -o tmp/small1 -M100 ../chr901.fa 
+subread-buildindex -B -F -o tmp/small1 -M100 ../chr901.fa
 subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-noerror-r1.fq \
     -o tmp/test-tmp.sam1 -H -J
 subread-align --SAMoutput -t0 -u -i tmp/small1 -r data/test-noerror-r1.fq \
@@ -44,13 +44,13 @@ subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-noerror-r1.fq \
 subread-align --SAMoutput -t0 -u -i tmp/small1 -r data/test-noerror-r1.fq \
     -R data/test-noerror-r2.fq -o tmp/test-tmp.sam4  -Q -J
 subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-error-r1.fq \
-    -R data/test-error-r2.fq -o tmp/test-tmp.sam5 -H -J 
+    -R data/test-error-r2.fq -o tmp/test-tmp.sam5 -H -J
 subread-align --SAMoutput -t0 -i tmp/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz \
     -R data/test-err-mut-r2.fq.gz -o tmp/test-tmp.sam6 -H -J \
     --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY
 
 cd $WORKDIR/exactSNP
-exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b 
+exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b
 
 
 if [ $# -eq 0 ]

-- 
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