1. odgi (1)
1.1. NAME
odgi - dynamic succinct variation graph tool
1.2. SYNOPSIS
odgi build -g graph.gfa -o graph.og
odgi stats -i graph.og -S
odgi sort -i graph.og -o graph.sorted.og -p bSnSnS
odgi view -i graph.og -g
odgi kmers -i graph.og -c -k 23 -e 34 -D 50
odgi unitig -i graph.og -f -t 1324 -l 120
odgi viz -i graph.og -o graph.og.png -x 1920 -y 1080 -R -t 28
odgi paths -i graph.og -f
odgi prune -i graph.og -o graph.pruned.og -c 3 -C 345 -T
odgi unchop -i graph.og -o graph.unchopped.og
odgi normalize -i graph.og -o graph.normalized.og -I 100 -d
odgi subset -i graph.og -o graph.subsetted.og -n 1 -t 28
odgi bin -i graph.og -j -w 100 -s -g
odgi matrix -i graph.og -e -d
odgi chop -i graph.og -o graph.choped.og -c 1000
odgi groom -i graph.og -o graph.groomed.og
odgi layout -i graph.og -o graph.svg -R 10 -m 100
odgi break -i graph.og -o graph.broken.og -s 100 -d
odgi pathindex -i graph.og -o graph.xp
odgi panpos -i graph.og -p Chr1 -n 4
odgi server -i graph.og -p 4000 -ip <IP_ADDRESS>
odgi test
odgi version
1.3. DESCRIPTION
odgi, the Optimized Dynamic (genome) Graph Interface, links a thrifty dynamic in-memory variation graph data model to a set of algorithms designed for scalable sorting, pruning, transformation, and visualization of very large genome graphs. odgi includes python bindings that can be used to directly interface with its data model. This odgi manual provides detailed information about its features and subcommands, including examples.
1.4. COMMANDS
Each command has its own man page which can be viewed using e.g. man odgi_build.1. Below we have a brief summary of syntax and subcommand description.
odgi build [-g, --gfa=FILE] [-o, --out=FILE] [OPTION]…
The odgi build(1) command constructs a succinct variation graph from a GFA. Currently, only GFA1 is supported. For details of the format please see https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md.
odgi stats [-i, --idx=FILE] [OPTION]…
The odgi stats(1) command produces statistics of a variation graph. Among other metrics, it can calculate the #nodes, #edges, #paths and the total nucleotide length of the graph. Various histogram summary options complement the tool. If [-B, --bed-multicov=BED] is set, the metrics will be produced for the intervals specified in the BED.
odgi sort [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi sort(1) command sorts a succinct variation graph. Odgi sort offers a diverse palette of sorting algorithms to
determine the node order:
-
A topological sort: A graph can be sorted via breadth-first search (BFS) or depth-first search (DFS). Optionally, a chunk size specifies how much of the graph to grab at once in each topological sorting phase. The sorting algorithm will continue the sort from the next node in the prior graph order that has not been sorted, yet. The cycle breaking algorithm applies a DFS sort until a cycle is found. We break and start a new DFS sort phase from where we stopped.
-
A random sort: The graph is randomly sorted. The node order is randomly shuffled from Mersenne Twister pseudo-random generated numbers.
-
A sparse matrix mondriaan sort: We can partition a hypergraph with integer weights and uniform hyperedge costs using the Mondriaan partitioner.
-
A 1D linear SGD sort: Odgi implements a 1D linear, variation graph adjusted, multi-threaded version of the Graph Drawing by Stochastic Gradient Descent algorithm. The force-directed graph drawing algorithm minimizes the graph’s energy function or stress level. It applies stochastic gradient descent (SGD) to move a single pair of nodes at a time.
-
An eades algorithmic sort: Use Peter Eades' heuristic for graph drawing.
Sorting the paths in a graph my refine the sorting process. For the users' convenience, it is possible to specify a whole pipeline of sorts within one parameter.
odgi view [-i, --idx=FILE] [OPTION]…
The odgi view(1) command can convert a graph in odgi format to GFAv1. It can reveal a graph’s internal structures for e.g. debugging processes.
odgi kmers [-i, --idx=FILE] [-c, --stdout] [OPTION]…
Given a kmer length, the odgi kmers(1) command can emit all kmers. The output can be refined by setting the maximum number
of furcations at edges or by not considering nodes above a given node degree limit.
odgi unitig [-i, --idx=FILE] [OPTION]…
The odgi unitig(1) command can print all unitigs of a given odgi graph to standard output in FASTA format. Unitigs can also be emitted
in a fixed sequence quality FASTQ format. Various parameters can refine the unitigs to print.
odgi viz [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi viz(1) command can produce a linear, static visualization of an odgi variation graph. It aggregates the pangenome into bins
and directly renders a raster image. The binning level depends on the target width of the PNG to emit. Can be used to produce visualizations for gigabase scale pangenomes. For more information
about the binning process, please refer to odgi bin. If reverse coloring was selected, only
the bins with a reverse rate of at least 0.5 are colored. Currently, there is no parameter to color according to the
sequence coverage in bins available.
odgi paths [-i, --idx=FILE] [OPTION]…
The odgi paths(1) command allows the investigation of paths of a given variation graph. It can calculate overlap statistics
of groupings of paths.
odgi prune [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi prune(1) command can remove complex parts of a graph. One can drop paths, nodes by a certain kind of edge coverage,
edges and graph tips. Specifying a kmer length and a maximum number of furcations, the graph can be broken at edges not
fitting into these conditions.
odgi unchop [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi unchop(1) command merges each unitig into a single node.
odgi normalize [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi normalize(1) command unchops a given variation graph and simplifies redundant furcations.
odgi subset [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
Extracting a node subset of a variation graph is the task of the odgi subset(1) command. Users can specify a node, a list of nodes
or a the context of which to generate a subset from.
odgi matrix [-i, --idx=FILE] [OPTION]…
The odgi matrix(1) command generates a sparse matrix format out of the graph topology of a given variation graph.
odgi bin [-i, --idx=FILE] [OPTION]…
The odgi bin(1) command bins a given variation graph. The pangenome sequence, the one-time traversal of all nodes from smallest to
largest node identifier, can be summed up into bins of a specified size. For each bin, the path metainformation is summarized.
This enables a summarized view of gigabase scale graphs. Each step of a path is a bin and connected to its next bin via a link.
A link has a start bin identifier and an end bin identifier.
The concept of odgi bin is also applied in odgi viz.
A demonstration of how the odgi bin JSON output can be used for an interactive visualization is realized in the Pantograph
project. Per default, odgi bin writes the bins to stdout in a tab-delimited format: path.name, path.prefix, path.suffix,
bin (bin identifier), mean.cov (mean coverage of the path in this bin), mean.inv (mean inversion rate of this path in this bin),
mean.pos (mean nucleotide position of this path in this bin), first.nucl (first nucleotide position of this path in this bin),
last.nucl (last nucleotide position of this path in this bin). These nucleotide ranges might span positions that are not present in the bin. Example:
A range of 1-100 means that the first nucleotide has position 1 and the last has position 100, but nucleotide 45 could be located in
another bin. For an exact positional output, please specify [-j, --json].
odgi chop [-i, --idx=FILE] [-o, --out=FILE] [-c, --chop-to=N] [OPTION]…
The odgi chop(1) command chops long nodes into short ones while preserving the graph topology.
odgi layout [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi layout(1) command draws 2D layouts of the graph using stochastic gradient descent (SGD). The input graph must be sorted
and id-compacted. The algorithm itself is described in Graph Drawing by Stochastic Gradient Descent.
