[med-svn] [diamond] 03/03: Wrote manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository diamond.

commit be0a4882420df457fbd17f9096c84ec48e547bbc
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jan 5 11:13:47 2017 +0100

    Wrote manpage
---
 debian/diamond.1 | 287 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/doc-base  |   2 +-
 debian/manpages  |   1 +
 3 files changed, 289 insertions(+), 1 deletion(-)

diff --git a/debian/diamond.1 b/debian/diamond.1
new file mode 100644
index 0000000..9ebd10a
--- /dev/null
+++ b/debian/diamond.1
@@ -0,0 +1,287 @@
+.TH DIAMOND "1" "January 2017" "diamond 0.8.31" "User Commands"
+.SH NAME
+diamond \- accelerated BLAST compatible local sequence aligner
+.SH SYNOPSIS
+.B diamond
+COMMAND [OPTIONS]
+.SH DESCRIPTION
+ DIAMOND is a sequence aligner for protein and translated DNA searches
+ and functions as a drop-in replacement for the NCBI BLAST software
+ tools. It is suitable for protein-protein search as well as DNA-protein
+ search on short reads and longer sequences including contigs and
+ assemblies, providing a speedup of BLAST ranging up to x20,000.
+.SH COMMANDS
+.TP
+makedb
+Build DIAMOND database from a FASTA file
+.TP
+blastp
+Align amino acid query sequences against a protein reference database
+.TP
+blastx
+Align DNA query sequences against a protein reference database
+.TP
+view
+View DIAMOND alignment archive (DAA) formatted file
+.TP
+help
+Produce help message
+.TP
+version
+Display version information
+.TP
+getseq
+Retrieve sequences from a DIAMOND database file
+.SH OPTIONS
+.SS General options:
+.TP
+\fB\-\-threads\fR (\fB\-p\fR)
+number of CPU threads
+.TP
+\fB\-\-db\fR (\fB\-d\fR)
+database file
+.TP
+\fB\-\-out\fR (\fB\-o\fR)
+output file
+.TP
+\fB\-\-outfmt\fR (\fB\-f\fR)
+output format
+.IP
+0	= BLAST pairwise
+.IP
+5	= BLAST XML
+.IP
+6	= BLAST tabular
+.IP
+100	= DIAMOND alignment archive (DAA)
+.IP
+101	= SAM
+.IP
+Value 6 may be followed by a space\-separated list of these keywords:
+.IP
+qseqid	means Query Seq \- id
+.IP
+qlen	means Query sequence length
+.IP
+sseqid	means Subject Seq \- id
+.IP
+sallseqid means All subject Seq \- id(s), separated by a ';'
+.IP
+slen means Subject sequence length
+.IP
+qstart means Start of alignment in query
+.IP
+qend means End of alignment in query
+.IP
+sstart means Start of alignment in subject
+.IP
+send means End of alignment in subject
+.IP
+qseq means Aligned part of query sequence
+.IP
+sseq means Aligned part of subject sequence
+.IP
+evalue means Expect value
+.IP
+bitscore means Bit score
+.IP
+score means Raw score
+.IP
+length means Alignment length
+.IP
+pident means Percentage of identical matches
+.IP
+nident means Number of identical matches
+.IP
+mismatch means Number of mismatches
+.IP
+positive means Number of positive \- scoring matches
+.IP
+gapopen means Number of gap openings
+.IP
+gaps means Total number of gaps
+.IP
+ppos means Percentage of positive \- scoring matches
+.IP
+qframe means Query frame
+.IP
+btop means Blast traceback operations(BTOP)
+.IP
+stitle means Subject Title
+.IP
+salltitles means All Subject Title(s), separated by a '<>'
+.IP
+qcovhsp means Query Coverage Per HSP
+.IP
+qtitle means Query title
+.IP
+Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
+.TP
+\fB\-\-verbose\fR (\fB\-v\fR)
+verbose console output
+.TP
+\fB\-\-log\fR
+enable debug log
+.TP
+\fB\-\-quiet\fR
+disable console output
+.SS Makedb options:
+.TP
+\fB\-\-in\fR
+input reference file in FASTA format
+.SS Aligner options:
+.TP
+\fB\-\-query\fR (\fB\-q\fR)
+input query file
+.TP
+\fB\-\-un\fR
+file for unaligned queries
+.TP
+\fB\-\-unal\fR
+report unaligned queries (0=no, 1=yes)
+.TP
+\fB\-\-max\-target\-seqs\fR (\fB\-k\fR)
+maximum number of target sequences to report alignments for
+.TP
+\fB\-\-top\fR
+report alignments within this percentage range of top alignment score (overrides \fB\-\-max\-target\-seqs\fR)
