1#! /bin/sh 2 3mkdir -p tests-data; cd tests-data 4. ../compat.sh 5 6sort -k2,2 > ${pref}.md5sum <<EOF 7864c0b0826854bdc72a85d170549b64b ${pref}_m15_s2M.histo 8864c0b0826854bdc72a85d170549b64b ${pref}_m15_s16M.histo 941fd8408dde0ea14bec7425b1a877140 ${pref}_m15.stats 10376761a6e273b57b3428c14e3b536edf ${pref}_binary.dump 11376761a6e273b57b3428c14e3b536edf ${pref}_text.dump 129251799dd5dbd3f617124aa2ff72112a ${pref}_binary.histo 13c30cba4fe2886cea4abb27f5c30ea35e ${pref}_binary.stats 149251799dd5dbd3f617124aa2ff72112a ${pref}_text.histo 15c30cba4fe2886cea4abb27f5c30ea35e ${pref}_text.stats 1694625cd2d59e278f08421a673eb0926a ${pref}_m15_s2M_L2_U3.histo 1794625cd2d59e278f08421a673eb0926a ${pref}_m15_s2M_L2_U3_automerge.histo 1845fb383344e0fb0b7540718339be4c03 ${pref}_query_one_count 19864c0b0826854bdc72a85d170549b64b ${pref}_m15_DOS.histo 20EOF 21 22# Count with in memory hash doubling 23$JF count -t $nCPUs -o ${pref}_m15_s2M.jf -s 2M -C -m 15 seq10m.fa 24$JF histo ${pref}_m15_s2M.jf > ${pref}_m15_s2M.histo 25$JF stats ${pref}_m15_s2M.jf > ${pref}_m15.stats 26 27# Count without size doubling 28$JF count -t $nCPUs -o ${pref}_m15_s16M.jf -s 16M -C -m 15 seq10m.fa 29$JF histo ${pref}_m15_s16M.jf > ${pref}_m15_s16M.histo 30 31# Count large merges in binary and text. Should agree 32$JF count -m 40 -t $nCPUs -o ${pref}_text.jf -s 2M --text seq1m_0.fa 33$JF count -m 40 -t $nCPUs -o ${pref}_binary.jf -s 2M seq1m_0.fa 34$JF histo ${pref}_text.jf > ${pref}_text.histo 35$JF stats ${pref}_text.jf > ${pref}_text.stats 36$JF histo ${pref}_binary.jf > ${pref}_binary.histo 37$JF stats ${pref}_binary.jf > ${pref}_binary.stats 38$JF dump -c ${pref}_text.jf | sort > ${pref}_text.dump 39$JF dump -c ${pref}_binary.jf | sort > ${pref}_binary.dump 40 41# Check the lower and upper count without merging 42$JF count -t $nCPUs -o ${pref}_m15_s2M_L2_U3.jf -s 2M -C -m 15 -L2 -U3 seq10m.fa 43$JF histo ${pref}_m15_s2M_L2_U3.jf > ${pref}_m15_s2M_L2_U3.histo 44 45# Check the lower and upper count limits with merging 46$JF count -t $nCPUs -o ${pref}_m15_s2M_L2_U3_automerge.jf -s 2M -C -m 15 -L2 -U3 --disk seq10m.fa 47$JF histo ${pref}_m15_s2M_L2_U3_automerge.jf > ${pref}_m15_s2M_L2_U3_automerge.histo 48 49# Check query 50$JF query ${pref}_binary.jf -s seq1m_0.fa | grep ' 1$' | wc -l | sed -e 's/ //g' > ${pref}_query_one_count 51# $JF query ${pref}_binary.jf -s seq1m_0.fa -C | grep ' 1$' | wc -l | sed -e 's/ //g' > ${pref}_query_canonical_one_count 52 53# $JF count -m 40 -t $nCPUs -o ${pref}_text -s 2M --text seq1m_0.fa 54# $JF info -s ${pref}_text0 | sort > ${pref}_text0_dump 55 56# $JF count -m 40 -t $nCPUs -o ${pref}_bin -s 2M seq1m_0.fa 57# $JF dump -c ${pref}_bin0 | sort > ${pref}_bin0_dump 58 59# $JF histo ${pref}_bin0 > ${pref}.histo 60 61# Count all k-mers 62# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \ 63# -s 10000000 --timing ${pref}.timing --stats ${pref}.stats seq10m.fa 64# # Output only counts >= 2 65# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o ${pref}_L \ 66# -s 10000000 --timing ${pref}.timing -L 2 seq10m.fa 67# # Stream output 68# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o /dev/fd/1 -O \ 69# -s 10000000 --timing ${pref}.timing --stats ${pref}.stats seq10m.fa | \ 70# cat > ${pref}_S 71 72# $JF histo -f ${pref}_0 > ${pref}.histo 73# $JF dump -c ${pref}_L_0 > ${pref}_L.dump 74# $JF dump -c -L 2 ${pref}_0 > ${pref}.dump 75# cat ${pref}_0 | $JF dump -c -L 2 /dev/fd/0 > ${pref}_stream.dump 76# echo "GCCATTTCGATTAAAGAATGAT TAGGCATGCAACGCTTCCCTTT" | $JF query ${pref}_0 > ${pref}.query 77# $JF dump -c ${pref}_0 > ${pref}_all.dump 78# $JF dump -c ${pref}_S > ${pref}_S_all.dump 79 80# Check DOS line ending 81if [ -n "$UNIX2DOS" ]; then 82 $JF count -t $nCPUs -o ${pref}_m15_DOS.jf -s 2M -C -m 15 seq10mDOS.fa 83 $JF histo ${pref}_m15_DOS.jf > ${pref}_m15_DOS.histo 84else 85 cp ${pref}_m15_s2M.histo ${pref}_m15_DOS.histo 86fi 87 88check ${pref}.md5sum 89 90