[med-svn] [gmap] 07/11: d/filter.pl: add regexps to brush up gmap manpages after using help2man d/manpages: deleted d/gmap_build.1: deleted use help2man instead d/rules: add help2man stanza for gsnap and gmap_build
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Sat Aug 22 06:25:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 0db83416f46b9fae9a92eaf3974804fc8b39bf99
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Aug 21 17:04:37 2015 +0200
d/filter.pl: add regexps to brush up gmap manpages after using help2man
d/manpages: deleted
d/gmap_build.1: deleted use help2man instead
d/rules: add help2man stanza for gsnap and gmap_build
---
debian/filter.pl | 26 +++++++++++---
debian/gmap_build.1 | 101 ----------------------------------------------------
debian/manpages | 1 -
debian/rules | 7 ++--
4 files changed, 27 insertions(+), 108 deletions(-)
diff --git a/debian/filter.pl b/debian/filter.pl
index 0edce16..89907e8 100755
--- a/debian/filter.pl
+++ b/debian/filter.pl
@@ -7,9 +7,9 @@ while ( <STDIN> ) {
#multiline regex
undef $/;
# remove colon from the name
- $_ =~ s/(^\.SH\sDESCRIPTION\n\.IP\n)(cat)/$2/gmxs;
-# $_ =~ s/(^\.PP\n)(Input\soptions.*)/.SH OPTIONS\n.SS $2/gmxs;
-# $_ =~ s/(^\.PP\n)(Computation\soptions.*)/.SS $2/gmxs;
+ $_ =~ s/(^\.SH\sDESCRIPTION\n.*\.IP\n)(cat)/$2/gmxs;
+ $_ =~ s/(^\.PP\n)(Input\soptions.*)/.SH OPTIONS\n.SS $2/gmxs;
+ # $_ =~ s/(^\.PP\n)(Computation\soptions.*)/.SS $2/gmxs;
$_ =~ s/(^Batch\smode\s\(default\s=\s2\)\n)(Mode.*)/$1\n $2/gmxs;
$_ =~ s/(^\.TP\n)(0)(\n)(see\snote.*)/ $2 $4/gmxs;
$_ =~ s/(^\.TP\n)(1)(\n)(see\snote.*)/ $2 $4/gmxs;
@@ -17,6 +17,24 @@ while ( <STDIN> ) {
$_ =~ s/(^3\s{6}see\snote.*)/ $1/gmxs;
$_ =~ s/(^4\s{6}see\snote.*)/ $1/gmxs;
$_ =~ s/(^5\s{6}expand\s.*)/ $1/gmxs;
-# $_ =~ s/(^\.TP\n)(Note:?\s.*)/\n$2/gmxs;
+ # lineup "-f format" option of gmap
+ $_ =~ s/(under\sOutput\stypes\)\:\n)(.*)\.PP\n/
+ my $q = $1;
+ my $p = $2;
+ $p =~ s"(\,\n)"$1 "gmxs;
+ $p = $q.' '.$p;
+ /egmsx;
+ # $_ =~ s/(^\.TP\n)(Note:?\s.*)/\n$2/gmxs;
+#gsnap aligning
+ #$_ =~ s/(^\.SH\sDESCRIPTION\n)GSNAP\sversion.*help\\fR\n\.IP/$1/gmsx;
+ $_ =~ s/(^\.TP\n)(\(default\))(\n\s+)(4\s{6}see\snote.*)/ $2 $4/gmxs;
+ $_ =~ s/(^\.TP\n)(2)(\n)(see\snote.*)/ $2 $4/gmxs;
+ $_ =~ s/(^\.TP\n)(3)(\n)(see\snote.*)/ $2 $4/gmxs;
+ $_ =~ s/(^5\s{6}see\snote\s.*)/ $1/gmxs;
+ $_ =~ s/(^Examples:\n\.TP)/\.TP\n$1/gmsx;
+ $_ =~ s/(.*be\schanged)\n\.TP\n(by\sproviding.*)/$1 $2/gmsx;
+ #fix gmap_build header
+ $_ =~ s/(^\.SH\sDESCRIPTION\n)Unknown.*\.PP/$1/gmsx;
print $_;
}
+print "\n\.TP\nOther tools of GMAP suite are located in \/usr\/lib\/gmap";
diff --git a/debian/gmap_build.1 b/debian/gmap_build.1
deleted file mode 100644
index 46f3e5e..0000000
--- a/debian/gmap_build.1
+++ /dev/null
@@ -1,101 +0,0 @@
-.TH GMAP_BUILD "1" "GMAP 2014-12-23" "User Commands"
-.SH NAME
-gmap_build \- create a genome database for GMAP or GSNAP
-.SH SYNOPSIS
-.B gmap_build
-[\fI\,options\/\fR...] \fI\,-d <genomename> <fasta_files>\/\fR
-.SH DESCRIPTION
-.PP
-.SH NAME
-gmap_build \- manual page for gmap_build 2014
-.SH SYNOPSIS
-.B gmap_build
-[\fI\,options\/\fR...] \fI\,-d <genomename> <fasta_files>\/\fR
-.SH DESCRIPTION
-Unknown option: help
-\fB\-k\fR flag not specified, so building with default 15\-mers
-Must specify genome database name with \fB\-d\fR flag. at \fI\,/usr/bin/gmap_build\/\fP line 67.
-.PP
-gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP.
-Part of GMAP package, version 2014\-12\-23.
-.PP
-A simplified alternative to using the program gmap_setup, which creates a Makefile.
