1#! /bin/sh 2 3cd tests 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 ${pref}_query_one_count 19EOF 20 21# Count with in memory hash doubling 22$JF count -t $nCPUs -o ${pref}_m15_s2M.jf -s 2M -C -m 15 seq10m.fa 23$JF histo ${pref}_m15_s2M.jf > ${pref}_m15_s2M.histo 24$JF stats ${pref}_m15_s2M.jf > ${pref}_m15.stats 25 26# Count without size doubling 27$JF count -t $nCPUs -o ${pref}_m15_s16M.jf -s 16M -C -m 15 seq10m.fa 28$JF histo ${pref}_m15_s16M.jf > ${pref}_m15_s16M.histo 29 30# Count large merges in binary and text. Should agree 31$JF count -m 40 -t $nCPUs -o ${pref}_text.jf -s 2M --text seq1m_0.fa 32$JF count -m 40 -t $nCPUs -o ${pref}_binary.jf -s 2M seq1m_0.fa 33$JF histo ${pref}_text.jf > ${pref}_text.histo 34$JF stats ${pref}_text.jf > ${pref}_text.stats 35$JF histo ${pref}_binary.jf > ${pref}_binary.histo 36$JF stats ${pref}_binary.jf > ${pref}_binary.stats 37$JF dump -c ${pref}_text.jf | sort > ${pref}_text.dump 38$JF dump -c ${pref}_binary.jf | sort > ${pref}_binary.dump 39 40# Check the lower and upper count without merging 41$JF count -t $nCPUs -o ${pref}_m15_s2M_L2_U3.jf -s 2M -C -m 15 -L2 -U3 seq10m.fa 42$JF histo ${pref}_m15_s2M_L2_U3.jf > ${pref}_m15_s2M_L2_U3.histo 43 44# Check the lower and upper count limits with merging 45$JF count -t $nCPUs -o ${pref}_m15_s2M_L2_U3_automerge.jf -s 2M -C -m 15 -L2 -U3 --disk seq10m.fa 46$JF histo ${pref}_m15_s2M_L2_U3_automerge.jf > ${pref}_m15_s2M_L2_U3_automerge.histo 47 48# Check query 49$JF query ${pref}_binary.jf -s seq1m_0.fa | grep ' 1$' | wc -l | sed -e 's/ //g' > ${pref}_query_one_count 50# $JF query ${pref}_binary.jf -s seq1m_0.fa -C | grep ' 1$' | wc -l | sed -e 's/ //g' > ${pref}_query_canonical_one_count 51 52# $JF count -m 40 -t $nCPUs -o ${pref}_text -s 2M --text seq1m_0.fa 53# $JF info -s ${pref}_text0 | sort > ${pref}_text0_dump 54 55# $JF count -m 40 -t $nCPUs -o ${pref}_bin -s 2M seq1m_0.fa 56# $JF dump -c ${pref}_bin0 | sort > ${pref}_bin0_dump 57 58# $JF histo ${pref}_bin0 > ${pref}.histo 59 60# Count all k-mers 61# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \ 62# -s 10000000 --timing ${pref}.timing --stats ${pref}.stats seq10m.fa 63# # Output only counts >= 2 64# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o ${pref}_L \ 65# -s 10000000 --timing ${pref}.timing -L 2 seq10m.fa 66# # Stream output 67# $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o /dev/fd/1 -O \ 68# -s 10000000 --timing ${pref}.timing --stats ${pref}.stats seq10m.fa | \ 69# cat > ${pref}_S 70 71# $JF histo -f ${pref}_0 > ${pref}.histo 72# $JF dump -c ${pref}_L_0 > ${pref}_L.dump 73# $JF dump -c -L 2 ${pref}_0 > ${pref}.dump 74# cat ${pref}_0 | $JF dump -c -L 2 /dev/fd/0 > ${pref}_stream.dump 75# echo "GCCATTTCGATTAAAGAATGAT TAGGCATGCAACGCTTCCCTTT" | $JF query ${pref}_0 > ${pref}.query 76# $JF dump -c ${pref}_0 > ${pref}_all.dump 77# $JF dump -c ${pref}_S > ${pref}_S_all.dump 78 79check ${pref}.md5sum 80 81# cat ${pref}.timing 82 83