1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
|
#!/bin/sh
unset GZIP
FQ=test.cnt.gz
rm -f ${FQ}{,.gbi}
lines=500000
python3 tests/make-test-fastq.py $lines | bgzip -c > $FQ
echo "indexing"
time grabix index $FQ
echo "indexed"
python3 tests/test-fastq.py $FQ
a=$(grabix grab test.cnt.gz $(($lines * 4)))
b=$(zless $FQ | tail -1)
if [ "$a" != "$b" ] ; then
echo FAIL last record
fi
rm -f ${FQ}{,.gbi}
for V in `find . -name *.vcf -type f` ; do
rm -f ${V}.*
bgzip -f $V
grabix index ${V}.gz
sleep 1
exp=$(zgrep -cv "#" $V.gz)
obs=$(grabix size $V.gz)
if [ "$exp" != "$obs" ] ; then
echo "FAIL: $V: expected $exp lines found $obs"
else
echo "OK $V"
fi
rm -f ${V}.*
done
|
