[med-svn] r19047 - trunk/packages/mummer/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Tue Apr 14 08:59:39 UTC 2015
Author: tille
Date: 2015-04-14 08:59:38 +0000 (Tue, 14 Apr 2015)
New Revision: 19047
Added:
trunk/packages/mummer/trunk/debian/show-diff.1
Modified:
trunk/packages/mummer/trunk/debian/changelog
trunk/packages/mummer/trunk/debian/control
trunk/packages/mummer/trunk/debian/delta2blocks.1
trunk/packages/mummer/trunk/debian/mummer.1
trunk/packages/mummer/trunk/debian/mummer.links
Log:
Fix manpage syntax and add missing manpage
Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2015-04-14 08:04:28 UTC (rev 19046)
+++ trunk/packages/mummer/trunk/debian/changelog 2015-04-14 08:59:38 UTC (rev 19047)
@@ -4,6 +4,7 @@
* Add some patches from mugsy enhancing functionality by adding two tools
* cme fix dpkg-control
* Remove SF privacy breach script from docs
+ * Fix manpage syntax and add missing manpage
-- Andreas Tille <tille at debian.org> Mon, 13 Apr 2015 22:29:27 +0200
Modified: trunk/packages/mummer/trunk/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control 2015-04-14 08:04:28 UTC (rev 19046)
+++ trunk/packages/mummer/trunk/debian/control 2015-04-14 08:59:38 UTC (rev 19047)
@@ -38,5 +38,17 @@
Section: doc
Depends: ${misc:Depends}
Description: Documentation for MUMmer
+ MUMmer is a system for rapidly aligning entire genomes, whether
+ in complete or draft form. For example, MUMmer 3.0 can find all
+ 20-basepair or longer exact matches between a pair of 5-megabase genomes
+ in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
+ computer. MUMmer can also align incomplete genomes; it handles the 100s
+ or 1000s of contigs from a shotgun sequencing project with ease, and
+ will align them to another set of contigs or a genome using the NUCmer
+ program included with the system. If the species are too divergent for
+ DNA sequence alignment to detect similarity, then the PROmer program
+ can generate alignments based upon the six-frame translations of both
+ input sequences.
+ .
This package contains the documentation for MUMmer, a system for rapidly
aligning entire genomes.
Modified: trunk/packages/mummer/trunk/debian/delta2blocks.1
===================================================================
--- trunk/packages/mummer/trunk/debian/delta2blocks.1 2015-04-14 08:04:28 UTC (rev 19046)
+++ trunk/packages/mummer/trunk/debian/delta2blocks.1 2015-04-14 08:59:38 UTC (rev 19047)
@@ -1,5 +1,5 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH DELTA2BLOCKS "1" "April 2015" "delta2blocks 3.23" "User Commands"
+.TH DELTA2BLOCKS "1" "April 2015" "mummer 3.23" "User Commands"
.SH NAME
delta2blocks \- extra tool for mummer from patch of mugsy to sort alignments
.br
Modified: trunk/packages/mummer/trunk/debian/mummer.1
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.1 2015-04-14 08:04:28 UTC (rev 19046)
+++ trunk/packages/mummer/trunk/debian/mummer.1 2015-04-14 08:59:38 UTC (rev 19047)
@@ -91,7 +91,7 @@
.SH DESCRIPTION
.SH OPTIONS
-All tools (exept for gaps) obey to the -h, --help, -V and --version options
+All tools (exept for gaps) obey to the \-h, \-\-help, \-V and \-\-version options
as one would expect. This help is excellent and makes these man pages basically obsolete.
