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commit 90ba178ac76759ec70861d509612821472e2345b Author: Afif Elghraoui <a...@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; \ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit