Update filter for man pages, update descriptions for tools

parent 8dbd32f4
...@@ -18,6 +18,8 @@ foreach my $f (@fields) { ...@@ -18,6 +18,8 @@ foreach my $f (@fields) {
while ( <STDIN> ) { while ( <STDIN> ) {
#multiline regex #multiline regex
undef $/; 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 # remove colon from the name
s/(\.TH\s([\w\d-]*)):/$1/gmxs; s/(\.TH\s([\w\d-]*)):/$1/gmxs;
# substitude unrecognized version string with the version # substitude unrecognized version string with the version
...@@ -25,17 +27,22 @@ while ( <STDIN> ) { ...@@ -25,17 +27,22 @@ while ( <STDIN> ) {
s/([\w\d]*)\:\sunrecognized\soption\s\'\\-\\-version\'/ $version/g; s/([\w\d]*)\:\sunrecognized\soption\s\'\\-\\-version\'/ $version/g;
# there are no invalid options # there are no invalid options
s/([\w\d]*)\:\sinvalid\soption\s--\s\'-\'/$1 $version/g; 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 # strip full path
s/\\fI\\,\/.*\/bin(\/utilities)?\///gmxs; s/\\fI\\,\/.*\/bin(\/utilities)?\///gmxs;
# tidy up help2man removeDuP output: # strip the header
s/Repeated\sRead\sRemoval.*accessible:\s\'\'//xms; 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; s/(.SH\sNAME\n[\w\d-]*):/$1/gxms;
# remove "./" from examples # remove "./" from examples
s/(\\\&\.\/)([\w\d-]*)/$2/gxms; 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; 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; print;
} }
...@@ -68,9 +68,16 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ ...@@ -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' \ $(HELP2MAN) --name='calculate the proportion of mapped reads/fragments' \
$(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1; $(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1;
for i in removeDup repair qualityScores ; do \ $(HELP2MAN) --name='retrieve Phred score for read bases' \
$(HELP2MAN) --name='a component of subread suite' $(utildir)/$$i | debian/filter.pl > $(mandir)/$$i.1; \ $(utildir)/qualityScores| debian/filter.pl > $(mandir)/qualityScores.1;
done
$(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 dh_auto_install
......
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