The force-directed graph drawing algorithm minimizes the graph’s energy function or stress level.
It applies SGD to move a single pair of nodes at a time. The rendered graph is written in SVG format.
odgi flatten [-i, --idx=FILE] [OPTION]…
The odgi flatten(1) command projects the graph sequence and paths into FASTA and BED.
odgi break [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi break(1) command finds cycles in a graph via breadth-first search (BFS) and breaks them, also dropping
the graph’s paths.
odgi pathindex [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi pathindex(1) command generates a path index of a graph. It uses succinct data structures to encode the index.
The path index represents a subset of the features of a fully realized xg index. Having a path index, we can use
odgi panpos to go from path:position → pangenome:position which is important when
navigating large graphs in an interactive manner like in the Pantograph project.
odgi panpos [-i, --idx=FILE] [-p, --path=STRING] [-n, --nuc-pos=N] [OPTION]…
The odgi panpos(1) command give a pangenome position for a given path and nucleotide position. It requires a path index,
which can be created with odgi pathindex. Going from path:position → pangenome:position is important when
navigating large graphs in an interactive manner like in the Pantograph project. All
input and output positions are 1-based.
odgi server [-i, --idx=FILE] [-p, --port=N] [OPTION]…
The odgi server(1) command starts an HTTP server with a given path index as input. The idea is that we can go from
path:position → pangenome:position via GET requests to the HTTP server. The server headers do not block cross origin requests.
Example GET request: http://localost:3000/path_name/nucleotide_position.
The required path index can be created with odgi pathindex. Going from path:position → pangenome:position is important when
navigating large graphs in an interactive manner like in the Pantograph project. All
input and output positions are 1-based. If no IP address is specified, the server will run on localhost.
odgi test [<TEST NAME|PATTERN|TAGS> …] [OPTION]…
The odgi test(1) command starts all unit tests that are implemented in odgi. For targeted testing, a subset of tests can
be selected. odgi test(1) depends on Catch2. In the default setting, all results are printed to stdout.
odgi version [OPTION]…
The odgi version(1) command prints the current git version with tags and codename to stdout (like v-44-g89d022b "back to old ABI"). Optionally, only the release, version or codename can be printed.
1.5. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
1.6. AUTHORS
Erik Garrison from the University of California Santa Cruz wrote the whole odgi tool. Simon Heumos from the Quantitative Biology Center Tübingen wrote odgi pathindex, odgi panpos, odgi server, and this documentation.
1.7. RESOURCES
Project web site: https://github.com/vgteam/odgi
Git source repository on GitHub: https://github.com/vgteam/odgi
GitHub organization: https://github.com/vgteam
Discussion list / forum: https://github.com/vgteam/odgi/issues
1.8. COPYING
The MIT License (MIT)
Copyright (c) 2019 Erik Garrison
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
2. odgi build(1)
2.1. NAME
odgi_build - construct a dynamic succinct variation graph
2.2. SYNOPSIS
odgi build [-g, --gfa=FILE] [-o, --out=FILE] [OPTION]…
2.3. DESCRIPTION
The odgi build(1) command constructs a succinct variation graph from a GFA. Currently, only GFA1 is supported. For details of the format please see https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md.
2.4. OPTIONS
2.4.1. Graph Files IO
- -g, --gfa=FILE
-
GFA1 file containing the nodes, edges and paths to build a dynamic succinct variation graph from.
- -o, --out=FILE
-
Write the dynamic succinct variation graph to this file. A file ending with .og is recommended.
2.4.2. Graph Sorting
- -s, --sort
-
Apply a general topological sort to the graph and order the node ids accordingly. A bidirected adaptation of Kahn’s topological sort (1962) is used, which can handle components with no heads or tails. Here, both heads and tails are taken into account.
2.4.3. Processing Information
- -p, --progress
-
Print progress updates to stdout.
- -d, --debug
-
Verbosely print graph information to stderr. This includes the maximum node_id, the minimum node_id, the handle to node_id mapping, the deleted nodes and the path metadata.
- --trace
-
Include backtrace information when reporting errors.
- -v, --verbose
-
Verbosely print processing information to stderr, including debug-level log messages.
- -w, --warnings
-
Turn on script warnings (applies to executed code).
- -t, --timings
-
Print timings report to stderr (time to read, parse, and convert).
2.4.4. Program Information
- -h, --help
-
Print a help message for odgi build.
2.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
2.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
2.7. AUTHORS
odgi build was written by Erik Garrison.
3. odgi stats(1)
3.1. NAME
odgi_stats - metrics describing variation graphs
3.2. SYNOPSIS
odgi stats [-i, --idx=FILE] [OPTION]…
3.3. DESCRIPTION
The odgi stats(1) command produces statistics of a variation graph. Among other metrics, it can calculate the #nodes, #edges, #paths and the total nucleotide length of the graph. Various histogram summary options complement the tool. If [-B, --bed-multicov=BED] is set, the metrics will be produced for the intervals specified in the BED.
3.4. OPTIONS
3.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to create statistics from. The file name usually ends with .og.
3.4.2. Summary Options
- -S, --summarize
-
Summarize the graph properties and dimensions. Print to stdout the #nucleotides, #nodes, #edges and #paths of the graph.
- -b, --base-content
-
Describe the base content of the graph. Print to stdout the #A, #C, #G and #T of the graph.
- -C, --coverage
-
Provide a histogram of path coverage over bases in the graph. Print three tab-delimited columns to stdout: type, cov, N. type is one of full or uniq and determines if the histogram corresponds to the full graph or only to a unique paths graph. cov implies the #paths. N implies the #nucleotides.
- -V, --set-coverage
-
Provide a histogram of coverage over unique set of paths. Print two tab-delimited columns to stdout: cov, sets. cov implies #nucleotides. sets lists the unique set of paths in a comma separated list. Sets with a cov of one and no paths in sets are listed, too.
- -M, --multi-coverage
-
Provide a histogram of coverage over unique multiset, the combination with possible repetition of paths. Print two tab-delimited columns to stdout: cov, sets. cov implies #nucleotides. sets lists the unique multisets of paths in a comma separated list. Multisets with a cov of one and no paths in sets are listed, too.
3.4.3. BED Interval
- -B, --bed-multicov=BED
-
For each BED entry, provide a table of path coverage over unique multisets of paths in the graph. Each unique multiset of paths overlapping a given BED interval is described in terms of its length relative to the total interval, the number of path traversals and unique paths involved in these traversals.
3.4.4. Threading
- -t, --threads=N
-
Number of threads to use.
3.4.5. Program Information
- -h, --help
-
Print a help message for odgi stats.
3.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
3.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
3.7. AUTHORS
odgi stats was written by Erik Garrison.
