mode merge: added -out option

muellan · Jul 8, 2022 · 4e482bc · 4e482bc
1 parent ffbe0ac
commit 4e482bc
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Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/docs/mode_merge.txt b/docs/mode_merge.txt
@@ -41,6 +41,12 @@ REQUIRED PARAMETERS
                       taxonomic data files)
 
 
+MERGING RESULTS OUTPUT
+
+    <file>            Redirect output to file <file>.
+                      If not specified, output will be written to stdout.
+
+
 CLASSIFICATION
 
     -lowest <rank>    Do not classify on ranks below <rank>
@@ -85,7 +91,7 @@ CLASSIFICATION
                       default: off
 
 
-GENERAL OUTPUT
+GENERAL OUTPUT FORMATTING
 
     -silent|-verbose  information level during build:
                       silent => none / verbose => most detailed

diff --git a/src/options.cpp b/src/options.cpp
@@ -1683,10 +1683,18 @@ merge_mode_cli(merge_options& opt, error_messages& err)
             % "directory with taxonomic hierarchy data (see NCBI's taxonomic data files)"
     )
     ,
+    "MERGING RESULTS OUTPUT" %
+    (   option("-out") &
+        value("file", qry.queryMappingsFile)
+            .if_missing([&]{ err += "Output filename missing after '-out'!"; })
+        % "Redirect output to file <file>.\n"
+          "If not specified, output will be written to stdout."
+    )
+    ,
     "CLASSIFICATION" %
         classification_params_cli(qry.classify, err)
     ,
-    "GENERAL OUTPUT" % (
+    "GENERAL OUTPUT FORMATTING" % (
         info_level_cli(opt.infoLevel, err)
         ,
         option("-no-summary", "-nosummary").set(qry.output.showSummary,false)