[med-svn] [snap-aligner] 01/01: build man page; fix typo; ITP#

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository snap-aligner.

commit a22233e938e128baf78276e44f8426a3bada12b4
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sun Sep 27 17:59:13 2015 -0700

    build man page; fix typo; ITP#
---
 debian/changelog                       |  2 +-
 debian/control                         |  3 ++-
 debian/manpages                        |  5 +++++
 debian/patches/series                  |  1 +
 debian/patches/spelling                | 13 +++++++++++++
 debian/rules                           | 19 +++++++++++++++++--
 debian/snap-aligner-index-man-include  |  3 +++
 debian/snap-aligner-paired-man-include |  3 +++
 debian/snap-aligner-single-man-include |  3 +++
 9 files changed, 48 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 3e3d932..187abae 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 snap-aligner (0.18~1.0~beta.18-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #800340)
 
  -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sat, 19 Sep 2015 20:20:26 -0700
diff --git a/debian/control b/debian/control
index 6de3937..e6eb30b 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+               help2man
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..79cff22
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1,5 @@
+debian/snap-aligner.1
+debian/snap-aligner-index.1
+debian/snap-aligner-single.1
+debian/snap-aligner-paired.1
+debian/SNAPCommand.1
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e057d52
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..b27c719
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,13 @@
+Author: Michael R. Crusoe
+Description: typo fix
+--- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
++++ snap-aligner/SNAPLib/AlignerOptions.cpp
+@@ -208,7 +208,7 @@
+ 
+     WriteErrorMessage("When specifying an input or output file, you can simply list the filename, in which case\n"
+                       "SNAP will infer the type of the file from the file extension (.sam or .bam for example),\n"
+-                      "or you can explicitly specify the file type by preceeding the filename with one of the\n"
++                      "or you can explicitly specify the file type by preceding the filename with one of the\n"
+                       " following type specifiers (which are case sensitive):\n"
+                       "    -fastq\n"
+                       "    -compressedFastq\n"
diff --git a/debian/rules b/debian/rules
index 55d0c84..a49d252 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,8 +4,8 @@
 
 # some helpful variables - uncomment them if needed
 # shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
 #DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
 #DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 #DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
@@ -21,3 +21,18 @@
 override_dh_auto_test:
 	dh_auto_test
 	./unit_tests
+
+override_dh_auto_build:
+	dh_auto_build
+	help2man --no-discard-stderr --no-info --version-string="${VERSION}" \
+		--name "scalable nucleotide alignment program" \
+		--help-option=" " snap-aligner > debian/snap-aligner.1
+	for option in index single paired; do help2man \
+		--no-discard-stderr --no-info --version-string="${VERSION}" \
+		--include=debian/snap-aligner-$${option}-man-include \
+		--help-option=" " "./snap-aligner $${option}" > \
+		debian/snap-aligner-$${option}.1; done
+	help2man --no-discard-stderr --no-info --version-string="${VERSION}" \
+		--name "scalable nucleotide alignment program" \
+		--help-option=" " SNAPCommand > debian/SNAPCommand.1
+
diff --git a/debian/snap-aligner-index-man-include b/debian/snap-aligner-index-man-include
new file mode 100644
index 0000000..7964efc
--- /dev/null
+++ b/debian/snap-aligner-index-man-include
@@ -0,0 +1,3 @@
+[NAME]
+snap-aligner_index \- scalable nucleotide alignment program
+
diff --git a/debian/snap-aligner-paired-man-include b/debian/snap-aligner-paired-man-include
new file mode 100644
index 0000000..4ba67a7
--- /dev/null
+++ b/debian/snap-aligner-paired-man-include
@@ -0,0 +1,3 @@
+[NAME]
+snap-aligner_paired \- scalable nucleotide alignment program
+
diff --git a/debian/snap-aligner-single-man-include b/debian/snap-aligner-single-man-include
new file mode 100644
index 0000000..31cd3e9
--- /dev/null
+++ b/debian/snap-aligner-single-man-include
@@ -0,0 +1,3 @@
+[NAME]
+snap-aligner_single \- scalable nucleotide alignment program
+

-- 
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