[med-svn] r14377 - trunk/packages/staden-io-lib/trunk/debian

Andreas Tille tille at alioth.debian.org
Wed Aug 7 19:11:02 UTC 2013 

Author: tille
Date: 2013-08-07 19:11:01 +0000 (Wed, 07 Aug 2013)
New Revision: 14377

Added:
   trunk/packages/staden-io-lib/trunk/debian/srf_dump_all.1
   trunk/packages/staden-io-lib/trunk/debian/srf_filter.1
Modified:
   trunk/packages/staden-io-lib/trunk/debian/changelog
   trunk/packages/staden-io-lib/trunk/debian/rules
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages
Log:
Provide some help2man created manpages


Modified: trunk/packages/staden-io-lib/trunk/debian/changelog
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/changelog	2013-08-07 18:01:51 UTC (rev 14376)
+++ trunk/packages/staden-io-lib/trunk/debian/changelog	2013-08-07 19:11:01 UTC (rev 14377)
@@ -18,6 +18,7 @@
   * debian/libstaden-read1.symbols: Deleted because it simply breaks build.
   * debian/rules: Make use of d-shlibs which should help closing bug
     #710225 because it raises a flag if there is a new ABI
+  * provide some help2man created manpages
 
  -- Andreas Tille <tille at debian.org>  Wed, 07 Aug 2013 14:31:36 +0200
 

Modified: trunk/packages/staden-io-lib/trunk/debian/rules
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/rules	2013-08-07 18:01:51 UTC (rev 14376)
+++ trunk/packages/staden-io-lib/trunk/debian/rules	2013-08-07 19:11:01 UTC (rev 14377)
@@ -2,6 +2,9 @@
 
 libpkg=libstaden-read
 devpkg=$(libpkg)-dev
+#version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
+#utils=staden-io-lib-utils
+#mandir=$(CURDIR)/debian/$(utils)/usr/share/man/man1/
 
 %:
 	dh $@
@@ -21,6 +24,13 @@
 		    --movedev "debian/tmp/usr/include" usr \
 		    debian/tmp/usr/lib/*/$(libpkg).so
 
+	# manpages need some post editing but in case it could be automated, this code would help
+	# mkdir -p $(mandir)
+	# help2man --no-discard-stderr --no-info --help-option='""' \
+	#	 --name='filter SRF files for various purposes' \
+	#	 --version-string="$(version)" \
+	#	 $(CURDIR)/debian/$(utils)/usr/bin/srf_filter > $(mandir)/srf_filter.1
+
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam

Added: trunk/packages/staden-io-lib/trunk/debian/srf_dump_all.1
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/srf_dump_all.1	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/srf_dump_all.1	2013-08-07 19:11:01 UTC (rev 14377)
@@ -0,0 +1,58 @@
+.\" Originally generated via:
+.\"  help2man --no-discard-stderr --no-info --name='dump data of SRF files' --version-string='1.13.2' srf_dump_all > srf_dump_all.1
+.TH SRF_DUMP_ALL "1" "August 2013" "srf_dump_all 1.13.2" "User Commands"
+.SH NAME
+srf_dump_all \- dump data of SRF files
+.SH SYNOPSIS
+.B srf_dump_all
+[\fI-c chunk_types\fR] [\fI-d destination_types\fR]  [\fI-f read_filter\fR] [\fI-n\fR] [\fI-o\fR] [\fI-t type_of_output\fR] \fIarchive_name\fR
+.SH OPTIONS
+.HP
+\fB\-c\fR chunk_types
+.IP
+Chunk types to output given as a comma delimited list of types.
+The following types are allowed: "all", "seq", "prb",
+"int", "nse", "sig2".
+The default is "all".
+.HP
+\fB\-d\fR destination_types
+.IP
+Distinations to output to.
+The following types are allowed: "console", "file", "none".
+The default is "console".  Console and file can be together,
+but none is exclusive.
+.HP
+\fB\-f\fR read_filter
+.TP
+The filter to apply to reads in the archive.
+If reads match the
+.IP
+filter they are dumped.
+The filter takes the form of <name>=<value>, where <name> can be
+"read", "prefix", "file".
+If the <name> is "read" the value is represents the name of a
+read to dump.  Only the matching read will be dumped.
+If the <name> is "prefix" the value is represents the prefix of
+the name of the reads to dump.  Only the matching reads will be
+dumped.
+If the <name> is "file" the value is a file name where any
+number of "read" and "prefix" name value pairs can be included,
+one per line.
+The default is no filter, which means all reads are dumped.
+.TP
+\fB\-n\fR
+Output the total number of reads at the bottom.
+.TP
+\fB\-o\fR
+Output the total number of reads only.  Nothing else is output.
+.HP
+\fB\-t\fR type_of_output
+.TP
+Type of output.
+Only one value allowed.
+.IP
+Currently "text" and "solexa" is supported.
+The default is "text".
+.TP
+\fB\-v\fR
+Print verbose messages.

Added: trunk/packages/staden-io-lib/trunk/debian/srf_filter.1
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/srf_filter.1	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/srf_filter.1	2013-08-07 19:11:01 UTC (rev 14377)
@@ -0,0 +1,52 @@
+.\" Originally generated via:
+.\" help2man --no-discard-stderr --no-info --help-option='""' --name='filter SRF files for various purposes' --version-string='1.13.2' srf_filter > srf_filter.1
+.TH SRF_FILTER "1" "August 2013" "srf_filter 1.13.2" "User Commands"
+.SH NAME
+srf_filter \- filter SRF files for various purposes
+.SH SYNOPSIS
+.B srf_filter
+[\fI-c chunk_types\fR] [\fI-f read_filter\fR] [\fI-C\fR] [\fI-o\fR] [\fI-v\fR] \fIinput(s) output\fR
+.SH OPTIONS
+.HP
+\fB\-c\fR chunk_types
+.IP
+Chunk types to output given as a comma delimited list of types.
+The following types are allowed: "ALL", "BASE", "CNF1", "CNF4"
+"SAMP", "SMP4".
+The default is "ALL".
+.HP
+\fB\-m\fR mdata_types
+.IP
+SAMP/SMP4 mdata types to output given as a comma delimited list of types.
+The following types are allowed: "ALL", "PROC", "SLXI", "SLXN"
+"0FAM", "1CY3", "2TXR", "3CY5".
+The default is "ALL".
+.HP
+\fB\-f\fR read_filter
+.TP
+The filter to apply to reads in the archive.
+If reads match the
+.IP
+filter they are dumped.
+The filter takes the form of <name>=<value>, where <name> can be
+"read", "prefix", "file".
+If the <name> is "read" the value is represents the name of a
+read to dump.  Only the matching read will be dumped.
+If the <name> is "prefix" the value is represents the prefix of
+the name of the reads to dump.  Only the matching reads will be
+dumped.
+If the <name> is "file" the value is a file name where any
+number of "read" and "prefix" name value pairs can be included,
+one per line.
+The default is no filter, which means all reads are dumped.
+.TP
+\fB\-b\fR
+exclude bad reads using readsFlags bitmask in data block header.
+.TP
+\fB\-2\fR cyc
+use this option to add a Illumina\-style REGN chunk.
+.TP
+\fB\-v\fR
+Print verbose messages.
+.PP
+Use '\-' for the input or output name to read from stdin or write to stdout.

Modified: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages	2013-08-07 18:01:51 UTC (rev 14376)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages	2013-08-07 19:11:01 UTC (rev 14377)
@@ -1 +1,2 @@
 man/man1/*1
+debian/*.1

More information about the debian-med-commit mailing list