[med-svn] [subread] 05/06: Update filter for man pages, update descriptions for tools

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit 412c5e8426fdefb120c5287ea1047025717f9de1
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Jul 28 14:08:06 2017 +0200

    Update filter for man pages, update descriptions for tools
---
 debian/filter.pl | 19 +++++++++++++------
 debian/rules     | 13 ++++++++++---
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/debian/filter.pl b/debian/filter.pl
index a7a9fac..367f95a 100755
--- a/debian/filter.pl
+++ b/debian/filter.pl
@@ -18,6 +18,8 @@ foreach my $f (@fields) {
 while ( <STDIN> ) {
     #multiline regex
     undef $/;
+    # remove indent and "boldify" the name
+    s/(\.SH\sUSAGE\n*)(\.IP\n|\s|\.TP\n)([\w\d\\-]*)/$1\\fB$3\\fR/xms;
     # remove colon from the name
     s/(\.TH\s([\w\d-]*)):/$1/gmxs;
     # substitude unrecognized version string with the version
@@ -25,17 +27,22 @@ while ( <STDIN> ) {
     s/([\w\d]*)\:\sunrecognized\soption\s\'\\-\\-version\'/ $version/g;
     # there are no invalid options
     s/([\w\d]*)\:\sinvalid\soption\s--\s\'-\'/$1 $version/g;
-    # strip the header or duplicated body of coverageCount
-    s/\.SH\s(DESCRIPTION|SYNOPSIS).*(Usage:\"?|genome\.\n\.PP)/.SH USAGE\n/gmxs;
     # strip full path
     s/\\fI\\,\/.*\/bin(\/utilities)?\///gmxs;
-    # tidy up help2man removeDuP output:
-    s/Repeated\sRead\sRemoval.*accessible:\s\'\'//xms;
+    # strip the header
+    s/\.SH\s(DESCRIPTION|SYNOPSIS).*?(Usage:\"?\n(\.IP|\.PP))/.SH USAGE\n\.PP/gmxs;
+    # tidy up help2man removeDup output:
+    s/Repeated\sRead\sRemoval.*?accessible:\s\'\'//gxms;
     s/(.SH\sNAME\n[\w\d-]*):/$1/gxms;
     # remove "./" from examples
     s/(\\\&\.\/)([\w\d-]*)/$2/gxms;
-    # remove indent and "boldify" the name
-    s/(\.SH\sUSAGE\n*)(\.IP\n|\s|\.TP\n)([\w\d\\-]*)/$1\\fB$3\\fR/xms;
     s/removeDup\\\\fR\/\\fP/removeDup\\fR/gmxs;
+    # massaging for coverageCount which displays help twice
+    s/(coverageCount\ Version.*?\n)(.*?)(coverageCount\ Version.*?\n\.IP)/.PP/xms;
+    # boldofy "usage" for coverageCount
+    s/(\.PP\n)(Usage\n\.IP)(\ncoverageCount)/$1.SH USAGE\n.PP $3/xms;
+    s/For\ more\ information\ about\ these\ arguments.*//xms;
+	# remove duplicated parts
+	s/Usage:\n\.IP.*//xms;
     print;
 }
diff --git a/debian/rules b/debian/rules
index 6b10b33..fdd42ff 100755
--- a/debian/rules
+++ b/debian/rules
@@ -68,9 +68,16 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
 	$(HELP2MAN) --name='calculate the proportion of mapped reads/fragments' \
 	$(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1;
 
-	for i in removeDup repair qualityScores ; do \
-	$(HELP2MAN) --name='a component of subread suite' $(utildir)/$$i | debian/filter.pl > $(mandir)/$$i.1; \
-	done
+	$(HELP2MAN) --name='retrieve Phred score for read bases' \
+	$(utildir)/qualityScores| debian/filter.pl > $(mandir)/qualityScores.1;
+
+	$(HELP2MAN) --name='Find reads that are from the same pair in the input and then place them next \
+to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
+The output file is compatible with featureCounts program' \
+	$(utildir)/repair| debian/filter.pl > $(mandir)/repair.1;
+
+	$(HELP2MAN) --name='Remove duplicated reads' \
+	$(utildir)/removeDup| debian/filter.pl > $(mandir)/removeDup.1;
 
 	dh_auto_install
 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git