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