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
34
35
36
37
38
39
40
41
42
43
44
45
|
#! /bin/sh
cd tests
. ./compat.sh
if ! grep -q '#define HAVE_HTSLIB' ../config.h; then
echo "Skip SAM/BAM/CRAM file format test"
exit 77
fi
sort -k2,2 > ${pref}.md5sum <<EOF
8f8a71e04c27cd88918f11d44d9b3852 ${pref}_sam.histo
8f8a71e04c27cd88918f11d44d9b3852 ${pref}_bam.histo
8f8a71e04c27cd88918f11d44d9b3852 ${pref}_cram.histo
f0faf797cc55add8b6e88ab67bbcf19b ${pref}_sam_qual.histo
f0faf797cc55add8b6e88ab67bbcf19b ${pref}_bam_qual.histo
f0faf797cc55add8b6e88ab67bbcf19b ${pref}_cram_qual.histo
EOF
comp_histo() {
set -x
suffix=$1
$JF count -t $nCPUs -m 20 -s 10M -o ${pref}_${suffix}.jf -C --sam seq10m.${suffix}
$JF histo ${pref}_${suffix}.jf > ${pref}_${suffix}.histo
$JF count -t $nCPUs -m 20 -s 10M -o ${pref}_${suffix}_qual.jf -C -Q D --sam seq10m.${suffix}
$JF histo ${pref}_${suffix}_qual.jf > ${pref}_${suffix}_qual.histo
}
comp_histo sam
if [ -f seq10m.bam ]; then
comp_histo bam
else
cp ${pref}_sam.histo ${pref}_bam.histo
cp ${pref}_sam_qual.histo ${pref}_bam_qual.histo
fi
if [ -f seq10m.cram ]; then
comp_histo cram
else
cp ${pref}_sam.histo ${pref}_cram.histo
cp ${pref}_sam_qual.histo ${pref}_cram_qual.histo
fi
check ${pref}.md5sum
|
