[med-svn] [pbgenomicconsensus] 02/06: Add manpages for remaining package executables

[Afif Elghraoui]

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

afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.

commit cf0fe579caa6b9d11ba557ad427d03679c8bb8ef
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Oct 13 20:44:11 2015 -0700

    Add manpages for remaining package executables
---
 debian/man/gffToBed.py.1           | 19 +++++++++++++++++++
 debian/man/gffToVcf.py.1           | 15 +++++++++++++++
 debian/man/makePbi.py.1            | 21 +++++++++++++++++++++
 debian/man/plurality.1             | 23 +++++++++++++++++++++++
 debian/man/summarizeConsensus.py.1 | 15 +++++++++++++++
 debian/pbgenomicconsensus.manpages |  1 +
 debian/rules                       |  5 +++++
 7 files changed, 99 insertions(+)

diff --git a/debian/man/gffToBed.py.1 b/debian/man/gffToBed.py.1
new file mode 100644
index 0000000..d48dbf2
--- /dev/null
+++ b/debian/man/gffToBed.py.1
@@ -0,0 +1,19 @@
+.TH GFFTOBED.PY 1 "October 2015"
+
+.SH NAME
+
+gffToBed.py \- converting PacBio variant GFF3 files to BED format
+
+.SH OPTIONS
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+
+.SH NOTES
+
+Currently supports regional coverage or variant .bed output.
+
+.SH SEE ALSO
+.BR pbgff (5)
+.BR quiver (1)
diff --git a/debian/man/gffToVcf.py.1 b/debian/man/gffToVcf.py.1
new file mode 100644
index 0000000..f13da82
--- /dev/null
+++ b/debian/man/gffToVcf.py.1
@@ -0,0 +1,15 @@
+.TH GFFTOVCF.PY 1 "October 2015"
+
+.SH NAME
+
+gffToVcf.py \- convert PacBio variant GFF3 files to 1000 Genomes VCF
+
+.SH OPTIONS
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+
+.SH SEE ALSO
+.BR pbgff (5)
+.BR quiver (1)
diff --git a/debian/man/makePbi.py.1 b/debian/man/makePbi.py.1
new file mode 100644
index 0000000..713c4f3
--- /dev/null
+++ b/debian/man/makePbi.py.1
@@ -0,0 +1,21 @@
+.TH MAKEPBI.PY 1 "October 2015"
+
+.SH NAME
+
+makePbi.py \- build PacBio BAM index for a
+.BR bam (5)
+file
+
+.SH OPTIONS
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+
+.SH BUGS
+
+This is a very inefficient reference implementation.
+
+.SH SEE ALSO
+.BR quiver (1)
+.BR blasr (1)
diff --git a/debian/man/plurality.1 b/debian/man/plurality.1
new file mode 100644
index 0000000..e12ab61
--- /dev/null
+++ b/debian/man/plurality.1
@@ -0,0 +1,23 @@
+.TH PLURALITY 1 "October 2015"
+
+.SH NAME
+
+plurality \- simple variant calling algorithm 
+
+.SH DESCRIPTION
+
+See
+.BR quiver-faq (7)
+for a more detailed description of \f[B]plurality\f[P].
+
+.SH OPTIONS
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+
+.SH SEE ALSO
+.BR quiver-faq (7)
+.BR quiver (1)
+.BR variantCaller.py (1)
+.BR blasr (1)
diff --git a/debian/man/summarizeConsensus.py.1 b/debian/man/summarizeConsensus.py.1
new file mode 100644
index 0000000..0c12f12
--- /dev/null
+++ b/debian/man/summarizeConsensus.py.1
@@ -0,0 +1,15 @@
+.TH SUMMARIZECONSENSUS.PY 1 "October 2015"
+
+.SH NAME
+
+summarizeConsensus.py \- augment the PacBio alignment_summary.gff with consensus and variants information
+
+.SH OPTIONS
+
+.TP
+.B \-h, \-\-help
+Show summary of options.
+
+.SH SEE ALSO
+.BR blasr (1)
+.BR quiver (1)
diff --git a/debian/pbgenomicconsensus.manpages b/debian/pbgenomicconsensus.manpages
new file mode 100644
index 0000000..19f429f
--- /dev/null
+++ b/debian/pbgenomicconsensus.manpages
@@ -0,0 +1 @@
+debian/man/*
diff --git a/debian/rules b/debian/rules
index 3044999..619c05e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -26,3 +26,8 @@ override_dh_install:
 		mv $$script $(BINDIR)/`basename $$script .py`; \
 		ln -s `basename $$script .py` $$script; \
 	done
+
+# Manpages for scripts with language extensions get installed to wrong
+# place unless we force the language as C here. See dh_installman(1)
+override_dh_installman:
+	dh_installman --language=C

-- 
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