.br
.B combineMUMs
@@ -101,18 +101,18 @@
multi-fasta file of the sequences matched against the
reference
.PP
- -D Only output to stdout the difference positions
+ \-D Only output to stdout the difference positions
and characters
- -n Allow matches only between nucleotides, i.e., ACGTs
- -N num Break matches at <num> or more consecutive non-ACGTs
- -q tag Used to label query match
- -r tag Used to label reference match
- -S Output all differences in strings
- -t Label query matches with query fasta header
- -v num Set verbose level for extra output
- -W file Reset the default output filename witherrors.gaps
- -x Don't output .cover files
- -e Set error-rate cutoff to e (e.g. 0.02 is two percent)
+ \-n Allow matches only between nucleotides, i.e., ACGTs
+ \-N num Break matches at <num> or more consecutive non-ACGTs
+ \-q tag Used to label query match
+ \-r tag Used to label reference match
+ \-S Output all differences in strings
+ \-t Label query matches with query fasta header
+ \-v num Set verbose level for extra output
+ \-W file Reset the default output filename witherrors.gaps
+ \-x Don't output .cover files
+ \-e Set error-rate cutoff to e (e.g. 0.02 is two percent)
.br
.B dnadiff
Run comparative analysis of two sequence sets using nucmer and its
@@ -122,13 +122,13 @@
.PP
.report - Summary of alignments, differences and SNPs
.delta - Standard nucmer alignment output
- .1delta - 1-to-1 alignment from delta-filter -1
- .mdelta - M-to-M alignment from delta-filter -m
- .1coords - 1-to-1 coordinates from show-coords -THrcl .1delta
- .mcoords - M-to-M coordinates from show-coords -THrcl .mdelta
- .snps - SNPs from show-snps -rlTHC .1delta
- .rdiff - Classified ref breakpoints from show-diff -rH .mdelta
- .qdiff - Classified qry breakpoints from show-diff -qH .mdelta
+ .1delta - 1-to-1 alignment from delta-filter \-1
+ .mdelta - M-to-M alignment from delta-filter \-m
+ .1coords - 1-to-1 coordinates from show-coords \-THrcl .1delta
+ .mcoords - M-to-M coordinates from show-coords \-THrcl .mdelta
+ .snps - SNPs from show-snps \-rlTHC .1delta
+ .rdiff - Classified ref breakpoints from show-diff \-rH .mdelta
+ .qdiff - Classified qry breakpoints from show-diff \-qH .mdelta
.unref - Unaligned reference IDs and lengths (if applicable)
.unqry - Unaligned query IDs and lengths (if applicable)
.PP
@@ -139,108 +139,108 @@
delta file Unfiltered .delta alignment file from nucmer
.PP
OPTIONS:
- -d|delta Provide precomputed delta file for analysis
- -h
- --help Display help information and exit
- -p|prefix Set the prefix of the output files (default "out")
- -V
- --version Display the version information and exit
+ \-d|delta Provide precomputed delta file for analysis
+ \-h
+ \-\-help Display help information and exit
+ \-p|prefix Set the prefix of the output files (default "out")
+ \-V
+ \-\-version Display the version information and exit
.br
.B delta-filter
- -e float For switches -g -r -q, keep repeats within e percent
+ \-e float For switches \-g \-r \-q, keep repeats within e percent
of the best LIS score [0, 100], no repeats by default
- -g Global alignment using length*identity weighted LIS.
+ \-g Global alignment using length*identity weighted LIS.
For every reference-query pair, leave only the aligns
which form the longest mutually consistent set
- -h Display help information
- -i float Set the minimum alignment identity [0, 100], default 0
- -l int Set the minimum alignment length, default 0
- -q Query alignment using length*identity weighted LIS.
+ \-h Display help information
+ \-i float Set the minimum alignment identity [0, 100], default 0
+ \-l int Set the minimum alignment length, default 0
+ \-q Query alignment using length*identity weighted LIS.
For each query, leave only the aligns which form the
longest consistent set for the query
- -r Reference alignment using length*identity weighted LIS.
+ \-r Reference alignment using length*identity weighted LIS.
