[INTERNAL] add hidden option not include versionnumber in outfile

Author: h-2

src/options.hpp

@@ -228,6 +228,7 @@ struct LambdaOptions : public SharedOptions
     std::bitset<64> samBamTags;
     bool            samWithRefHeader;
     unsigned        samBamSeq;
+    bool            versionInformationToOutputFile;
 
     unsigned        queryPart = 0;
 
@@ -470,7 +471,15 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
     setDefaultValue(parser, "sam-bam-tags", "AS NM ZE ZI ZF");
     setAdvanced(parser, "sam-bam-tags");
 
-        addSection(parser, "General Options");
+    addOption(parser, ArgParseOption("", "version-to-outputfile",
+        "Write the Lambda program tag and version number to the output file.",
+        ArgParseArgument::STRING,
+        "STR"));
+    setValidValues(parser, "version-to-outputfile", "on off");
+    setDefaultValue(parser, "version-to-outputfile", "on");
+    hideOption(parser, "version-to-outputfile");
+
+    addSection(parser, "General Options");
 #ifdef _OPENMP
     addOption(parser, ArgParseOption("t", "threads",
         "number of threads to run concurrently.",
@@ -851,6 +860,9 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
         (!options.samBamTags[SamBamExtraTags<>::Q_AA_CIGAR]))
         options.samBamSeq = 0;
 
+    getOptionValue(buffer, parser, "version-to-outputfile");
+    options.versionInformationToOutputFile = (buffer == "on");
+
     clear(buffer);
     getOptionValue(options.seedLength, parser, "seed-length");
     if ((!isSet(parser, "seed-length")) &&

src/output.hpp

@@ -261,6 +261,16 @@ myWriteHeader(TGH & globalHolder, TLambdaOptions const & options)
     {
         open(globalHolder.outfile, toCString(options.output));
         context(globalHolder.outfile).fields = options.columns;
+        auto & versionString = context(globalHolder.outfile).versionString;
+        clear(versionString);
+        append(versionString, _programTagToString(globalHolder.blastProgram));
+        append(versionString, " 2.2.26+ [created by LAMBDA");
+        if (options.versionInformationToOutputFile)
+        {
+            append(versionString, "-");
+            append(versionString, SEQAN_APP_VERSION);
+        }
+        append(versionString, ", see http://seqan.de/lambda and please cite correctly in your academic work]");
         writeHeader(globalHolder.outfile);
     } else // SAM or BAM
     {
@@ -305,13 +315,16 @@ myWriteHeader(TGH & globalHolder, TLambdaOptions const & options)
         appendValue(header, firstRecord);
 
         // Fill program header line.
-        BamHeaderRecord pgRecord;
-        pgRecord.type = BAM_HEADER_PROGRAM;
-        appendValue(pgRecord.tags, TTag("ID", "lambda"));
-        appendValue(pgRecord.tags, TTag("PN", "lambda"));
-        appendValue(pgRecord.tags, TTag("VN", SEQAN_APP_VERSION));
-        appendValue(pgRecord.tags, TTag("CL", options.commandLine));
-        appendValue(header, pgRecord);
+        if (options.versionInformationToOutputFile)
+        {
+            BamHeaderRecord pgRecord;
+            pgRecord.type = BAM_HEADER_PROGRAM;
+            appendValue(pgRecord.tags, TTag("ID", "lambda"));
+            appendValue(pgRecord.tags, TTag("PN", "lambda"));
+            appendValue(pgRecord.tags, TTag("VN", SEQAN_APP_VERSION));
+            appendValue(pgRecord.tags, TTag("CL", options.commandLine));
+            appendValue(header, pgRecord);
+        }
 
         // Fill homepage header line.
         BamHeaderRecord hpRecord0;

tests/maintests.sh

@@ -73,9 +73,10 @@ fi
 gunzip < "${SRCDIR}/tests/queries_${QALPHIN}.fasta.gz" > queries.fasta
 [ $? -eq 0 ] || errorout "Could not unzip queries.fasta"
 
-${BINDIR}/bin/lambda -d db.fasta -di ${DI} -p ${PROG} -q queries.fasta -t 1 -o output_${PROG}_${DI}.${EXTENSION}
+${BINDIR}/bin/lambda -d db.fasta -di ${DI} -p ${PROG} -q queries.fasta -t 1 --version-to-outputfile off -o output_${PROG}_${DI}.${EXTENSION}
 [ $? -eq 0 ] || errorout "Search failed."
 
 openssl md5 output_${PROG}_${DI}.${EXTENSION} >> /tmp/checksums
 ## TODO compare checksums instead of generating them
 
+