[med-svn] [transrate-tools] 01/01: ITP; manpage; VCS URLs; builddep fixes; drop cruft

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository transrate-tools.

commit 468e4ad4deebdab924c4fb3b1520bda18346be5c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Mon Sep 28 20:44:03 2015 -0700

    ITP; manpage; VCS URLs; builddep fixes; drop cruft
---
 debian/bam-read-man-include | 18 ++++++++++++++++++
 debian/bam-read.1           | 32 ++++++++++++++++++++++++++++++++
 debian/changelog            |  2 +-
 debian/control              |  8 +++++---
 debian/manpages             |  1 +
 debian/rules                | 21 ++++-----------------
 debian/upstream/metadata    | 12 ------------
 7 files changed, 61 insertions(+), 33 deletions(-)

diff --git a/debian/bam-read-man-include b/debian/bam-read-man-include
new file mode 100644
index 0000000..538e632
--- /dev/null
+++ b/debian/bam-read-man-include
@@ -0,0 +1,18 @@
+[NAME]
+bam-read \- Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.
+
+[SYNOPSIS]
+Currently captured:
+
+ - name
+ - bases mapped
+ - edit distance
+ - bridges
+ - length
+ - reads mapped
+ - both mapped
+ - proper pair
+ - good
+ - uncovered bases
+ - mean mapq
+ - probability of coverage not being segmented
diff --git a/debian/bam-read.1 b/debian/bam-read.1
new file mode 100644
index 0000000..af419e4
--- /dev/null
+++ b/debian/bam-read.1
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.2.
+.TH BAM-READ "1" "September 2015" "bam-read version 1.0.0" "User Commands"
+.SH NAME
+bam-read \- Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.
+.SH SYNOPSIS
+Currently captured:
+
+ - name
+ - bases mapped
+ - edit distance
+ - bridges
+ - length
+ - reads mapped
+ - both mapped
+ - proper pair
+ - good
+ - uncovered bases
+ - mean mapq
+ - probability of coverage not being segmented
+.SH DESCRIPTION
+bam\-read version 1.0.0
+Usage:
+bam\-read <bam_file> <output_csv> <nullprior (optional)>
+.PP
+example:
+bam\-read in.bam out.csv 0.95
+.PP
+Usage:
+bam\-read <bam_file> <output_csv> <nullprior (optional)>
+.PP
+example:
+bam\-read in.bam out.csv 0.95
diff --git a/debian/changelog b/debian/changelog
index d1691cd..272e391 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 transrate-tools (1.0.0-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #800412)
 
  -- Michael R. Crusoe <crusoe at ucdavis.edu>  Fri, 18 Sep 2015 17:38:02 -0700
diff --git a/debian/control b/debian/control
index 1eaa7d4..d292a65 100644
--- a/debian/control
+++ b/debian/control
@@ -5,10 +5,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
 Build-Depends: debhelper (>= 9),
                cmake,
-               libbamtools-dev
+               libbamtools-dev,
+               zlib1g-dev,
+               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/
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/transrate-tools.git
+Vcs-Git: git://anonscm.debian.org/debian-med/transrate-tools.git
 Homepage: https://github.com/Blahah/transrate-tools
 
 Package: transrate-tools
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..fa170d6
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/bam-read.1
diff --git a/debian/rules b/debian/rules
index 1d11ebc..6ea5baf 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,22 +1,9 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
-
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG        := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables, you can
-#  include /usr/share/dpkg/default.mk
-# and use what is set there.
-
 %:
 	dh $@
 
-#get-orig-source:
-#	. debian/get-orig-source
+override_dh_auto_install:
+	dh_auto_install
+	help2man --no-info --include debian/bam-read-man-include \
+	       obj*/src/bam-read > debian/bam-read.1
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index d8b5812..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,12 +0,0 @@
-Reference:
-  Author: 
-  Title: 
-  Journal: 
-  Year: 
-  Volume: 
-  Number: 
-  Pages: 
-  DOI: 
-  PMID:
-  URL: 
-  eprint: 

-- 
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