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VDB-3864: Filter out KClientHttpOpen, KLockAcquire, KFileReadAll_v1, …
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…certificate messages; Updated some expected library messages
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Andrew Klymenko committed Aug 2, 2019
1 parent f4d4b3a commit f2a5169
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4 changes: 2 additions & 2 deletions tools/ref-variation/test/expected/ref-variation.out
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Original file line number Diff line number Diff line change
Expand Up @@ -157,8 +157,8 @@ info: processed 100%
info: percent="0"
info: processed 0%
: Seeding the random number generator
: Loading CA root certificates
: Parsing text for default CA root certificates
: Configuring SSl defaults
: Seeding the random number generator
: Configuring SSl defaults
info: Found indel box at pos=36662041, length=10
info: reference: ...CAACA[ATAATTATAA]GATTC...
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36 changes: 19 additions & 17 deletions tools/ref-variation/test/ref-variation.sh
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Expand Up @@ -5,24 +5,26 @@ then
echo "ref-variation test is disabled for Mac"
else
rm -f ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -r NC_000013.10 -p 100635036 --query ACC -l 0 SRR793062 SRR795251 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000002.11 -p 73613071 --query "C" -l 1 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -t 16 -r NC_000007.13 -p 117292900 --query "-" -l 4 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 SRR867061 SRR867131 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c --count-strand counteraligned -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 SRR867061 SRR867131 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000671.1 -p 136131022 --query "T" -l 1 SRR1601768 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -r NC_000013.10 -p 100635036 --query ACC -l 0 SRR793062 SRR795251 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000002.11 -p 73613071 --query "C" -l 1 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -t 16 -r NC_000007.13 -p 117292900 --query "-" -l 4 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 SRR867061 SRR867131 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c --count-strand counteraligned -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 SRR867061 SRR867131 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000671.1 -p 136131022 --query "T" -l 1 SRR1601768 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
# the following run generates warnings from KDyldLoad; no idea why, filtering them out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r NC_000001.11 -p 136131022 --query "T" -l 1 SRR1601768 2>&1 | grep -v KDyldLoad | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -t 16 -c -r CM000671.1 -p 136131021 --query "T" -l 1 SRR1596639 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000002.11 -p 73613030 --query "AT[1-3]" -l 3 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000664.1 -p 234668879 -l 14 --query "ATATATATATATAT" SRR1597895 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000664.1 -p 234668879 -l 14 --query "AT[1-8]" SRR1597895 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000001.10 -p 1064999 -l 1 --query A 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000020.10 -p 137534 -l 2 --query - 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -c -r CM000663.1 -p 123452 -l 7 --query "GGGAGAAAT" 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vvv -r CM000684.1 -p 36662045 --query - -l 6 -vvv -c SRR1597729 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000001.10 -p 570000 -l 1 --query A 2>&1 | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L err -v -c -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 -i ref-variation.in >> ref-variation.out 2>&1
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r NC_000001.11 -p 136131022 --query "T" -l 1 SRR1601768 2>&1 | grep -v ': KClientHttpOpen - ' | grep -v ':KLockAcquire:' | grep -v KDyldLoad | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -t 16 -c -r CM000671.1 -p 136131021 --query "T" -l 1 SRR1596639 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000002.11 -p 73613030 --query "AT[1-3]" -l 3 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
#echo 1 >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000664.1 -p 234668879 -l 14 --query "ATATATATATATAT" SRR1597895 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
#echo 2 >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -v -c -r CM000664.1 -p 234668879 -l 14 --query "AT[1-8]" SRR1597895 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000001.10 -p 1064999 -l 1 --query A 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000020.10 -p 137534 -l 2 --query - 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -c -r CM000663.1 -p 123452 -l 7 --query "GGGAGAAAT" 2>&1 | grep -v ': KClientHttpOpen - ' | grep -v ' CA root certificate' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vvv -r CM000684.1 -p 36662045 --query - -l 6 -vvv -c SRR1597729 2>&1 | grep -v ': KClientHttpOpen - ' | grep -v ': KFileReadAll_v1 ' | grep -v 'CA root certificate' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L info -vv -r NC_000001.10 -p 570000 -l 1 --query A 2>&1 | grep -v ': KClientHttpOpen - ' | sed "s/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}T[0-9]\{2\}\:[0-9]\{2\}\:[0-9]\{2\}[ \t]*ref-variation\.[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?[ \t]*//" >> ref-variation.out
$BINDIR/ref-variation --no-user-settings --algorithm=ra -L err -v -c -t 1 -r NC_000002.11 -p 73613067 --query "-" -l 3 -i ref-variation.in | grep -v ': KClientHttpOpen - ' >> ref-variation.out 2>&1
diff expected/ref-variation.out ref-variation.out
EXIT_CODE=$?
#rm ref-variation.out
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