For each reference, leave only the aligns which form
the longest consistent set for the reference
- -u float Set the minimum alignment uniqueness, i.e. percent of
+ \-u float Set the minimum alignment uniqueness, i.e. percent of
the alignment matching to unique reference AND query
sequence [0, 100], default 0
- -o float Set the maximum alignment overlap for -r and -q options
+ \-o float Set the maximum alignment overlap for \-r and \-q options
as a percent of the alignment length [0, 100], default 100
.PP
Reads a delta alignment file from either nucmer or promer and
filters the alignments based on the command-line switches, leaving
only the desired alignments which are output to stdout in the same
delta format as the input. For multiple switches, order of operations
-is as follows: -i -l -u -q -r -g. If an alignment is excluded by a
+is as follows: \-i \-l \-u \-q \-r \-g. If an alignment is excluded by a
preceding operation, it will be ignored by the succeeding operations
.PP
- An important distinction between the -g option and the -r -q
-options is that -g requires the alignments to be mutually consistent
-in their order, while the -r -q options are not required to be
+ An important distinction between the \-g option and the \-r \-q
+options is that \-g requires the alignments to be mutually consistent
+in their order, while the \-r \-q options are not required to be
mutually consistent and therefore tolerate translocations,
-inversions, etc. Thus, -r provides a one-to-many, -q a many-to-one,
--r -q a one-to-one local mapping, and -g a one-to-one global mapping
+inversions, etc. Thus, \-r provides a one-to-many, \-q a many-to-one,
+\-r \-q a one-to-one local mapping, and \-g a one-to-one global mapping
of reference and query bases respectively.
.br
.B mapview
.br
- -h
+ \-h
.br
- --help Display help information and exit
+ \-\-help Display help information and exit
.br
- -m|mag Set the magnification at which the figure is rendered,
+ \-m|mag Set the magnification at which the figure is rendered,
this is an option for fig2dev which is used to generate
the PDF and PS files (default 1.0)
.br
- -n|num Set the number of output files used to partition the
+ \-n|num Set the number of output files used to partition the
output, this is to avoid generating files that are too
large to display (default 10)
.br
- -p|prefix Set the output file prefix
+ \-p|prefix Set the output file prefix
(default "PROMER_graph or NUCMER_graph")
.br
- -v
- --verbose Verbose logging of the processed files
+ \-v
+ \-\-verbose Verbose logging of the processed files
.br
- -V
- --version Display the version information and exit
+ \-V
+ \-\-version Display the version information and exit
.br
- -x1 coord Set the lower coordinate bound of the display
+ \-x1 coord Set the lower coordinate bound of the display
.br
- -x2 coord Set the upper coordinate bound of the display
+ \-x2 coord Set the upper coordinate bound of the display
.br
- -g|ref If the input file is provided by 'mgaps', set the
+ \-g|ref If the input file is provided by 'mgaps', set the
reference sequence ID (as it appears in the first column
of the UTR/CDS coords file)
.br
- -I Display the name of query sequences
+ \-I Display the name of query sequences
.br
- -Ir Display the name of reference genes
+ \-Ir Display the name of reference genes
.br
.B mummer
Find and output (to stdout) the positions and length of all
sufficiently long maximal matches of a substring in
<query-file> and <reference-file>
- -mum compute maximal matches that are unique in both sequences
- -mumcand same as -mumreference
- -mumreference compute maximal matches that are unique in
+ \-mum compute maximal matches that are unique in both sequences
+ \-mumcand same as \-mumreference
+ \-mumreference compute maximal matches that are unique in
the reference-sequence but not necessarily
in the query-sequence (default)
- -maxmatch compute all maximal matches regardless of their uniqueness
- -n match only the characters a, c, g, or t
+ \-maxmatch compute all maximal matches regardless of their uniqueness
+ \-n match only the characters a, c, g, or t
they can be in upper or in lower case
- -l set the minimum length of a match
+ \-l set the minimum length of a match
if not set, the default value is 20
- -b compute forward and reverse complement matches
- -r only compute reverse complement matches
- -s show the matching substrings
- -c report the query-position of a reverse complement match
+ \-b compute forward and reverse complement matches
+ \-r only compute reverse complement matches
+ \-s show the matching substrings
