[med-svn] [rapmap] 01/01: Add manpages

Wed Sep 7 07:52:55 UTC 2016

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tille pushed a commit to branch master
in repository rapmap.

commit c5fb4e52199f55c1bb3f7a561e4f8c95a80ae84b
Author: Andreas Tille <tille at debian.org>
Date:   Wed Sep 7 09:52:44 2016 +0200

    Add manpages
---
 debian/man/rapmap.1             | 29 ++++++++++++++++++
 debian/man/rapmap_pseudoindex.1 | 43 ++++++++++++++++++++++++++
 debian/man/rapmap_pseudomap.1   | 62 +++++++++++++++++++++++++++++++++++++
 debian/man/rapmap_quasiindex.1  | 54 ++++++++++++++++++++++++++++++++
 debian/man/rapmap_quasimap.1    | 68 +++++++++++++++++++++++++++++++++++++++++
 debian/manpages                 |  1 +
 6 files changed, 257 insertions(+)

diff --git a/debian/man/rapmap.1 b/debian/man/rapmap.1
new file mode 100644
index 0000000..6593a1d
--- /dev/null
+++ b/debian/man/rapmap.1
@@ -0,0 +1,29 @@
+.TH RAPMAP "1" "September 2016" "rapmap 0.3.0" "User Commands"
+.SH NAME
+rapmap \- rapid sensitive and accurate DNA read mapping via quasi-mapping
+.SH SYNOPSIS
+.B rapmap
+\fI[pseudoindex|pseudomap|quasiindex|quasimap]\fR \fI<options>\fR
+.SH DESCRIPTION
+RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+pseudo) transcriptome alignment. That means that, at this point, it is
+somewhat experimental. The develop branch will have the latest
+improvements and additions, but is not guaranteed to be stable between
+commits. Breaking changes to the master branch will be accompanied by a
+tag to the version before the breaking change. Currently, RapMap is a
+stand-alone quasi-mapper that can be used with other tools. It is also
+being used as part of Sailfish and Salmon. Eventually, the hope is to
+create and stabilize an API so that it can be used as a library from
+other tools.
+.SH OPTIONS
+Rapmap contains 4 subcommands:
+.IP
+pseudoindex - builds a k-mer-based index (see rapmap_pseudoindex(1))
+.IP
+pseudomap - map reads using a k-mer-based index (see rapmap_pseudomap(1))
+.IP
+quasiindex - builds a suffix array-based (SA) index (see rapmap_quasiindex(1))
+.IP
+quasimap - map reads using the SA-based index (see rapmap_quasimap(1))
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/man/rapmap_pseudoindex.1 b/debian/man/rapmap_pseudoindex.1
new file mode 100644
index 0000000..a3cf2be
--- /dev/null
+++ b/debian/man/rapmap_pseudoindex.1
@@ -0,0 +1,43 @@
+.TH RAPMAP_PSEUDOINDEX "1" "September 2016" "rapmap_pseudoindex 0.3.0" "User Commands"
+.SH NAME
+rapmap_pseudoindex \- rapmap module to build a k-mer-based index
+.SH SYNOPSIS
+.B rapmap pseudoindex
+[\-k <positive integer less than 32>] \fB\-i\fR <path> \fB\-t\fR
+<path> [\-\-] [\-\-version] [\-h]
+.SH DESCRIPTION
+RapMap Indexer
+.P
+RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+pseudo) transcriptome alignment. That means that, at this point, it is
+somewhat experimental. The develop branch will have the latest
+improvements and additions, but is not guaranteed to be stable between
+commits. Breaking changes to the master branch will be accompanied by a
+tag to the version before the breaking change. Currently, RapMap is a
+stand-alone quasi-mapper that can be used with other tools. It is also
+being used as part of Sailfish and Salmon. Eventually, the hope is to
+create and stabilize an API so that it can be used as a library from
+other tools.
+.SH OPTIONS
+.TP
+\fB\-k\fR, \fB\-\-klen\fR <positive integer less than 32>
+The length of k\-mer to index
+.TP
+\fB\-i\fR, \fB\-\-index\fR <path>
+(required)
+The location where the index should be written
+.TP
+\fB\-t\fR, \fB\-\-transcripts\fR <path>
+(required)
+The transcript file to be indexed
+.TP
+\fB\-\-\fR, \fB\-\-ignore_rest\fR
