Run all tests

parent 0f575508
......@@ -22,41 +22,9 @@ else
WORKDIR=${TMPDIR}/adt_test
fi
cd $WORKDIR/featureCounts
#featureCounts -a data/test-minimum.GTF -o test-minimum.FC data/test-minimum.sam
#bash data/compare.sh data/corner-INDEL.sam data/corner-INDEL.ora data/test-minimum.GTF "-p" "indel reads"
bash featureCounts-test.sh
cd $WORKDIR/subjunc
#mkdir tmp
bash subjunc-test.sh
#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 \
#-r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions
cd $WORKDIR/subread-align
mkdir tmp
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 \
-o tmp/test-tmp.sam2 -H -J
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 --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
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
bash exactSNP-test.sh
cd $WORKDIR
bash test_all.sh
if [ $# -eq 0 ]
then
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment