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From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Subject: Normalize some command line help to generate better manual pages
Forwarded: https://github.com/seqan/seqan/pull/1999
--- seqan2.orig/apps/micro_razers/micro_razers.cpp
+++ seqan2/apps/micro_razers/micro_razers.cpp
@@ -212,6 +212,7 @@
ArgumentParser parser("micro_razers");
+ setShortDescription(parser, "Map small RNA reads possibly containing 3' adapter sequence");
addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIREADS FILE\\fP>");
addDescription(parser, "MicroRazerS uses a prefix-based mapping strategy to map "
"small RNA reads possibly containing 3' adapter sequence. ");
--- seqan2.orig/apps/sgip/sgip.cpp
+++ seqan2/apps/sgip/sgip.cpp
@@ -168,7 +168,7 @@
void _setupParser(TParser & parser)
{
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
- addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
+ setShortDescription(parser, "Solution of Graph Isomorphism Problem");
addUsageLine(parser, "-o <original graph> [Option]");
addSection(parser, "Mandatory Options");
addOption(parser, ArgParseOption("o", "original", "File containing original graph", ArgParseArgument::INPUT_FILE,"IN"));
--- seqan2.orig/apps/splazers/splazers.cpp
+++ seqan2/apps/splazers/splazers.cpp
@@ -303,6 +303,7 @@
#ifdef RAZERS_MATEPAIRS
addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIREADS FILE 1\\fP> <\\fIREADS FILE 2\\fP>");
#endif
+ setShortDescription(parser, "Split-map read sequences");
addDescription(parser,
"SplazerS uses a prefix-suffix mapping strategy to split-map read sequences."
"If a SAM file of mapped reads is given as input, all unmapped but anchored"
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