+ \-c report the query-position of a reverse complement match
relative to the original query sequence
- -F force 4 column output format regardless of the number of
+ \-F force 4 column output format regardless of the number of
reference sequence inputs
- -L show the length of the query sequences on the header line
+ \-L show the length of the query sequences on the header line
.br
.B nuncmer
nucmer generates nucleotide alignments between two mutli-FASTA input
@@ -253,41 +253,41 @@
Reference Set the input reference multi-FASTA filename
Query Set the input query multi-FASTA filename
- --mum Use anchor matches that are unique in both the reference
+ \-\-mum Use anchor matches that are unique in both the reference
and query
- --mumcand Same as --mumreference
- --mumreference Use anchor matches that are unique in in the reference
+ \-\-mumcand Same as \-\-mumreference
+ \-\-mumreference Use anchor matches that are unique in in the reference
but not necessarily unique in the query (default behavior)
- --maxmatch Use all anchor matches regardless of their uniqueness
+ \-\-maxmatch Use all anchor matches regardless of their uniqueness
- -b|breaklen Set the distance an alignment extension will attempt to
+ \-b|breaklen Set the distance an alignment extension will attempt to
extend poor scoring regions before giving up (default 200)
- -c|mincluster Sets the minimum length of a cluster of matches (default 65)
- --[no]delta Toggle the creation of the delta file (default --delta)
- --depend Print the dependency information and exit
- -d|diagfactor Set the clustering diagonal difference separation factor
+ \-c|mincluster Sets the minimum length of a cluster of matches (default 65)
+ \-\-[no]delta Toggle the creation of the delta file (default \-\-delta)
+ \-\-depend Print the dependency information and exit
+ \-d|diagfactor Set the clustering diagonal difference separation factor
(default 0.12)
- --[no]extend Toggle the cluster extension step (default --extend)
- -f
- --forward Use only the forward strand of the Query sequences
- -g|maxgap Set the maximum gap between two adjacent matches in a
+ \-\-[no]extend Toggle the cluster extension step (default \-\-extend)
+ \-f
+ \-\-forward Use only the forward strand of the Query sequences
+ \-g|maxgap Set the maximum gap between two adjacent matches in a
cluster (default 90)
- -h
- --help Display help information and exit
- -l|minmatch Set the minimum length of a single match (default 20)
- -o
- --coords Automatically generate the original NUCmer1.1 coords
+ \-h
+ \-\-help Display help information and exit
+ \-l|minmatch Set the minimum length of a single match (default 20)
+ \-o
+ \-\-coords Automatically generate the original NUCmer1.1 coords
output file using the 'show-coords' program
- --[no]optimize Toggle alignment score optimization, i.e. if an alignment
+ \-\-[no]optimize Toggle alignment score optimization, i.e. if an alignment
extension reaches the end of a sequence, it will backtrack
to optimize the alignment score instead of terminating the
- alignment at the end of the sequence (default --optimize)
- -p|prefix Set the prefix of the output files (default "out")
- -r
- --reverse Use only the reverse complement of the Query sequences
- --[no]simplify Simplify alignments by removing shadowed clusters. Turn
+ alignment at the end of the sequence (default \-\-optimize)
+ \-p|prefix Set the prefix of the output files (default "out")
+ \-r
+ \-\-reverse Use only the reverse complement of the Query sequences
+ \-\-[no]simplify Simplify alignments by removing shadowed clusters. Turn
this option off if aligning a sequence to itself to look
- for repeats (default --simplify)
+ for repeats (default \-\-simplify)
.br
.B promer
@@ -303,81 +303,81 @@
Reference Set the input reference multi-FASTA DNA file
Query Set the input query multi-FASTA DNA file
- --mum Use anchor matches that are unique in both the reference
+ \-\-mum Use anchor matches that are unique in both the reference
and query
- --mumcand Same as --mumreference
- --mumreference Use anchor matches that are unique in in the reference
+ \-\-mumcand Same as \-\-mumreference
+ \-\-mumreference Use anchor matches that are unique in in the reference
but not necessarily unique in the query (default behavior)
- --maxmatch Use all anchor matches regardless of their uniqueness
+ \-\-maxmatch Use all anchor matches regardless of their uniqueness
- -b|breaklen Set the distance an alignment extension will attempt to
+ \-b|breaklen Set the distance an alignment extension will attempt to
extend poor scoring regions before giving up, measured in
amino acids (default 60)