4. odgi sort(1)
4.1. NAME
odgi_sort - sort a variation graph
4.2. SYNOPSIS
odgi sort [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
4.3. DESCRIPTION
The odgi sort(1) command sorts a succinct variation graph. Odgi sort offers a diverse palette of sorting algorithms to determine the node order:
-
A topological sort: A graph can be sorted via breadth-first search (BFS) or depth-first search (DFS). Optionally, a chunk size specifies how much of the graph to grab at once in each topological sorting phase. The sorting algorithm will continue the sort from the next node in the prior graph order that has not been sorted, yet. The cycle breaking algorithm applies a DFS sort until a cycle is found. We break and start a new DFS sort phase from where we stopped.
-
A random sort: The graph is randomly sorted. The node order is randomly shuffled from Mersenne Twister pseudo-random generated numbers.
-
A sparse matrix mondriaan sort: We can partition a hypergraph with integer weights and uniform hyperedge costs using the Mondriaan partitioner.
-
A 1D linear SGD sort: Odgi implements a 1D linear, variation graph adjusted, multi-threaded version of the Graph Drawing by Stochastic Gradient Descent algorithm. The force-directed graph drawing algorithm minimizes the graph’s energy function or stress level. It applies stochastic gradient descent (SGD) to move a single pair of nodes at a time.
-
An eades algorithmic sort: Use Peter Eades' heuristic for graph drawing.
Sorting the paths in a graph my refine the sorting process. For the users' convenience, it is possible to specify a whole pipeline of sorts within one parameter.
4.4. OPTIONS
4.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to sort. The file name usually ends with .og.
- -o, --out=FILE
-
Write the sorted dynamic succinct variation graph to this file. A file ending with .og is recommended.
- -s, --sort-order=FILE
-
File containing the sort order. Each line contains one node identifier.
4.4.2. Topological Sorts
- -b, --breadth-first
-
Use a (chunked) breadth first topological sort.
- -B, --breadth-first-chunk=N
-
Chunk size for breadth first topological sort. Specify how many nucleotides to grap at once in each BFS phase.
- -z, --depth-first
-
Use a (chunked) depth first topological sort.
- -Z, --depth-first-chunk=N
-
Chunk size for the depth first topological sort. Specify how many nucleotides to grap at once in each DFS phace.
- -w, --two-way
-
Use a two-way topological algorithm for sorting. It is a maximum of head-first and tail-first topological sort.
- -n, --no-seeds
-
Don’t use heads or tails to seed topological sort.
- -c, --cycle-breaking
-
Use a cycle breaking sort.
4.4.3. Random Sort
- -r, --random
-
Randomly sort the graph.
4.4.4. Mondriaan Sort
- -m, --mondriaan
-
Use the sparse matrix diagonalization to sort the graph.
- -N, --mondriaan-n-parts=N
-
Number of partitions for the mondriaan sort.
- -E, --mondriaan-epsilon=N
-
Set the epsilon parameter for the mondriaan sort.
- -W, --mondriaan-path-weight
-
Weight the mondriaan input matrix by the path coverage of edges.
4.4.5. 1D Linear SGD Sort
- -S, --linear-sgd
-
Apply 1D linear SGD algorithm to sort the graph.
- -O, --sgd-bandwidth=sgd-bandwidth
-
Bandwidth of linear SGD model. The default value is 1000.
- -Q, --sgd-sampling-rate=sgd-sampling-rate
-
Sample pairs of nodes with probability distance between them divided by the sampling rate. The default value is 20.
- -K, --sgd-use-paths
-
Use the paths to structure the distances between nodes in SGD.
- -T, --sgd-iter-max=sgd_iter-max
-
The maximum number of iterations for the linear SGD model. The default value is 30.
- -V, --sgd-eps=sgd-eps
-
The final learning rate for the linear SGD model. The default value is 0.01.
- -C, --sgd-delta=sgd-delta
-
The threshold of the maximum node displacement, approximately in base pairs, at which to stop SGD.
4.4.6. Eades Sort
- -e, --eades
-
Use eades algorithm.
4.4.7. Path Sorting Options
- -L, --paths-min
-
Sort paths by their lowest contained node identifier.
- -M, --paths-max
-
Sort paths by their highest contained node identifier.
- -A, --paths-avg
-
Sort paths by their average contained node identifier.
- -R, --paths-avg-rev
-
Sort paths in reverse by their average contained node identifier.
- -D, --path-delim=path-delim
-
Sort paths in bins by their prefix up to this delimiter.
4.4.8. Pipeline Sorting
- -p, --pipeline=STRING
-
Apply a series of sorts, based on single character command line arguments given to this command. The default sort is s. The reverse sort would be specified via f.
4.4.9. Additional Parameters
- -d, --dagify-sort
-
Sort on the basis of a DAGified graph.
- -O, --Optimize
-
Use the MutableHandleGraph::optimize method to compact the node identifier space.
4.4.10. Threading
- -t, --threads=N
-
Number of threads to use for parallel sorting in SGD. Only specify this argument in combination with -S, --linear-sgd. No multi-threading support for any other sorting algorithm.
4.4.11. Processing Information
- -P, --progress
-
Print sort progress to stdout.
4.4.12. Program Information
- -h, --help
-
Print a help message for odgi sort.
4.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
4.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
4.7. AUTHORS
odgi sort was written by Erik Garrison.
5. odgi view(1)
5.1. NAME
odgi_view - projection of graphs into other formats
5.2. SYNOPSIS
odgi view [-i, --idx=FILE] [OPTION]…
5.3. DESCRIPTION
The odgi view(1) command can convert a graph in odgi format to GFAv1. It can reveal a graph’s internal structures for e.g. debugging processes.
5.4. OPTIONS
5.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to convert from. The file name usually ends with .og.
- -g, --to-gfa
-
Write the graph in GFAv1 format to standard output.
5.4.2. Summary Options
- -d, --display
-
Show the internal structures of a graph. Print to stdout the maximum node identifier, the minimum node identifier, the nodes vector, the delete nodes bit vector and the path metadata, each in a separate line.
5.4.3. Program Information
- -h, --help
-
Print a help message for odgi view.
5.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
5.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
5.7. AUTHORS
odgi view was written by Erik Garrison.
6. odgi kmers(1)
6.1. NAME
odgi_kmers - show and characterize the kmer space of the graph
6.2. SYNOPSIS
odgi kmers [-i, --idx=FILE] [-c, --stdout] [OPTION]…
6.3. DESCRIPTION
Given a kmer length, the odgi kmers(1) command can emit all kmers. The output can be refined by setting the maximum number of furcations at edges or by not considering nodes above a given node degree limit.
6.4. OPTIONS
6.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to convert from. The file name usually ends with .og.
- -c, --stdout=
-
Write the kmers to standard output. Kmers are line-separated.
6.4.2. Kmer Options
- -k, --kmer-length=N
-
The kmer length to generate kmers from.
- -e, --max-furcations=N
-
Break at edges that would induce this many furcations when generating a kmer.
- -D, --max-degree=N
-
Don’t take nodes into account that have a degree greater than N.
6.4.3. Threading
- -t, --threads=N
-
Number of threads to use.
