1#! /bin/sh
2
3mkdir -p tests-data; cd tests-data
4. ../compat.sh
5
6if ! grep -q '#define HAVE_HTSLIB' ../config.h; then
7    echo "Skip SAM/BAM/CRAM file format test"
8    exit 77
9fi
10
11sort -k2,2 > ${pref}.md5sum <<EOF
128f8a71e04c27cd88918f11d44d9b3852 ${pref}_sam.histo
138f8a71e04c27cd88918f11d44d9b3852 ${pref}_bam.histo
148f8a71e04c27cd88918f11d44d9b3852 ${pref}_cram.histo
15f0faf797cc55add8b6e88ab67bbcf19b ${pref}_sam_qual.histo
16f0faf797cc55add8b6e88ab67bbcf19b ${pref}_bam_qual.histo
17f0faf797cc55add8b6e88ab67bbcf19b ${pref}_cram_qual.histo
18EOF
19
20comp_histo() {
21    set -x
22    suffix=$1
23    $JF count -t $nCPUs -m 20 -s 10M -o ${pref}_${suffix}.jf -C --sam seq10m.${suffix}
24    $JF histo ${pref}_${suffix}.jf > ${pref}_${suffix}.histo
25    $JF count -t $nCPUs -m 20 -s 10M -o ${pref}_${suffix}_qual.jf -C -Q D --sam seq10m.${suffix}
26    $JF histo ${pref}_${suffix}_qual.jf > ${pref}_${suffix}_qual.histo
27}
28
29comp_histo sam
30
31if [ -f seq10m.bam ]; then
32    comp_histo bam
33else
34    cp ${pref}_sam.histo ${pref}_bam.histo
35    cp ${pref}_sam_qual.histo ${pref}_bam_qual.histo
36fi
37
38if [ -f seq10m.cram ]; then
39    comp_histo cram
40else
41    cp ${pref}_sam.histo ${pref}_cram.histo
42    cp ${pref}_sam_qual.histo ${pref}_cram_qual.histo
43fi
44
45check ${pref}.md5sum
46