- -c|mincluster Sets the minimum length of a cluster of matches, measured in
+ \-c|mincluster Sets the minimum length of a cluster of matches, measured in
amino acids (default 20)
- --[no]delta Toggle the creation of the delta file (default --delta)
- --depend Print the dependency information and exit
- -d|diagfactor Set the clustering diagonal difference separation factor
+ \-\-[no]delta Toggle the creation of the delta file (default \-\-delta)
+ \-\-depend Print the dependency information and exit
+ \-d|diagfactor Set the clustering diagonal difference separation factor
(default .11)
- --[no]extend Toggle the cluster extension step (default --extend)
- -g|maxgap Set the maximum gap between two adjacent matches in a
+ \-\-[no]extend Toggle the cluster extension step (default \-\-extend)
+ \-g|maxgap Set the maximum gap between two adjacent matches in a
cluster, measured in amino acids (default 30)
- -l|minmatch Set the minimum length of a single match, measured in amino
+ \-l|minmatch Set the minimum length of a single match, measured in amino
acids (default 6)
- -m|masklen Set the maximum bookend masking lenth, measured in amino
+ \-m|masklen Set the maximum bookend masking lenth, measured in amino
acids (default 8)
- -o
- --coords Automatically generate the original PROmer1.1 ".coords"
+ \-o
+ \-\-coords Automatically generate the original PROmer1.1 ".coords"
output file using the "show-coords" program
- --[no]optimize Toggle alignment score optimization, i.e. if an alignment
+ \-\-[no]optimize Toggle alignment score optimization, i.e. if an alignment
extension reaches the end of a sequence, it will backtrack
to optimize the alignment score instead of terminating the
- alignment at the end of the sequence (default --optimize)
+ alignment at the end of the sequence (default \-\-optimize)
- -p|prefix Set the prefix of the output files (default "out")
- -x|matrix Set the alignment matrix number to 1 [BLOSUM 45],
+ \-p|prefix Set the prefix of the output files (default "out")
+ \-x|matrix Set the alignment matrix number to 1 [BLOSUM 45],
2 [BLOSUM 62] or 3 [BLOSUM 80] (default 2)
.br
.B repeat-match
Find all maximal exact matches in <genome-file>
- -E Use exhaustive (slow) search to find matches
- -f Forward strand only, don't use reverse complement
- -n # Set minimum exact match length to #
- -t Only output tandem repeats
- -V # Set level of verbose (debugging) printing to #
+ \-E Use exhaustive (slow) search to find matches
+ \-f Forward strand only, don't use reverse complement
+ \-n # Set minimum exact match length to #
+ \-t Only output tandem repeats
+ \-V # Set level of verbose (debugging) printing to #
.br
.B show-aligns
- -h Display help information
- -q Sort alignments by the query start coordinate
- -r Sort alignments by the reference start coordinate
- -w int Set the screen width - default is 60
- -x int Set the matrix type - default is 2 (BLOSUM 62),
+ \-h Display help information
+ \-q Sort alignments by the query start coordinate
+ \-r Sort alignments by the reference start coordinate
+ \-w int Set the screen width - default is 60
+ \-x int Set the matrix type - default is 2 (BLOSUM 62),
other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
note: only has effect on amino acid alignments
.br
.B show-coords
- -b Merges overlapping alignments regardless of match dir
+ \-b Merges overlapping alignments regardless of match dir
or frame and does not display any idenitity information.
- -B Switch output to btab format
- -c Include percent coverage information in the output
- -d Display the alignment direction in the additional
+ \-B Switch output to btab format
+ \-c Include percent coverage information in the output
+ \-d Display the alignment direction in the additional
FRM columns (default for promer)
- -g Deprecated option. Please use 'delta-filter' instead
- -h Display help information
- -H Do not print the output header
- -I float Set minimum percent identity to display
- -k Knockout (do not display) alignments that overlap
+ \-g Deprecated option. Please use 'delta-filter' instead
+ \-h Display help information
+ \-H Do not print the output header
+ \-I float Set minimum percent identity to display
+ \-k Knockout (do not display) alignments that overlap
another alignment in a different frame by more than 50%
of their length, AND have a smaller percent similarity
or are less than 75% of the size of the other alignment
(promer only)
- -l Include the sequence length information in the output
- -L long Set minimum alignment length to display
- -o Annotate maximal alignments between two sequences, i.e.
