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ChunShowChunShow
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error fix and undate regression results
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8 files changed

+92
-20
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8 files changed

+92
-20
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‎regression/run_cluster.sh

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#!/bin/sh -e
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CLUDB="${RESULTS}/clu"
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"${MMSEQS}" createdb "${DATADIR}/clu.fasta" "${CLUDB}" --shuffle 0
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"${MMSEQS}" cluster "${CLUDB}" "$RESULTS/results_clu" "$RESULTS/tmp" --min-seq-id 0.3 -s 2 --cluster-steps 3
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"${MMSEQS}" createtsv "${CLUDB}" "${CLUDB}" "$RESULTS/results_clu" "$RESULTS/results_cluster.tsv"
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="15691"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎regression/run_cluster_update.sh

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#!/bin/sh -e
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SEQCLUDB1="${RESULTS}/clu1"
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SEQCLUDB2="${RESULTS}/clu2"
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awk 'NR%4==1 || NR%4==2{print}' "${DATADIR}/clu.fasta" > "$RESULTS/clu1.fasta"
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awk 'NR%4==3 || NR%4==0{print}' "${DATADIR}/clu.fasta" > "$RESULTS/clu2.fasta"
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head -n 2 "$RESULTS/clu1.fasta" >> "$RESULTS/clu2.fasta"
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cat "$RESULTS/clu1.fasta" "$RESULTS/clu2.fasta" > "$RESULTS/cluCombined.fasta"
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"${MMSEQS}" createdb "$RESULTS/clu1.fasta" "${SEQCLUDB1}"
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"${MMSEQS}" createdb "$RESULTS/cluCombined.fasta" "${SEQCLUDB2}"
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"${MMSEQS}" linclust "${SEQCLUDB1}" "$RESULTS/results_clu" "$RESULTS/tmp" --cov-mode 1 -a -c 0.50 --min-seq-id 0.50
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"${MMSEQS}" clusterupdate "${SEQCLUDB1}" "${SEQCLUDB2}" "$RESULTS/results_clu" "$RESULTS/seqdb_update" "$RESULTS/clu_updated" "$RESULTS/tmp" --cov-mode 1 -c 0.50 --min-seq-id 0.50
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"${MMSEQS}" createtsv "$RESULTS/seqdb_update" "$RESULTS/seqdb_update" "$RESULTS/clu_updated" "$RESULTS/clu_updated.tsv"
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CLUSTERMEMEBER=$(wc -l "$RESULTS/clu_updated.tsv" | awk '{print $1}')
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CLUSTER=$(echo $(cut -f1 "$RESULTS/clu_updated.tsv" | sort -u | wc -l))
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UPDATEDSEQCNT=$(wc -l "$RESULTS/seqdb_update.index" | awk '{print $1}')
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TARGET="32132 24733 32132"
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ACTUAL="$CLUSTERMEMEBER $CLUSTER $UPDATEDSEQCNT"
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awk -v actual="$ACTUAL" -v target="$TARGET" 'BEGIN { print (actual == target) ? "GOOD" : "BAD"; \
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print "Expected: ", target; \
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print "Actual: ", actual; }' > "${RESULTS}.report"

‎regression/run_easy_cluster.sh

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#!/bin/sh -e
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"${MMSEQS}" easy-cluster "${DATADIR}/clu.fasta" "$RESULTS/results" "$RESULTS/tmp" --min-seq-id 0.3 -s 2 --cluster-steps 3
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="15691"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎regression/run_easy_cluster_reassign.sh

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#!/bin/sh -e
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cat "${DATADIR}/clu.fasta" | "${MMSEQS}" easy-cluster stdin "$RESULTS/results" "$RESULTS/tmp" --min-seq-id 0.3 -s 2 -c 0.8 --cov-mode 1 --cluster-reassign 1
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="17231"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎regression/run_easy_linclust.sh

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#!/bin/sh -e
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"${MMSEQS}" easy-linclust "${DATADIR}/clu.fasta" "$RESULTS/results" "$RESULTS/tmp" --cov-mode 1 --cluster-mode 0 -c 0.90 --min-seq-id 0.50
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="26146"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎regression/run_linclust.sh

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#!/bin/sh -e
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CLUDB=
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"${MMSEQS}" createdb "${DATADIR}/clu.fasta" "${RESULTS}/clu"
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"${MMSEQS}" linclust "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/tmp" --cov-mode 1 --cluster-mode 0 -c 0.90 --min-seq-id 0.50
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"${MMSEQS}" createtsv "${RESULTS}/clu" "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/results_cluster.tsv"
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="26135"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎regression/run_linclust_split.sh

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#!/bin/sh -e
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"${MMSEQS}" createdb "${DATADIR}/clu.fasta" "${RESULTS}/clu"
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"${MMSEQS}" linclust "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/tmp" --cov-mode 1 --cluster-mode 0 -c 0.90 --min-seq-id 0.50 --split-memory-limit 10M
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"${MMSEQS}" createtsv "${RESULTS}/clu" "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/results_cluster.tsv"
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awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
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ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
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TARGET="26135"
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awk -v actual="$ACTUAL" -v target="$TARGET" \
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'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
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> "${RESULTS}.report"

‎src/linclust/kmermatcher.cpp

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@@ -54,26 +54,6 @@ KmerPosition<T, IncludeAdjacentSeq> *initKmerPositionMemory(size_t size) {
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return hashSeqPair;
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}
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void maskSequence(int maskMode, int maskLowerCase, float maskProb, Sequence &seq, int maskLetter, ProbabilityMatrix * probMatrix){
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if (maskMode == 1) {
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tantan::maskSequences((char*)seq.numSequence,
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(char*)(seq.numSequence + seq.L),
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50 /*options.maxCycleLength*/,
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probMatrix->probMatrixPointers,
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0.005 /*options.repeatProb*/,
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0.05 /*options.repeatEndProb*/,
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0.5 /*options.repeatOffsetProbDecay*/,
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0, 0,
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maskProb /*options.minMaskProb*/, probMatrix->hardMaskTable);
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}
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if(maskLowerCase == 1 && (Parameters::isEqualDbtype(seq.getSequenceType(), Parameters::DBTYPE_AMINO_ACIDS) ||
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Parameters::isEqualDbtype(seq.getSequenceType(), Parameters::DBTYPE_NUCLEOTIDES))) {
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const char * charSeq = seq.getSeqData();
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for (int i = 0; i < seq.L; i++) {
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seq.numSequence[i] = (islower(charSeq[i])) ? maskLetter : seq.numSequence[i];
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}
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}
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}
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template <int TYPE, typename T, bool IncludeAdjacentSeq>
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std::pair<size_t, size_t> fillKmerPositionArray(KmerPosition<T, IncludeAdjacentSeq> * kmerArray, size_t kmerArraySize, DBReader<unsigned int> &seqDbr, Parameters & par, BaseMatrix * subMat, bool hashWholeSequence, size_t hashStartRange, size_t hashEndRange, size_t * hashDistribution){
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}
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MPI_Barrier(MPI_COMM_WORLD);
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if(mpiRank == 0){
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std::string splitBufferName;
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for(size_t split = 0; split < splits; split++) {
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std::string splitFileName = par.db2 + "_split_" +SSTR(split);
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splitFiles.push_back(splitFileName);

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