6.4.4. Program Information
- -h, --help
-
Print a help message for odgi kmers.
6.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
6.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
6.7. AUTHORS
odgi kmers was written by Erik Garrison.
7. odgi unitig(1)
7.1. NAME
odgi_unitig - output unitigs of the graph
7.2. SYNOPSIS
odgi unitig [-i, --idx=FILE] [OPTION]…
7.3. DESCRIPTION
The odgi unitig(1) command can print all unitigs of a given odgi graph to standard output in FASTA format. Unitigs can also be emitted in a fixed sequence quality FASTQ format. Various parameters can refine the unitigs to print.
7.4. OPTIONS
7.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to convert from. The file name usually ends with .og.
7.4.2. FASTQ Options
- -f, --fake-fastq
-
Write the unitigs in FASTQ format to stdout with a fixed quality value of I.
7.4.3. Unitig Options
- -t, --sample-to=N
-
Continue unitigs with a random walk in the graph so that they have at least the given N length.
- -p, --sample-plus=N
-
Continue unitigs with a random walk in the graph by N past their natural end.
- -l, --min-begin-node-length=N
-
Only begin unitigs collection from nodes which have at least length N.
7.4.4. Program Information
- -h, --help
-
Print a help message for odgi unitig.
7.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
7.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
7.7. AUTHORS
odgi unitig was written by Erik Garrison.
8. odgi viz(1)
8.1. NAME
odgi_viz - variation graph visualizations
8.2. SYNOPSIS
odgi viz [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
8.3. DESCRIPTION
The odgi viz(1) command can produce a linear, static visualization of an odgi variation graph. It can aggregate the pangenome into bins and directly renders a raster image. The binning level can be specified in input or it is calculated from the target width of the PNG to emit. Can be used to produce visualizations for gigabase scale pangenomes. For more information about the binning process, please refer to odgi bin. If reverse coloring was selected, only the bins with a reverse rate of at least 0.5 are colored. Currently, there is no parameter to color according to the sequence coverage in bins available.
8.4. OPTIONS
8.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to convert from. The file name usually ends with .og.
- -o, --out=FILE
-
Write the visualization in PNG format to this file.
8.4.2. Visualization Options
- -x, --width=N
-
Set the width in pixels of the output image.
- -y, --height=N
-
Set the height in pixels of the output image.
- -P, --path-height=N
-
The height in pixels for a path.
- -X, --path-x-padding=N
-
The padding in pixels on the x-axis for a path.
- -R, --pack-paths
-
Pack all paths rather than displaying a single path per row.
- -L, --link-path-pieces=FLOAT
-
Show thin links of this relative width to connect path pieces.
- -A, --alignment-prefix=STRING
-
Apply alignment related visual motifs to paths which have this name prefix.
- -S, --show-strand
-
Use red and blue coloring to display forward and reverse alignments. This parameter should only be set in combination with [-A, --alignment-prefix=STRING].
8.4.3. Binned Mode Options
- -b, --binned-mode=N
-
The variation graph is binned before its visualization. Each pixel in the output image will correspond to a bin. For more information about the binning process, please refer to odgi bin.
- -w, --bin-width=N
-
The bin width specifies the size of each bin in the binned mode. If it is not specified, the bin width is calculated from the width in pixels of the output image.
- -g, --no-gap-links
-
We divide links into 2 classes:
-
Class: The links which help to follow complex variations. They need to be drawn, else one could not follow the sequence of a path.
-
Class: The links helping to follow simple variations. Such links solely connecting a path from left to right may not be relevant to understand a path’s traversal through the bins. Therefore, they are not drawn in the binned mode.
-
8.4.4. Threading
- -t, --threads=N
-
Number of threads to use.
8.4.5. Program Information
- -h, --help
-
Print a help message for odgi viz.
8.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
8.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
8.7. AUTHORS
odgi viz was written by Erik Garrison.
9. odgi paths(1)
9.1. NAME
odgi_paths - embedded path interrogation
9.2. SYNOPSIS
odgi paths [-i, --idx=FILE] [OPTION]…
9.3. DESCRIPTION
The odgi paths(1) command allows the investigation of paths of a given variation graph. It can calculate overlap statistics of groupings of paths.
9.4. OPTIONS
9.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to investigate the paths from. The file name usually ends with .og.
- -O, --overlaps=FILE
-
Read in the path grouping file to generate the overlap statistics from. The file must be tab-delimited. The first column lists a grouping and the second the path itself. Each line has one path entry. For each group the pairwise overlap statistics for each pairing will be calculated and printed to stdout.
9.4.2. Investigation Options
- -L, --list-paths
-
Print the paths in the graph to stdout. Each path is printed in its own line.
- -H, --haplotypes
-
Print to stdout the paths in an approximate binary haplotype matrix based on the graph’s sort order. The output is tab-delimited: path.name, path.length, node.count, node.1, node.2, node.n. Each path entry is printed in its own line.
- -D, --delim=CHAR
-
The part of each path name before this delimiter is a group identifier. This parameter should only be set in combination with [-H, --haplotypes]. Prints an additional, first column group.name to stdout.
- -d, --distance
-
Provides a sparse distance matrix for paths. If [-D, --delim] is set, it will be path groups distances.
- -f, --fasta
-
Print paths in FASTA format to stdout.
9.4.3. Threading
- -t, --threads=N
-
Number of threads to use.
9.4.4. Program Information
- -h, --help
-
Print a help message for odgi paths.
9.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
9.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
9.7. AUTHORS
odgi paths was written by Erik Garrison.
10. odgi prune(1)
10.1. NAME
odgi_prune - remove complex parts of the graph
10.2. SYNOPSIS
odgi prune [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
10.3. DESCRIPTION
The odgi prune(1) command can remove complex parts of a graph. One can drop paths, nodes by a certain kind of edge coverage, edges and graph tips. Specifying a kmer length and a maximum number of furcations, the graph can be broken at edges not fitting into these conditions.
10.4. OPTIONS
10.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to load in. The file name usually ends with .og.
- -o, --out=FILE
-
Write the pruned graph to FILE. The file name should end with .og.
10.4.2. Kmer Options
- -k, --kmer-length=N
-
The length of the kmers to consider.
- -e, --max-furcations=N
-
Break at edges that would induce N many furcations in a kmer.
10.4.3. Node Options
- -d, --max-degree=N
-
Remove nodes that have a higher node degree than N.
- -c, --min-coverage=N
-
Remove nodese covered by fewer than N number of path steps.
- -C, --max-coverage=N
-
Remove nodes covered by more than N number of path steps.
- -T, --cut-tips=N
-
Remove nodes which are graph tips.
10.4.4. Edge Options
- -E, --edge-coverage
-
Remove edges outside of the minimum and maximum coverage rather than nodes. Only set this argument in combination with [-c, --min-coverage=N] and [-C, --max-coverage=N].
- -b, --best-edges=N
-
Only keep the N most covered inbound and output edges of each node.
10.4.5. Path Options
- -D, --drop-paths
-
Remove the paths from the graph.
10.4.6. Threading
- -t, --threads=N
-
Number of threads to use.
10.4.7. Program Information
- -h, --help
-
Print a help message for odgi prune.