+ \-l Include the sequence length information in the output
+ \-L long Set minimum alignment length to display
+ \-o Annotate maximal alignments between two sequences, i.e.
overlaps between reference and query sequences
- -q Sort output lines by query IDs and coordinates
- -r Sort output lines by reference IDs and coordinates
- -T Switch output to tab-delimited format
+ \-q Sort output lines by query IDs and coordinates
+ \-r Sort output lines by reference IDs and coordinates
+ \-T Switch output to tab-delimited format
Input is the .delta output of either the "nucmer" or the
"promer" program passed on the command line.
@@ -390,19 +390,19 @@
will be ordered as found in the <deltafile> input.
.br
.B show-snps
- -C Do not report SNPs from alignments with an ambiguous
+ \-C Do not report SNPs from alignments with an ambiguous
mapping, i.e. only report SNPs where the [R] and [Q]
columns equal 0 and do not output these columns
- -h Display help information
- -H Do not print the output header
- -I Do not report indels
- -l Include sequence length information in the output
- -q Sort output lines by query IDs and SNP positions
- -r Sort output lines by reference IDs and SNP positions
- -S Specify which alignments to report by passing
+ \-h Display help information
+ \-H Do not print the output header
+ \-I Do not report indels
+ \-l Include sequence length information in the output
+ \-q Sort output lines by query IDs and SNP positions
+ \-r Sort output lines by reference IDs and SNP positions
+ \-S Specify which alignments to report by passing
'show-coords' lines to stdin
- -T Switch to tab-delimited format
- -x int Include x characters of surrounding SNP context in the
+ \-T Switch to tab-delimited format
+ \-x int Include x characters of surrounding SNP context in the
output, default 0
Input is the .delta output of either the nucmer or promer program
@@ -410,47 +410,47 @@
.PP
Output is to stdout, and consists of a list of SNPs (or amino acid
substitutions for promer) with positions and other useful info.
-Output will be sorted with -r by default and the [BUFF] column will
+Output will be sorted with \-r by default and the [BUFF] column will
always refer to the sequence whose positions have been sorted. This
value specifies the distance from this SNP to the nearest mismatch
(end of alignment, indel, SNP, etc) in the same alignment, while the
[DIST] column specifies the distance from this SNP to the nearest
sequence end. SNPs for which the [R] and [Q] columns are greater than
0 should be evaluated with caution, as these columns specify the
-number of other alignments which overlap this position. Use -C to
+number of other alignments which overlap this position. Use \-C to
assure SNPs are only reported from unique alignment regions.
.B show-tiling
- -a Describe the tiling path by printing the tab-delimited
+ \-a Describe the tiling path by printing the tab-delimited
alignment region coordinates to stdout
- -c Assume the reference sequences are circular, and allow
+ \-c Assume the reference sequences are circular, and allow
tiled contigs to span the origin
- -g int Set maximum gap between clustered alignments [-1, INT_MAX]
- A value of -1 will represent infinity
+ \-g int Set maximum gap between clustered alignments [\-1, INT_MAX]
+ A value of \-1 will represent infinity
(nucmer default = 1000)
- (promer default = -1)
- -i float Set minimum percent identity to tile [0.0, 100.0]
+ (promer default = \-1)
+ \-i float Set minimum percent identity to tile [0.0, 100.0]
(nucmer default = 90.0)
(promer default = 55.0)
- -l int Set minimum length contig to report [-1, INT_MAX]
- A value of -1 will represent infinity
+ \-l int Set minimum length contig to report [\-1, INT_MAX]
+ A value of \-1 will represent infinity
(common default = 1)
- -p file Output a pseudo molecule of the query contigs to 'file'
- -R Deal with repetitive contigs by randomly placing them
- in one of their copy locations (implies -V 0)
- -t file Output a TIGR style contig list of each query sequence
+ \-p file Output a pseudo molecule of the query contigs to 'file'
+ \-R Deal with repetitive contigs by randomly placing them
+ in one of their copy locations (implies \-V 0)
+ \-t file Output a TIGR style contig list of each query sequence
that sufficiently matches the reference (non-circular)
- -u file Output the tab-delimited alignment region coordinates
+ \-u file Output the tab-delimited alignment region coordinates
of the unusable contigs to 'file'
- -v float Set minimum contig coverage to tile [0.0, 100.0]
+ \-v float Set minimum contig coverage to tile [0.0, 100.0]
(nucmer default = 95.0) sum of individual alignments
(promer default = 50.0) extent of syntenic region
- -V float Set minimum contig coverage difference [0.0, 100.0]
+ \-V float Set minimum contig coverage difference [0.0, 100.0]
i.e. the difference needed to determine one alignment
is 'better' than another alignment
(nucmer default = 10.0) sum of individual alignments
(promer default = 30.0) extent of syntenic region
- -x Describe the tiling path by printing the XML contig
+ \-x Describe the tiling path by printing the XML contig
linking information to stdout
Input is the .delta output of the nucmer program, run on very
@@ -461,7 +461,7 @@
each aligning query contig as mapped to the reference sequences.
