Fix some CLI parameters

epi2me-labs · Sep 4, 2023 · 681b3ab · 681b3ab
1 parent 7f5b2d9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.1.7]
+### Fixed
+- Several CLI options did not correctly require a value.
+
 ## [v0.1.6]
 ### Fixed
 - Memory mapping CLI option was setting translated search mode not enabling memory mapping!

diff --git a/server/kraken2_server.cc b/server/kraken2_server.cc
@@ -224,12 +224,12 @@ void ParseCommandLine(int argc, char **argv, Options &opts) {
         {"report-zero", no_argument, NULL, 'Z'},
         {"translated-search", no_argument, NULL, 't'},
         {"translated-search", no_argument, NULL, 'T'},
-        {"confidence", no_argument, NULL, 'c'},
-        {"confidence", no_argument, NULL, 'C'},
-        {"min-quality", no_argument, NULL, 'q'},
-        {"min-quality", no_argument, NULL, 'Q'},
-        {"hit-groups", no_argument, NULL, 'g'},
-        {"hit-groups", no_argument, NULL, 'G'},
+        {"confidence", required_argument, NULL, 'c'},
+        {"confidence", required_argument, NULL, 'C'},
+        {"min-quality", required_argument, NULL, 'q'},
+        {"min-quality", required_argument, NULL, 'Q'},
+        {"hit-groups", required_argument, NULL, 'g'},
+        {"hit-groups", required_argument, NULL, 'G'},
         {"memory-mapping", no_argument, NULL, 'o'},
         {"memory-mapping", no_argument, NULL, 'O'},
         {"wait", required_argument, NULL, 'w'},