10.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
10.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
10.7. AUTHORS
odgi prune was written by Erik Garrison.
11. odgi unchop(1)
11.1. NAME
odgi_unchop - merge unitigs into single nodes
11.2. SYNOPSIS
odgi unchop [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
11.3. DESCRIPTION
The odgi unchop(1) command merges each unitig into a single node.
11.4. OPTIONS
11.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to unchop. The file name usually ends with .og.
- -o, --out=FILE
-
Write the unchopped dynamic succinct variation graph to this file. A file ending with .og is recommended.
11.4.2. Program Information
- -h, --help
-
Print a help message for odgi unchop.
11.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
11.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
11.7. AUTHORS
odgi unchop was written by Erik Garrison.
12. odgi normalize(1)
12.1. NAME
odgi_normalize - compact unitigs and simplify redundant furcations
12.2. SYNOPSIS
odgi normalize [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
12.3. DESCRIPTION
The odgi normalize(1) command unchops a given variation graph and simplifies redundant furcations.
12.4. OPTIONS
12.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to normalize. The file name usually ends with .og.
- -o, --out=FILE
-
Write the normalized dynamic succinct variation graph to this file. A file ending with .og is recommended.
- -I, --max-iterations=N
-
Iterate the normalization up to N many times. The default is 10.
12.4.2. Program Debugging
- -d, --debug
-
Print information about the normalization process to stdout.
12.4.3. Program Information
- -h, --help
-
Print a help message for odgi normalize.
12.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
12.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
12.7. AUTHORS
odgi normalize was written by Erik Garrison.
13. odgi subset(1)
13.1. NAME
odgi_subset - extract subsets of the graph as defined by query criteria
13.2. SYNOPSIS
odgi subset [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
13.3. DESCRIPTION
Extracting a node subset of a variation graph is the task of the odgi subset(1) command. Users can specify a node, a list of nodes or a context of which to generate a subset from.
13.4. OPTIONS
13.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to subset. The file name usually ends with .og.
- -o, --out=FILE
-
Write the subset to this file.
13.4.2. Traversal Options
- -l, --node-list=FILE
-
A file with one node identifier per line. All nodes specified here will be extract as a subset.
- -n, --node=N
-
Specify the node identifier from which our traversal should begin.
- -c, --context=N
-
The number of steps away from which to begin our traversal.
13.4.3. Threading
- -t, --threads=N
-
Number of threads to use.
13.4.4. Program Information
- -h, --help
-
Print a help message for odgi subset.
13.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
13.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
13.7. AUTHORS
odgi subset was written by Erik Garrison.
14. odgi bin(1)
14.1. NAME
odgi_bin - binning of pangenome sequence and path information in the graph
14.2. SYNOPSIS
odgi bin [-i, --idx=FILE] [OPTION]…
14.3. DESCRIPTION
The odgi bin(1) command bins a given variation graph. The pangenome sequence, the one-time traversal of all nodes from smallest to
largest node identifier, can be summed up into bins of a specified size. For each bin, the path metainformation is summarized.
This enables a summarized view of gigabase scale graphs. Each step of a path is a bin and connected to its next bin via a link.
A link has a start bin identifier and an end bin identifier.
The concept of odgi bin is also applied in odgi viz.
A demonstration of how the odgi bin JSON output can be used for an interactive visualization is realized in the Pantograph
project. Per default, odgi bin writes the bins to stdout in a tab-delimited format: path.name, path.prefix, path.suffix,
bin (bin identifier), mean.cov (mean coverage of the path in this bin), mean.inv (mean inversion rate of this path in this bin),
mean.pos (mean nucleotide position of this path in this bin), first.nucl (first nucleotide position of this path in this bin),
last.nucl (last nucleotide position of this path in this bin). These nucleotide ranges might span positions that are not present in the bin. Example:
A range of 1-100 means that the first nucleotide has position 1 and the last has position 100, but nucleotide 45 could be located in
another bin. For an exact positional output, please specify [-j, --json].
14.4. OPTIONS
14.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to investigate the bin from. The file name usually ends with .og.
14.4.2. FASTA Options
- -f, --fasta=FILE
-
Write the pangenome sequence to FILE in FASTA format.
14.4.3. Bin Options
- -n, --number-bins=N
-
The number of bins the pangenome sequence should be chopped up to.
- -w, --bin-width=N
-
The bin width specifies the size of each bin.
- -D, --path-delim=STRING
-
Annotate rows by prefix and suffix of this delimiter.
- -a, --aggregate-delim
-
Aggregate on path prefix delimiter. Argument depends on [-D, --path-delim=STRING].
- -j, --json
-
Print bins and links to stdout in pseudo JSON format. Each line is a valid JSON object, but the whole file is not a valid JSON! First, each bin including its pangenome sequence is printed to stdout per line. Second, for each path in the graph, its traversed bins including metainformation: bin (bin identifier), mean.cov (mean coverage of the path in this bin), mean.inv (mean inversion rate of this path in this bin), mean.pos (mean nucleotide position of this path in this bin), and an array of ranges determining the nucleotide position of the path in this bin. Switching first and last nucleotide in a range represents a complement reverse orientation of that particular sequence.
- -s, --no-seqs
-
If [-j, --json] is set, no nucleotide sequences will be printed to stdout in order to save disk space.
- -g, --no-gap-links
-
Links connecting a path from left to right may not be relevant to understand a path’s traversal through the bins. They can be left out saving disk space.
14.4.4. Program Information
- -h, --help
-
Print a help message for odgi bin.
14.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
14.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
14.7. AUTHORS
odgi bin was written by Erik Garrison.
15. odgi matrix(1)
15.1. NAME
odgi_matrix - write the graph topology in sparse matrix formats
15.2. SYNOPSIS
odgi matrix [-i, --idx=FILE] [OPTION]…
15.3. DESCRIPTION
The odgi matrix(1) command generates a sparse matrix format out of the graph topology of a given variation graph.
15.4. OPTIONS
15.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to create the sparse matrix from. The file name usually ends with .og.
15.4.2. Matrix Options
- -e, --edge-depth-weight
-
Weigh edges by their path depth.
- -d, --delta-weight
-
Weigh edges by their inverse id delta.
15.4.3. Program Information
- -h, --help
-
Print a help message for odgi matrix.
15.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
15.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
15.7. AUTHORS
odgi matrix was written by Erik Garrison.
16. odgi chop(1)
16.1. NAME
odgi_chop - divide nodes into smaller pieces
16.2. SYNOPSIS
odgi chop [-i, --idx=FILE] [-o, --out=FILE] [-c, --chop-to=N] [OPTION]…
16.3. DESCRIPTION
The odgi chop(1) command chops long nodes into short ones while preserving the graph topology.
16.4. OPTIONS
16.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to chop. The file name usually ends with .og.
- -o, --out=FILE
-
Write the choped succinct variation graph to FILE. The file name usually ends with .og.
16.4.2. Chop Options
- -c, --chop-to=N
-
Divide nodes that longer than N into nodes no longer than N while maintaining graph topology.
16.4.3. Processing Information
- -d, --debug
-
Print information about the components to stdout.