These coordinates reference the extent of the entire query contig,
even when only a certain percentage of the contig was actually
-aligned (unless the -a option is used). Columns are, start in ref,
+aligned (unless the \-a option is used). Columns are, start in ref,
end in ref, distance to next contig, length of this contig, alignment
coverage, identity, orientation, and ID respectively.
Modified: trunk/packages/mummer/trunk/debian/mummer.links
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.links 2015-04-14 08:04:28 UTC (rev 19046)
+++ trunk/packages/mummer/trunk/debian/mummer.links 2015-04-14 08:59:38 UTC (rev 19047)
@@ -17,4 +17,4 @@
usr/share/man/man1/mummer.1 usr/share/man/man1/show-coords.1
usr/share/man/man1/mummer.1 usr/share/man/man1/show-snps.1
usr/share/man/man1/mummer.1 usr/share/man/man1/show-tiling.1
-usr/share/man/man1/delta2blocks.1 usr/share/man/man1/delta2man.1
+usr/share/man/man1/delta2blocks.1 usr/share/man/man1/delta2maf.1
Added: trunk/packages/mummer/trunk/debian/show-diff.1
===================================================================
--- trunk/packages/mummer/trunk/debian/show-diff.1 (rev 0)
+++ trunk/packages/mummer/trunk/debian/show-diff.1 2015-04-14 08:59:38 UTC (rev 19047)
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH SHOW-DIFF "1" "April 2015" "mummer 3.23" "User Commands"
+.SH NAME
+show-diff \- show diff information (part of mummer package)
+.SH SYNOPSIS
+.B show\-diff
+.RI [options] <deltafile>
+.SH DESCRIPTION
+.TP
+\fB\-f\fR Output diff information as AMOS features
+.TP
+\fB\-h\fR Display help information
+.TP
+\fB\-H\fR Do not show header
+.TP
+\fB\-q\fR Show diff information for queries
+.TP
+\fB\-r\fR Show diff information for references (default)
+.PP
+Outputs a list of structural differences for each sequence in
+the reference and query, sorted by position. For a reference
+sequence R, and its matching query sequence Q, differences are
+categorized as GAP (gap between two mutually consistent alignments),
+DUP (inserted duplication), BRK (other inserted sequence), JMP
+(rearrangement), INV (rearrangement with inversion), SEQ
+(rearrangement with another sequence). The first five columns of
+the output are seq ID, feature type, feature start, feature end,
+and feature length. Additional columns are added depending on the
+feature type. Negative feature lengths indicate overlapping adjacent
+alignment blocks.
+.TP
+IDR GAP gap\-start gap\-end gap\-length\-R gap\-length\-Q gap\-diff
+.TP
+IDR DUP dup\-start dup\-end dup\-length
+.TP
+IDR BRK gap\-start gap\-end gap\-length
+.TP
+IDR JMP gap\-start gap\-end gap\-length
+.TP
+IDR INV gap\-start gap\-end gap\-length
+.TP
+IDR SEQ gap\-start gap\-end gap\-length prev\-sequence next\-sequence
+.PP
+Positions always reference the sequence with the given ID. The
+sum of the fifth column (ignoring negative values) is the total
+amount of inserted sequence. Summing the fifth column after removing
+DUP features is total unique inserted sequence. Note that unaligned
+sequence are not counted, and could represent additional "unique"
+sequences. See documentation for tips on how to interpret these
+alignment break features.
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