[med-svn] [seqan2] 02/05: Normalize some command line help to generate better manual pages

[Michael Crusoe]

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misterc-guest pushed a commit to branch debian-experimental
in repository seqan2.

commit 6578992eb74ac1c80123f6ab140cfc854ddd7d91
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sun Oct 9 06:30:17 2016 -0700

    Normalize some command line help to generate better manual pages
---
 debian/patches/series            |  2 ++
 debian/patches/short-description | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 5299247..366f163 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
 spelling.patch
+short-description
+
diff --git a/debian/patches/short-description b/debian/patches/short-description
new file mode 100644
index 0000000..cca8f8f
--- /dev/null
+++ b/debian/patches/short-description
@@ -0,0 +1,33 @@
+From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
+Subject: Normalize some command line help to generate better manual pages
+--- 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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