16.4.4. Program Information
- -h, --help
-
Print a help message for odgi chop.
16.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
16.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
16.7. AUTHORS
odgi chop was written by Erik Garrison.
17. odgi layout(1)
17.1. NAME
odgi_layout - use SGD to make 2D layouts of the graph
17.2. SYNOPSIS
odgi layout [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
17.3. DESCRIPTION
The odgi layout(1) command draws 2D layouts of the graph using stochastic gradient descent (SGD). The input graph must be sorted and id-compacted. The algorithm itself is described in Graph Drawing by Stochastic Gradient Descent. The force-directed graph drawing algorithm minimizes the graph’s energy function or stress level. It applies SGD to move a single pair of nodes at a time. The rendered graph is written in SVG format.
17.4. OPTIONS
17.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to layout. The file name usually ends with .og.
- -o, --out=FILE
-
Write the rendered layout in SVG format to FILE.
17.4.2. SGD Options
- -m, --iter-max=N
-
The maximum number of iterations to run the layout. Default is 30.
- -p, --n-pivots=N
-
The number of pivots for sparse layout. Default is 0 leading to a non-sparse layout.
- -e, --eps=N
-
The learning rate for SGD layout. Default is 0.01.
17.4.3. SVG Options
- -x, --x-padding=N
-
The padding between the connected component layouts. Default is 10.0.
- -R, --render-scale=N
-
SVG scaling Default is 5.0.
17.4.4. Processing Information
- -d, --debug
-
Print information about the components to stdout.
17.4.5. Program Information
- -h, --help
-
Print a help message for odgi layout.
17.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
17.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
17.7. AUTHORS
odgi layout was written by Erik Garrison.
18. odgi flatten(1)
18.1. NAME
odgi_flatten - generate linearization of the graph
18.2. SYNOPSIS
odgi flatten [-i, --idx=FILE] [OPTION]…
18.3. DESCRIPTION
The odgi flatten(1) command projects the graph sequence and paths into FASTA and BED.
18.4. OPTIONS
18.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to flatten. The file name usually ends with .og.
18.4.2. Output Options
- -f, --fasta=FILE
-
Write the concatenated node sequences in FASTA format to FILE.
- -n, --name-seq=STRING
-
The name to use for the concatenated graph sequence. Default is the name of the input file which was specified via [-i, --idx=FILE].
- -b, --bed=FILE
-
Write the mapping between graph paths and the linearized FASTA sequence in BED format to FILE.
18.4.3. Program Information
- -h, --help
-
Print a help message for odgi flatten.
18.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
18.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
18.7. AUTHORS
odgi flatten was written by Erik Garrison.
19. odgi break(1)
19.1. NAME
odgi_break - break cycles in the graph and drop its paths
19.2. SYNOPSIS
odgi break [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
19.3. DESCRIPTION
The odgi break(1) command finds cycles in a graph via breadth-first search (BFS) and breaks them, also dropping the graph’s paths.
19.4. OPTIONS
19.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to break. The file name usually ends with .og.
- -o, --out=FILE
-
Write the broken graph to FILE.
19.4.2. Cycle Options
- -c, --cycle-max-bp=N
-
The maximum cycle length at which to break.
- -s, --max-search-bp=N
-
The maximum search space of each BFS given in number of base pairs.
- -u, --repeat-up-to=N
-
Iterate cycle breaking up to N times or stop if no new edges are removed.
- -d, --show
-
Print the edges we would remove to stdout.
19.4.3. Program Information
- -h, --help
-
Print a help message for odgi break.
19.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
19.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
19.7. AUTHORS
odgi break was written by Erik Garrison.
20. odgi pathindex(1)
20.1. NAME
odgi_pathindex - create a path index for a given path
20.2. SYNOPSIS
odgi pathindex [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
20.3. DESCRIPTION
The odgi pathindex(1) command generates a path index of a graph. It uses succinct data structures to encode the index. The path index represents a subset of the features of a fully realized xg index. Having a path index, we can use odgi panpos to go from path:position → pangenome:position which is important when navigating large graphs in an interactive manner like in the Pantograph project.
20.4. OPTIONS
20.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph to generate a path index from. The file name usually ends with .og.
- -o, --out=FILE
-
Write the path index to FILE.
20.4.2. Program Information
- -h, --help
-
Print a help message for odgi pathindex.
20.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
20.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
20.7. AUTHORS
odgi pathindex was written by Simon Heumos.
21. odgi panpos(1)
21.1. NAME
odgi_panpos - get the pangenome position of a given path and nucleotide position (1-based)
21.2. SYNOPSIS
odgi panpos [-i, --idx=FILE] [-p, --path=STRING] [-n, --nuc-pos=N] [OPTION]…
21.3. DESCRIPTION
The odgi panpos(1) command give a pangenome position for a given path and nucleotide position. It requires a path index, which can be created with odgi pathindex. Going from path:position → pangenome:position is important when navigating large graphs in an interactive manner like in the Pantograph project. All input and output positions are 1-based.
21.4. OPTIONS
21.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph index to find the pangenome position in. The file name usually ends with .xp.
21.4.2. Position Options
- -p, --path=STRING
-
The path name of the query.
- -n, --nuc-pos=STRING
-
The nucleotide sequence of the query.
21.4.3. Program Information
- -h, --help
-
Print a help message for odgi panpos.
21.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
21.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
21.7. AUTHORS
odgi panpos was written by Simon Heumos.
22. odgi server(1)
22.1. NAME
odgi_server - start a HTTP server with a given index file to query a pangenome position
22.2. SYNOPSIS
odgi server [-i, --idx=FILE] [-p, --port=N] [OPTION]…
22.3. DESCRIPTION
The odgi server(1) command starts an HTTP server with a given path index as input. The idea is that we can go from
path:position → pangenome:position via GET requests to the HTTP server. The server headers do not block cross origin requests.
Example GET request: http://localost:3000/path_name/nucleotide_position.
The required path index can be created with odgi pathindex. Going from path:position → pangenome:position is important when
navigating large graphs in an interactive manner like in the Pantograph project. All
input and output positions are 1-based. If no IP address is specified, the server will run on localhost.
22.4. OPTIONS
22.4.1. Graph Files IO
- -i, --idx=FILE
-
File containing the succinct variation graph index to host in a HTTP server. The file name usually ends with .xp.
22.4.2. HTTP Options
- -p, --port=N
-
Run the server under this port.
- -a, --ip=IP
-
Run the server under this IP address. If not specified, IP will be localhost.
22.4.3. Program Information
- -h, --help
-
Print a help message for odgi server.
22.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
22.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
22.7. AUTHORS
odgi server was written by Simon Heumos.
23. odgi test(1)
23.1. NAME
odgi_test - run odgi unit tests
23.2. SYNOPSIS
odgi test [<TEST NAME|PATTERN|TAGS> …] [OPTION]…
23.3. DESCRIPTION
The odgi test(1) command starts all unit tests that are implemented in odgi. For targeted testing, a subset of tests can be selected. odgi test(1) depends on Catch2. In the default setting, all results are printed to stdout.
23.4. OPTIONS
23.4.1. Testing Options
- -l, --list-tests
-
List all test cases. If a pattern was specified, all matching test cases are listed.