-.SH OPTIONS
-.TP
-\fB\-D\fR, \fB\-\-dir\fR=\fI\,STRING\/\fR
-Destination directory for installation (defaults to gmapdb directory specified at configure time)
-.TP
-\fB\-d\fR, \fB\-\-db\fR=\fI\,STRING\/\fR
-Genome name
-.TP
-\fB\-n\fR, \fB\-\-names\fR=\fI\,STRING\/\fR
-Substitute names for chromosomes, provided in a file. The file should have one line
-for each chromosome name to be changed, with the original FASTA name in column 1 and
-the desired chromosome name in column 2. This provides an easy way to change the
-names of chromosomes, for example, to add or remove the "chr" prefix. Column 2 may
-be blank, which indicates no name change. This file can also be combined with
-\fB\-\-sort\fR=\fI\,names\/\fR to provide a particular order for the chromosomes in the genome index.
-.TP
-\fB\-M\fR, \fB\-\-mdflag\fR=\fI\,STRING\/\fR
-Use MD file from NCBI for mapping contigs to chromosomal coordinates
-.TP
-\fB\-C\fR, \fB\-\-contigs\-are\-mapped\fR
-Find a chromosomal region in each FASTA header line. Useful for contigs that have been mapped
-to chromosomal coordinates. Ignored if the \fB\-\-mdflag\fR is provided.
-.TP
-\fB\-z\fR, \fB\-\-compression\fR=\fI\,STRING\/\fR
-Use given compression types (separated by commas; default is bitpack64)
-bitpack64 \- optimized for modern computers with SIMD instructions (recommended)
-all \- create all available compression types, currently bitpack64
-none \- do not compress offset files (I believe this is no longer supported)
-.TP
-\fB\-k\fR, \fB\-\-kmer\fR=\fI\,INT\/\fR
-k\-mer value for genomic index (allowed: 15 or less, default is 15)
-.TP
-\fB\-q\fR INT
-sampling interval for genomoe (allowed: 1\-3, default 3)
-.TP
-\fB\-s\fR, \fB\-\-sort\fR=\fI\,STRING\/\fR
-Sort chromosomes using given method:
-none \- use chromosomes as found in FASTA file(s)
-alpha \- sort chromosomes alphabetically (chr10 before chr 1)
-numeric\-alpha \- chr1, chr1U, chr2, chrM, chrU, chrX, chrY
-chrom \- chr1, chr2, chrM, chrX, chrY, chr1U, chrU
-names \- sort chromosomes based on file provided to \fB\-\-names\fR flag
-.TP
-\fB\-g\fR, \fB\-\-gunzip\fR
-Files are gzipped, so need to gunzip each file first
-.TP
-\fB\-E\fR, \fB\-\-fasta\-pipe\fR=\fI\,STRING\/\fR
-Interpret argument as a command, instead of a list of FASTA files
-.TP
-\fB\-w\fR INT
-Wait (sleep) this many seconds after each step (default 2)
-.TP
-\fB\-c\fR, \fB\-\-circular\fR=\fI\,STRING\/\fR
-Circular chromosomes (either a list of chromosomes separated by a comma, or
-a filename containing circular chromosomes, one per line). If you use the
-\fB\-\-names\fR feature, then you should use the original name of the chromosome,
-not the substitute name, for this option.
-.TP
-\fB\-e\fR, \fB\-\-nmessages\fR=\fI\,INT\/\fR
-Maximum number of messages (warnings, contig reports) to report (default 50)
-.TP
-\fB\-\-no\-sarray\fR
-Skip build of suffix array
-.SS "Obsolete options:"
-.TP
-\fB\-T\fR STRING
-Temporary build directory (may need to specify if you run out of space in your current directory)
-This is no longer necessary, since gmap_build now builds directly in the destination
-(or \fB\-D\fR) directory.
-.SH AUTHOR
-Thomas D. Wu and Colin K. Watanabe
-.SH "REPORTING BUGS"
-Report bugs to Thomas Wu <twu at gene.com>.
-.SH COPYRIGHT
-Copyright 2005 Genentech, Inc. All rights reserved.
-.SH "SEE ALSO"
-\fBgmap\fR(1), \fBgsnap\fR(1)
-.br
-http://research-pub.gene.com/gmap/
diff --git a/debian/manpages b/debian/manpages
deleted file mode 100644
index e0f0a2d..0000000
--- a/debian/manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/gmap_build.1
diff --git a/debian/rules b/debian/rules
index 18fd4f6..1852b9d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -15,13 +15,14 @@ ifeq ($(DEB_HOST_ARCH), i386)
EXTRA_CONFIGURE_ARGS += --enable-sse4.1=no --disable-simd
endif
-HELP2MAN = /usr/bin/help2man --no-info --help-option="''" --version-string="$(version)"
+HELP2MAN = /usr/bin/help2man --no-info --version-string="$(version)"
%:
dh $@ --parallel --with autotools_dev
override_dh_auto_configure:
- dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap $(EXTRA_CONFIGURE_ARGS)
+ dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap \
+ --bindir=/usr/lib/gmap $(EXTRA_CONFIGURE_ARGS)
override_dh_auto_install:
mkdir -p $(mandir)
@@ -29,6 +30,8 @@ override_dh_auto_install:
$(bindir)/gmap |debian/filter.pl >$(mandir)/gmap.1;
$(HELP2MAN) --name='Genomic Short-read Nucleotide Alignment Program' \
$(bindir)/gsnap |debian/filter.pl >$(mandir)/gsnap.1;
+ $(HELP2MAN) --name='Tool for genome database creation for GMAP or GSNAP' \
+ $(utildir)/gmap_build |debian/filter.pl >$(mandir)/gmap_build.1;
dh_auto_install
override_dh_install:
--
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