+Ignores the rest of the labeled arguments following this flag.
+.TP
+\fB\-\-version\fR
+Displays version information and exits.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays usage information and exits.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/man/rapmap_pseudomap.1 b/debian/man/rapmap_pseudomap.1
new file mode 100644
index 0000000..5d3d840
--- /dev/null
+++ b/debian/man/rapmap_pseudomap.1
@@ -0,0 +1,62 @@
+.TH RAPMAP_PSEUDOMAP "1" "September 2016" "rapmap_pseudomap 0.3.0" "User Commands"
+.SH NAME
+rapmap_pseudomap \- rapmap module to map reads using a k-mer-based index
+.SH SYNOPSIS
+,B rapmap pseudomap
+[\-e] [\-m <positive integer>] [\-t <positive integer>]
+[\-o <path>] [\-r <path>] [\-2 <path>] [\-1 <path>] [\-n] \fB\-i\fR
+<path> [\-\-] [\-\-version] [\-h]
+.SH DESCRIPTION
+RapMap Mapper
+.P
+RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+pseudo) transcriptome alignment. That means that, at this point, it is
+somewhat experimental. The develop branch will have the latest
+improvements and additions, but is not guaranteed to be stable between
+commits. Breaking changes to the master branch will be accompanied by a
+tag to the version before the breaking change. Currently, RapMap is a
+stand-alone quasi-mapper that can be used with other tools. It is also
+being used as part of Sailfish and Salmon. Eventually, the hope is to
+create and stabilize an API so that it can be used as a library from
+other tools.
+.SH OPTIONS
+.TP
+\fB\-e\fR,  \fB\-\-endCollector\fR
+Use the simpler (and faster) "end" collector as opposed to the more
+sophisticated "skipping" collector
+.TP
+\fB\-m\fR, \fB\-\-maxNumHits\fR <positive integer>
+Reads mapping to more than this many loci are discarded
+.TP
+\fB\-t\fR, \fB\-\-numThreads\fR <positive integer>
+Number of threads to use
+.TP
+\fB\-o\fR, \fB\-\-output\fR <path>
+The output file (default: stdout)
+.TP
+\fB\-r\fR, \fB\-\-unmatedReads\fR <path>
+The location of single\-end reads
+.TP
+\fB\-2\fR, \fB\-\-rightMates\fR <path>
+The location of the right paired\-end reads
+.TP
+\fB\-1\fR, \fB\-\-leftMates\fR <path>
+The location of the left paired\-end reads
+.TP
+\fB\-n\fR, \fB\-\-noOutput\fR
+Don't write out any alignments (for speed testing purposes)
+.TP
+\fB\-i\fR, \fB\-\-index\fR <path>
+(required)
+The location of the pseudoindex
+.TP
+\fB\-\-\fR,  \fB\-\-ignore_rest\fR
+Ignores the rest of the labeled arguments following this flag.
+.TP
+\fB\-\-version\fR
+Displays version information and exits.
+.TP
+\fB\-h\fR,  \fB\-\-help\fR
+Displays usage information and exits.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/man/rapmap_quasiindex.1 b/debian/man/rapmap_quasiindex.1
new file mode 100644
index 0000000..36e482c
--- /dev/null
+++ b/debian/man/rapmap_quasiindex.1
@@ -0,0 +1,54 @@
+.TH RAPMAP_QUASIINDEX "1" "September 2016" "rapmap_quasiindex 0.3.0" "User Commands"
+.SH NAME
+rapmap_quasiindex \- rapmap module to build a suffix array-based (SA) index
+.SH SYNOPSIS
+.B rapmap quasiindex
+[\-x <positive integer <= # cores>] [\-p] [\-n] [\-k
+<positive integer less than 32>] \fB\-i\fR <path> \fB\-t\fR <path>
+[\-\-] [\-\-version] [\-h]
+.SH DESCRIPTION
+RapMap Indexer
+.P
+RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+pseudo) transcriptome alignment. That means that, at this point, it is
+somewhat experimental. The develop branch will have the latest
+improvements and additions, but is not guaranteed to be stable between
+commits. Breaking changes to the master branch will be accompanied by a
+tag to the version before the breaking change. Currently, RapMap is a
+stand-alone quasi-mapper that can be used with other tools. It is also
+being used as part of Sailfish and Salmon. Eventually, the hope is to