- -t, --list-tags
-
List all tags. If a pattern was specified, all matching tags are listed.
- -s, --success
-
Include successful tests in output.
- -b, --break
-
Break into debugger mode upon failed test.
- -e, --nothrow
-
Skip exception tests.
- -i, --invisibles
-
Show invisibles like tabs or newlines.
- -o, --out=FILE
-
Write all output to FILE.
- -r, --reporter=STRING
-
Reporter to use. Default is console.
- -n, --name=STRING
-
Suite name.
- -a, --abort
-
Abort at first failure.
- -x, --abortx=N
-
Abort after N failures.
- -w, --warn=STRING
-
Enable warnings.
- -d, --durations=yes|no
-
Show test durations. Default is no.
- -f, --input-file=FILE
-
Load test names from a file.
- -#, --filenames-as-tags
-
Adds a tag for the file name.
- -c, --section=STRING
-
Specify the section to run the tests on.
- -v, --verosity=quiet|normal|high
-
Set output verbosity. Default is normal.
- --list-test-names-only
-
List all test cases names only. If a pattern was specified, all matching test cases are listed.
- --list-reporters
-
List all reporters.
- --order=decl|lex|rand
-
Test case order. Default ist decl.
- --rng-seed=time|number
-
Set a specific seed for random numbers.
- --use-color=yes|no
-
Should the output be colorized? Default is yes.
- --libidentify
-
Report name and version according to libidentify.
- --wait-for-keypress=start|exit|both
-
Waits for a keypress before start|exit|both.
- --benchmark-resolution-multiple
-
Multiple of clock resolution to run benchmarks.
23.4.2. Program Information
- -?, -h, --help
-
Print a help message for odgi test.
23.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
23.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
23.7. AUTHORS
odgi test was written by Erik Garrison and Simon Heumos.
24. odgi version(1)
24.1. NAME
odgi_version - display the version of odgi
24.2. SYNOPSIS
odgi version [OPTION]…
24.3. DESCRIPTION
The odgi version(1) command prints the current git version with tags and codename to stdout (like v-44-g89d022b "back to old ABI"). Optionally, only the release, version or codename can be printed.
24.4. OPTIONS
24.4.1. Version Options
- -v, --version=
-
Print only the version (like v-44-g89d022b).
- -c, --codename
-
Print only the codename (like back to old ABI).
- -r, --release
-
Print only the release (like v).
24.4.2. Program Information
- -h, --help
-
Print a help message for odgi version.
24.5. EXIT STATUS
- 0
-
Success.
- 1
-
Failure (syntax or usage error; parameter error; file processing failure; unexpected error).
24.6. BUGS
Refer to the odgi issue tracker at https://github.com/vgteam/odgi/issues.
24.7. AUTHORS
odgi version was written by Simon Heumos.


FLIPPER A film review by Michael John Legeros Copyright 1996 Michael John Legeros
(Universal) Directed by Alan Shapiro Written by Alan Shaprio, based on the television series Cast Elijah Wood, Paul Hogan, Chelsea Field, and Jessica Wesson MPAA Rating "PG" Running Time 97 minutes
==
We lasted thirty minutes in this one. FLIPPER is what I call a "cinematic black hole," a film so utterly flat-- so completely non- compelling-- that almost nothing escapes from the screen for the audience to connect with. As a teenager spending the summer with his Florida fisherman uncle, Elijah Wood (THE WAR) is a comatose kid walking. He speaks without a hint of inflection in his voice and barely animates the muscles in his face. What, was he afraid to outperform the fish? Or did he learn a little too much from his WAR co-star Kevin Costner? Paul Hogan isn't much better. The Aussie actor displays about, oh, one-tenth of the screen charisma that he brought to the role of "Crocodile" Dundee. The minimalist plot has something to do with a dolphin, a hurricane, and a Red Hot Chili Peppers concert. Oh yeah, and we heard the word "dioxin" mentioned. For those kids who have never seen underwater footage nor visited an aquarium nor vacationed at Sea World, FLIPPER might be worth a watch. As for the rest of the western world... well, I can't think of a single reason to sit through this movie.
Grade: W/O (walked out)
--
Mike Legeros - Raleigh, NC
<EMAIL_ADDRESS>(h) -<EMAIL_ADDRESS>(w)
Visit me in MOVIE HELL
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


Recommended usage of qform and sform
THIS PAGE IS CURRENTLY UNDER CONSTRUCTION
Purpose of the qform and sform
The qform and sform stored in a nifti file are intended to fulfil the following functions:
- specify the handedness of the coordinate system (important for getting left and right correct)
- specify the original scanner coordinates (qform only; figure)
- specify standard space coordinates (sform only)
- specify a relationship with another image's coordinates (sform only)
The qform and sform should never specify coordinates with different handedness (i.e. have determinants of different signs). Otherwise it is not possible to tell left from right.
The qform_code should be set to either NIFTI_XFORM_UNKNOWN or NIFTI_XFORM_SCANNER_ANAT.
The sform code should be set to either NIFTI_XFORM_UNKNOWN, NIFTI_XFORM_ALIGNED_ANAT, NIFTI_XFORM_TALAIRACH or NIFTI_XFORM_MNI_152.
Using the qform and sform in applications
In applications that involve spatial transformations, it is not always clear how to use, copy of modify these fields. The following is a brief set of guidelines. A more detailed description also exists.
- Estimating a transformation (i.e. registration of two images without resampling):
- the qform and/or sform of the two images may be used for initialising the alignment
- the sform would normally be set to a transformed version of the target image's sform
(e.g. estimating the transformation between an image and the MNI152 standard space template: afterwards the image would have its sform_code set to NIFTI_XFORM_MNI152 and the sform set to map the voxel coordinates from the image into the MNI152 standard coordinates)
- Resampling an image (i.e. applying a spatial transformation):
- the resampled image should inherit a transformed version of the sform matrix (if it set originally) and the sform_code should remain the same
- the qform of the resampled image need not be set (although a transformed version could be used)
- if the resampling is non-linear (not affine) then both sform and qform should be set to NIFTI_XFORM_UNKNOWN
- Combined estimation and resampling (i.e. registration of two images with resampling):
- the qform and/or sform of the two images may be used for initialising the alignment
- the sform is set to a transformed version of the target image's sform
- if the target image's sform is unknown, then apply the transformation to the original image's sform instead (by postmultiplication with the voxel-voxel transformation - see details on transformations)
- Applying a spatial transformation to a single image (i.e. not a registration of two images):
- the qform and/or sform is postmultiplied by the transformation matrix relating the initial and final voxel coordinates (see details on transformations)
- if the initial and final voxel coordinates do not have a known relationship then the qform and sform can be left unaltered (this might be an option available to the user)
Transforming the qform and sform
Consider applying a transformation which can be expressed as an affine
mapping between voxel coordinates as:
V' = A * V
where V' and V are column vectors representing voxel coordinates
in the new and old image respectively, and A is an affine matrix.
