[med-svn] [subread] 05/08: d/tests/subread-tests: update tests with parameters introduced in the new version

[Alex Mestiashvili]

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

commit d6574990b59e4724c5382c86cd5cadcfd8c82e40
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Nov 6 16:06:59 2015 +0100

     d/tests/subread-tests: update tests with parameters introduced in the new version
---
 debian/tests/subread-tests | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/debian/tests/subread-tests b/debian/tests/subread-tests
index 9975593..ddddcd2 100755
--- a/debian/tests/subread-tests
+++ b/debian/tests/subread-tests
@@ -27,25 +27,25 @@ 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 
-subjunc -i tmp/small1 -o junctions.sam -r data/junction-reads-A.fq \
+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 --BAMoutput \
+subjunc -i tmp/small1 -o junctionsNfusions.bam \
 -r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions
 
 cd $WORKDIR/subread-align
 mkdir tmp
-subread-buildindex -o tmp/small1 -M100 ../chr901.fa 
-subread-align -i tmp/small1 -r data/test-noerror-r1.fq \
+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 -u -i tmp/small1 -r data/test-noerror-r1.fq \
+subread-align --SAMoutput -t0 -u -i tmp/small1 -r data/test-noerror-r1.fq \
     -o tmp/test-tmp.sam2 -H -J
-subread-align -i tmp/small1 -r data/test-noerror-r1.fq \
+subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-noerror-r1.fq \
     -R data/test-noerror-r2.fq -o tmp/test-tmp.sam3 -H -J
-subread-align -u -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 -i tmp/small1 -r data/test-error-r1.fq \
+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 
-subread-align -i tmp/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz \
+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
 

-- 
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