+.TP
+\fB\-\-compress\fR
+compression for output files (0=none, 1=gzip)
+.TP
+\fB\-\-evalue\fR (\fB\-e\fR)
+maximum e\-value to report alignments
+.TP
+\fB\-\-min\-score\fR
+minimum bit score to report alignments (overrides e\-value setting)
+.TP
+\fB\-\-id\fR
+minimum identity% to report an alignment
+.TP
+\fB\-\-query\-cover\fR
+minimum query cover% to report an alignment
+.TP
+\fB\-\-subject\-cover\fR
+minimum subject cover% to report an alignment
+.TP
+\fB\-\-sensitive\fR
+enable sensitive mode (default: fast)
+.TP
+\fB\-\-more\-sensitive\fR
+enable more sensitive mode (default: fast)
+.TP
+\fB\-\-block\-size\fR (\fB\-b\fR)
+sequence block size in billions of letters (default=2.0)
+.TP
+\fB\-\-index\-chunks\fR (\fB\-c\fR)
+number of chunks for index processing
+.TP
+\fB\-\-tmpdir\fR (\fB\-t\fR)
+directory for temporary files
+.TP
+\fB\-\-gapopen\fR
+gap open penalty (default=11 for protein)
+.TP
+\fB\-\-gapextend\fR
+gap extension penalty (default=1 for protein)
+.TP
+\fB\-\-matrix\fR
+score matrix for protein alignment (default=BLOSUM62)
+.TP
+\fB\-\-custom\-matrix\fR
+file containing custom scoring matrix
+.TP
+\fB\-\-lambda\fR
+lambda parameter for custom matrix
+.TP
+\fB\-\-K\fR
+K parameter for custom matrix
+.TP
+\fB\-\-comp\-based\-stats\fR
+enable composition based statistics (0/1=default)
+.TP
+\fB\-\-seg\fR
+enable SEG masking of queries (yes/no)
+.TP
+\fB\-\-query\-gencode\fR
+genetic code to use to translate query (see user manual)
+.TP
+\fB\-\-salltitles\fR
+print full subject titles in output files
+.TP
+\fB\-\-no\-self\-hits\fR
+suppress reporting of identical self hits
+.SS Advanced options:
+.TP
+\fB\-\-min\-orf\fR (\fB\-l\fR)
+ignore translated sequences without an open reading frame of at least this length
+.TP
+\fB\-\-freq\-sd\fR
+number of standard deviations for ignoring frequent seeds
+.TP
+\fB\-\-id2\fR
+minimum number of identities for stage 1 hit
+.TP
+\fB\-\-window\fR (\fB\-w\fR)
+window size for local hit search
+.TP
+\fB\-\-xdrop\fR (\fB\-x\fR)
+xdrop for ungapped alignment
+.TP
+\fB\-\-ungapped\-score\fR
+minimum alignment score to continue local extension
+.TP
+\fB\-\-hit\-band\fR
+band for hit verification
+.TP
+\fB\-\-hit\-score\fR
+minimum score to keep a tentative alignment
+.TP
+\fB\-\-gapped\-xdrop\fR (\fB\-X\fR)
+xdrop for gapped alignment in bits
+.TP
+\fB\-\-band\fR
+band for dynamic programming computation
+.TP
+\fB\-\-shapes\fR (\fB\-s\fR)
+number of seed shapes (0 = all available)
+.TP
+\fB\-\-shape\-mask\fR
+seed shapes
+.TP
+\fB\-\-index\-mode\fR
+index mode (0=4x12, 1=16x9)
+.TP
+\fB\-\-fetch\-size\fR
+trace point fetch size
+.TP
+\fB\-\-rank\-factor\fR
+include subjects within this range of max\-target\-seqs
+.TP
+\fB\-\-rank\-ratio\fR
+include subjects within this ratio of last hit
+.TP
+\fB\-\-max\-hsps\fR
+maximum number of HSPs per subject sequence to save for each query
+.TP
+\fB\-\-dbsize\fR
+effective database size (in letters)
+.TP
+\fB\-\-no\-auto\-append\fR
+disable auto appending of DAA and DMND file extensions
+.TP
+\fB\-\-target\-fetch\-size\fR
+number of target sequences to fetch for seed extension
+.SS View options
+.TP
+\fB\-\-daa\fR (\fB\-a\fR)
+DIAMOND alignment archive (DAA) file
+.TP
+\fB\-\-forwardonly\fR
+only show alignments of forward strand
+.SS Getseq options
+.TP
+\fB\-\-seq\fR
+Sequence numbers to display.
+.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/doc-base b/debian/doc-base
index 573120e..284b04e 100644
--- a/debian/doc-base
+++ b/debian/doc-base
@@ -1,5 +1,5 @@
 Document: diamond
-Title: Benjamin Buchfink <buchfink at gmail.com>
+Title: The DIAMOND sequence aligner
 Author: Benjamin Buchfink <buchfink at gmail.com>
 Abstract: accelerated BLAST compatible local sequence aligner
  DIAMOND is a sequence aligner for protein and translated DNA searches
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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