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Copy file name to clipboardExpand all lines: src/commons/LocalParameters.h
+6-6Lines changed: 6 additions & 6 deletions
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@@ -67,8 +67,8 @@ class LocalParameters : public Parameters {
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PARAMETER(PARAM_WRITE_FRAG_COORDS)
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int writeFragCoords;
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PARAMETER(PARAM_LEN_SEARCH_START)
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intlenSearchStart;
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PARAMETER(PARAM_LEN_SCAN_FOR_START)
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intlenScanForStart;
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private:
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LocalParameters() :
@@ -87,7 +87,7 @@ class LocalParameters : public Parameters {
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PARAM_ALLOW_OVERLAP(PARAM_ALLOW_OVERLAP_ID,"--overlap", "allow same-strand overlaps", "allow predictions to overlap another on the same strand. when not allowed (default), only the prediction with better E-value will be retained [0,1]", typeid(int), (void *) &overlapAllowed, "^[0-1]{1}$"),
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PARAM_WRITE_TKEY(PARAM_WRITE_TKEY_ID,"--target-key", "write target key instead of accession", "write the target key (internal DB identifier) instead of its accession. By default (0) target accession will be written [0,1]", typeid(int), (void *) &writeTargetKey, "^[0-1]{1}$"),
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PARAM_WRITE_FRAG_COORDS(PARAM_WRITE_FRAG_COORDS_ID,"--write-frag-coords", "write fragment contig coords", "write the contig coords of the stop-to-stop fragment in which putative exon lies. By default (0) only putative exon coords will be written [0,1]", typeid(int), (void *) &writeFragCoords, "^[0-1]{1}$"),
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PARAM_LEN_SEARCH_START(PARAM_LEN_SEARCH_START_ID,"--len-search-start", "length to search for start codon", "length to search for a start codon before the first exon and in the same frame. By default (0) no search", typeid(int), (void *) &lenSearchStart, "^[0-9]+$")
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PARAM_LEN_SCAN_FOR_START(PARAM_LEN_SCAN_FOR_START_ID,"--len-scan-for-start", "length to scan for start codon", "length to scan for a start codon before the first exon and in the same frame. By default (0) no scan", typeid(int), (void *) &lenScanForStart, "^[0-9]+$")
@@ -155,8 +155,8 @@ class LocalParameters : public Parameters {
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// default value 0 means only coords of putative exon are written
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writeFragCoords = 0;
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// default value 0 means no searching before the first exon
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lenSearchStart = 0;
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// default value 0 means no scanning before the first exon
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lenScanForStart = 0;
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citations.emplace(CITATION_METAEUK, "Levy Karin E, Mirdita M, Soeding J: MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics. biorxiv, 851964 (2019).");
if ((par.translationTable != 1) && (par.lenSearchStart > 0)) {
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Debug(Debug::WARNING) << "Selected translation table is not canonical and search for start is turned on. Please note that only ATG/atg is considered a start codon for the search!\n";
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if ((par.translationTable != 1) && (par.lenScanForStart > 0)) {
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Debug(Debug::WARNING) << "Selected translation table is not canonical and scan for start is turned on. Please note that only ATG/atg is considered a start codon for the scan!\n";
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}
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// for now, opting to use only ATG/atg as start codon because:
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