[med-svn] [pbgenomicconsensus] 01/06: Generate manpage for variantCaller.py from upstream doc

[Afif Elghraoui]

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commit 90ba178ac76759ec70861d509612821472e2345b
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Oct 13 19:38:37 2015 -0700

    Generate manpage for variantCaller.py from upstream doc
---
 debian/patches/manpages.patch | 131 ++++++++++++++++++++++++++++++++++++++++++
 debian/rules                  |   1 +
 2 files changed, 132 insertions(+)

diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index b2cb2c4..6e9d1c1 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -323,3 +323,134 @@ Last-Update: 2015-10-06
 +**plurality**\ (1)
 +**variantCaller.py**\ (1)
 +**pbgff**\ (5)
+--- pbgenomicconsensus.orig/doc/VariantCallerFunctionalSpecification.rst
++++ pbgenomicconsensus/doc/VariantCallerFunctionalSpecification.rst
+@@ -1,35 +1,17 @@
++================
++variantCaller.py
++================
++
++-----------------------------------------------------
++variant-calling algorithms for PacBio sequencing data
++-----------------------------------------------------
++
++:Date: October 2015
++:Version: 1.0.0
++:Manual section: 1		 
+ 
+-
+-Variant Caller Functional Specification
+-=======================================
+-
+-Version 2.2
+-
+-
+-Introduction
+-------------
+-
+-This document describes the interface, input/output, and performance
+-characteristics of ``variantCaller.py``, a variant calling tool
+-provided by the ``GenomicConsensus`` package.
+-
+-
+-Software Overview
+------------------
+-
+-The ``GenomicConsensus`` package provides a command-line tool,
+-``variantCaller.py``, which provides several variant-calling algorithms for
+-PacBio sequencing data.  ``variantCaller.py`` replaces ``EviCons`` and
+-``SmrtBayes``, the previous (haploid, diploid---respectively) variant callers
+-at PacBio.
+-
+-
+-
+-Functional Requirements
+------------------------
+-
+-Command-line interface
+-``````````````````````
++SYNOPSIS
++========
+ 
+ ``variantCaller.py`` is invoked from the command line.  For example, a simple
+ invocation is::
+@@ -44,23 +26,24 @@
+ - employing the **quiver** algorithm,
+ - taking input from the file ``aligned_reads.cmp.h5``,
+ - using the FASTA file ``lambdaNEB.fa`` as the reference,
+-- and writing output to ``variants.gff``.
++- and writing output to ``variants.gff`` (see **pbgff**\ (5)).
+ 
+ A particularly useful option is ``--referenceWindow/-w``: this option
+ allows the user to direct the tool to perform variant calling
+ exclusively on a *window* of the reference genome, where the
+ 
+ 
+-Invoking
++OPTIONS
++=======
+ 
+ ::
+ 
+     variantCaller.py --help
+ 
+-will provide a help message explaining all available options; they will be
+-documented here shortly.
+-
++will provide a help message explaining all available options.
+ 
++NOTES
++=====
+ 
+ Input and output
+ ````````````````
+@@ -82,7 +65,7 @@
+         be sorted.  An unsorted file can be sorting using the tool
+         ``cmpH5Sort.py``.
+ 
+-        The *quiver* algorithm in ``variantCaller.py`` requires its
++        The **quiver**\ (1) algorithm in ``variantCaller.py`` requires its
+         input cmp.h5 file to have the following *pulse features*:
+             - ``InsQV``,
+             - ``SubsQV``,
+@@ -90,7 +73,7 @@
+             - ``DelTag``,
+             - ``MergeQV``.
+ 
+-        The *plurality* algorithm can be run on cmp.h5 files that lack
++        The **plurality**\ (1) algorithm can be run on cmp.h5 files that lack
+         these features.
+ 
+ The input file is the main argument to ``variantCaller.py``, while the output
+@@ -147,19 +130,6 @@
+ fewer errors at low coverage), and should provide greater variant detection
+ power at a given error level.
+ 
+-
+-Software interfaces
+-```````````````````
+-The ``GenomicConsensus`` module has two essential dependencies:
+-
+-1. **pbcore**, the PacBio Python bioinformatics library
+-2. **ConsensusCore**, a C++ library with SWIG bindings that provides access to
+-   the same algorithms used in circular consensus sequencing.
+-
+-Both of these modules are easily installed using their ``setup.py`` scripts,
+-which is the canonical means of installing Python packages.
+-
+-
+ Confidence values
+ -----------------
+ 
+@@ -209,3 +179,11 @@
+ The amount of core memory (RAM) used among all the python processes launched
+ by a ``variantCaller.py`` run should not exceed the size of the uncompressed
+ input ``.cmp.h5`` file.
++
++SEE ALSO
++========
++
++**quiver**\ (1)
++**plurality**\ (1)
++**pbgff**\ (5)
++**blasr**\ (1)
diff --git a/debian/rules b/debian/rules
index 6bb7597..3044999 100755
--- a/debian/rules
+++ b/debian/rules
@@ -18,6 +18,7 @@ override_dh_install:
 	dh_install
 	mkdir -p $(MANDIR)/man5 $(MANDIR)/man1 $(MANDIR)/man7
 	rst2man doc/VariantsGffSpecification.rst > $(MANDIR)/man5/pbgff.5
+	rst2man doc/VariantCallerFunctionalSpecification.rst > $(MANDIR)/man1/variantCaller.py.1
 	rst2man doc/HowToQuiver.rst > $(MANDIR)/man1/quiver.1
 	rst2man doc/QuiverFAQ.rst > $(MANDIR)/man7/quiver-faq.7
 	for script in $(BINDIR)/*.py; \

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