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Set default for tax. workflow to top1 mode, change top1 mode so that …

…same scoring hits are considered
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martin-steinegger committed May 10, 2019
1 parent 11c1e58 commit a6e1b91961288c67bc92dcaee0db13f226da7e93
Showing with 6 additions and 5 deletions.
  1. +5 −2 data/taxonomy.sh
  2. +1 −3 src/commons/Parameters.cpp
@@ -36,8 +36,11 @@ LCA_SOURCE="${TMP_PATH}/first"

# top hip mode
if [ -n "${TOP_HIT}" ]; then
"$MMSEQS" filterdb "${TMP_PATH}/first" "${TMP_PATH}/top1" --extract-lines 1 \
|| fail "Filterdb died"

if [ ! -e "${TMP_PATH}/top1" ]; then
"$MMSEQS" filterdb "${TMP_PATH}/first" "${TMP_PATH}/top1" --beats-first --filter-column 4 --comparison-operator le \
|| fail "First filterdb died"
fi
LCA_SOURCE="${TMP_PATH}/top1"
else
# 2bLCA mode
@@ -997,8 +997,6 @@ Parameters::Parameters():
taxonomy.push_back(&PARAM_LCA_MODE);
taxonomy.push_back(&PARAM_TAX_OUTPUT_MODE);
taxonomy.push_back(&PARAM_USESEQID);
taxonomy.push_back(&PARAM_REMOVE_TMP_FILES);
taxonomy.push_back(&PARAM_RUNNER);
// easy taxonomy
easytaxonomy = combineList(taxonomy, addtaxonomy);
@@ -1747,7 +1745,7 @@ void Parameters::setDefaults() {
expansionMode = 1;

// taxonomy
taxonomySearchMode = Parameters::TAXONOMY_2BLCA_APPROX;
taxonomySearchMode = Parameters::TAXONOMY_TOP_HIT;
taxonomyOutpuMode = Parameters::TAXONOMY_OUTPUT_LCA;
}

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