+create and stabilize an API so that it can be used as a library from
+other tools.
+.SH OPTIONS
+.TP
+\fB\-x\fR, \fB\-\-numThreads\fR <positive integer <= #cores>
+Use this many threads to build the perfect hash function
+.TP
+\fB\-p\fR, \fB\-\-perfectHash\fR
+Use a perfect hash instead of dense hash \fB\-\-\-\fR somewhat slows
+construction, but uses less memory
+.TP
+\fB\-n\fR, \fB\-\-noClip\fR
+Don't clip poly\-A tails from the ends of target sequences
+.TP
+\fB\-k\fR, \fB\-\-klen\fR <positive integer less than 32>
+The length of k\-mer to index
+.TP
+\fB\-i\fR, \fB\-\-index\fR <path>
+(required)
+The location where the index should be written
+.TP
+\fB\-t\fR, \fB\-\-transcripts\fR <path>
+(required)
+The transcript file to be indexed
+.TP
+\fB\-\-\fR, \fB\-\-ignore_rest\fR
+Ignores the rest of the labeled arguments following this flag.
+.TP
+\fB\-\-version\fR
+Displays version information and exits.
+.TP
+\fB\-h\fR,  \fB\-\-help\fR
+Displays usage information and exits.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/man/rapmap_quasimap.1 b/debian/man/rapmap_quasimap.1
new file mode 100644
index 0000000..b83a8b9
--- /dev/null
+++ b/debian/man/rapmap_quasimap.1
@@ -0,0 +1,68 @@
+.TH RAPMAP_QUASIMAP "1" "September 2016" "rapmap_quasimap 0.3.0" "User Commands"
+.SH NAME
+rapmap_quasimap \- rapmap module to map reads using the SA-based index
+.SH SYNOPSIS
+.B rapmap quasimap
+[\-c] [\-f] [\-s] [\-m <positive integer>] [\-t <positive
+integer>] [\-o <path>] [\-r <path>] [\-2 <path>] [\-1
+<path>] [\-n] \fB\-i\fR <path> [\-\-] [\-\-version] [\-h]
+.SH DESCRIPTION
+RapMap Mapper (SA\-based)
+.P
+RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+pseudo) transcriptome alignment. That means that, at this point, it is
+somewhat experimental. The develop branch will have the latest
+improvements and additions, but is not guaranteed to be stable between
+commits. Breaking changes to the master branch will be accompanied by a
+tag to the version before the breaking change. Currently, RapMap is a
+stand-alone quasi-mapper that can be used with other tools. It is also
+being used as part of Sailfish and Salmon. Eventually, the hope is to
+create and stabilize an API so that it can be used as a library from
+other tools.
+.SH OPTIONS
+.TP
+\fB\-c\fR, \fB\-\-consistentHits\fR
+Ensure that the hits collected are consistent (co\-linear)
+.TP
+\fB\-f\fR, \fB\-\-fuzzyIntersection\fR
+Find paired\-end mapping locations using fuzzy intersection
+.TP
+\fB\-s\fR, \fB\-\-strictCheck\fR
+Perform extra checks to try and assure that only equally "best"
+mappings for a read are reported
+.TP
+\fB\-m\fR, \fB\-\-maxNumHits\fR <positive integer>
+Reads mapping to more than this many loci are discarded
+.TP
+\fB\-t\fR, \fB\-\-numThreads\fR <positive integer>
+Number of threads to use
+.TP
+\fB\-o\fR, \fB\-\-output\fR <path>
+The output file (default: stdout)
+.TP
+\fB\-r\fR, \fB\-\-unmatedReads\fR <path>
+The location of single\-end reads
+.TP
+\fB\-2\fR, \fB\-\-rightMates\fR <path>
+The location of the right paired\-end reads
+.TP
+\fB\-1\fR, \fB\-\-leftMates\fR <path>
+The location of the left paired\-end reads
+.TP
+\fB\-n\fR, \fB\-\-noOutput\fR
+Don't write out any alignments (for speed testing purposes)
+.TP
+\fB\-i\fR, \fB\-\-index\fR <path>
+(required)
+The location of the quasiindex
+.TP
+\fB\-\-\fR, \fB\-\-ignore_rest\fR
+Ignores the rest of the labeled arguments following this flag.
+.TP
+\fB\-\-version\fR
+Displays version information and exits.
+.TP
+\fB\-h\fR,  \fB\-\-help\fR
+Displays usage information and exits.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..19f429f
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*

-- 
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