The qform and sform matrices for the new image are given by:
- sform' = sform * B
- qform' = qform * B
The above can only be used
- for the qform when the transformation is rigid-body
- for the sform when the transformation is affine
For example:
- applying an affine transformation can modify sform but should set the qform to UNKNOWN.
- applying a non-linear transformation should set both qform and sform to UNKNOWN, unless a registration was performed in which case the sform should take the value of the target image's sform (as in a non-linear registration to a standard image)
If a single transformation is applied which would result in both qform and sform being set to unknown, the handedness of the coordinate system is lost. To avoid this, it is preferrable, when possible, to set the sform with a matrix that encodes the correct handedness (even if the coordinates themselves are not useful) and set the sform_code to NIFTI_XFORM_ALIGNED_ANAT.
For more information and examples, see the more detailed description.
Author: Mark Jenkinson


WebRTC RTCRtpScriptTransforms (
draft Spec
) Trial.
Please try with Safari 16, Firefox 117(beta) or later.
use Audio
Start Video
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Connect
Disconnect
Sender
Receiver
XOR Sender data
XOR Receiver data


Boston considering "outside of the box" approach to help create affordable housing
by John MonahanBOSTON - As a building boom in Boston changes the city skyline, a unique take on housing that makes city living possible for everyone may be in the works.
Boston Mayor Marty Walsh tells Boston 25 News, with federal building funds drying up, that the city is looking "outside of the box" to pay for renovation projects.
Related Headlines
"Every major city in America is dealing with this. They're old housing stock and they need to be refurbished and rebuilt," Mayor Walsh said.
One idea is mixing housing of different economic levels through a public/private partnership. Through this concept, private developers work with the city to build the mixed housing.
The city gets desperately needed affordable housing, while the developer sells high-end units for profit. The high-end units help pay for the entire project.
The model is currently being used to breathe new life into two of Boston's oldest public housing developments: The Bunker Hill housing development in Charlestown and the Maryellen McCormack development in South Boston. Both were built more than 75 years ago and need significant updating.
"This is a way for the city to bring these units up to code…and then also with the newer units coming in those will help to pay for all the construction," said Boston City Councilor Frank Baker.
The new developments would triple the amount of current units, to include a mix of low, middle and high-priced housing.
Current residents who spoke to Boston 25 News say the like the idea of updated apartments and an economic mix of residents.
"It is needed. For me, we have problems with the building itself and we keep waiting to see if they'll adjust it or fix the problems," one Bunker Hill resident said.
But there are some concerns about how current residents will be displaced during construction, and how they will be reintegrated into the project.
"I don't want to leave. I've been here most of my life. My son is 42-years-old and he was 5 when I moved in here so…. It's home," said South Boston resident Anna Williams.
Councilor Baker says residents will have a say on where they move during construction. The projects will each take 10 years or more to complete.
"I think it's a good thing and I think it's also a wave of the future," Baker said.


BBNaija superstar Tacha arrives in Ghana, gets a hero’s welcome
by Nana YawBig Brother Naija 2019 housemate, Anita Natacha Akide aka Tacha has touched down in Ghana for a holiday visit.
Tacha in a post on Twitter at about an hour ago shared her joy upon heading to Ghana and that she’s looking forward to having a good time.
‘I’M SO EXCITED!🇬🇭 TOUCH DOWN MOTHERLAND TODAY!☺ MEET AND GREET TOMORROW 8PM KiKiBees EAST LEGON! •Can’t wait Y’ALL!! #AkwaabaTacha,” she posted on Twitter.
Well, the Nigeria star arrived in Ghana moments ago and was well-received at the Kotoka International Airport.
See photos and video below:


Messi Sends Gifts To 15yo African-Born Wonderkid
by SL InternationalAn African wonderkid, who has been smashing records for Borussia Dortmund's youth sides recently, received a surprise in the post for his birthday from none other than FC Barcelona superstar Lionel Messi.
Read: Europe's Top 10 Dribblers Revealed
Dortmund's 15-year-old wonderkid Youssoufa Moukoko celebrated his birthday in style on Wednesday after receiving a gift from Messi, a player he has previously named as his idol.
The Cameroon-born German youth international posted an image on his official Instagram account showing off the boxed gift he had received from Messi this week.
Moukoko is widely regarded as one of football's hottest young talents, and recently became the youngest player ever to score in the UEFA Youth League.
Earn Airtime & Data With Soccer Laduma's Social Media App - Download Now
Earlier this month, Soccer Laduma spoke to BVB assistant manager Jorg Heinrich, who reserved praise for the club's burgeoning talent.
"There are very few players who can play the way he (Moukoko) does and skip through the youth teams," the 49-year-old shared.
"I'm convinced that if he continues to develop as he has done since joining Dortmund, then he'll play for the first team one day.
"As a player, you need physical attributes to compete with your teammates, so if you skip the youth teams you need to develop your physical attributes to be on par with your older teammates.
"Here are some young players who play for the first team and he'll be motivated because he can see it's possible to get the chance to play for Dortmund."
Read: 'Lewandowski Playing On Messi & Ronaldo's Level'
Moukoko is said to have scored more than 40 goals for Dortmund's U17 side last season, and has broken countless records for the club at age-group level.


Projeto TR2 - Proxy Server
Public Attributes
|
List of all members
headerList Struct Reference
Public Attributes
char *
headerFieldName
char *
value
struct
headerList
*
next
Member Data Documentation
◆
headerFieldName
char* headerList::headerFieldName
String para armazenar o "campo"
◆
value
char* headerList::value
String para armazenar o valor do "campo"
The documentation for this struct was generated from the following file:
C:/Users/User/Documents/GitHub/ProxyServer/ProxyFabre/include/
estruturas.h
Generated by
1.8.13


Before Change
self.skipTest("Requires a POSIX shell for the stub script.")
self._stub_tensorboard(
name="fail-with-77",
program=textwrap.dedent(
r
//!/bin/sh
printf >&2 "fatal: something bad happened\n"
printf "also some stdout\n"
exit 77
.lstrip(),
),
)
start_result = manager.start(["--logdir=./logs", "--port=0"])
self.assertIsInstance(start_result, manager.StartFailed)
After Change
self.skipTest("Requires a POSIX shell for the stub script.")
self._stub_tensorboard(
name="fail-with-77",
program=textwrap.dedent(
r
//!/bin/sh
printf >&2 "fatal: something bad happened\n"
printf "also some stdout\n"
exit 77
).lstrip(),
)
start_result = manager.start(["--logdir=./logs", "--port=0"])
self.assertIsInstance(start_result, manager.StartFailed)


The following is a speech I gave in the presence of attendees of the “Melayu 2.0” meetup, an interest group supported by Mendaki that sought to engage the community to write a better future for Singapore Malays.
Dear friends.
In the past 10 years of Malay history, our community has seen through many challenges that has made our progress difficult and minute. When we ask ourselves, what has the Malay people achieved, there is little that we can be proud of. When Natasha Nabila, a PSLE candidate from a working class family broke records, our community celebrated as if we, individually, had something to do with her success. A Malay adage would aptly describe, “Bak ayam telur sebiji, riuh sekampung”. That would probably show how desperate the Malay community needs a success story.
The community’s reputation in all kinds of problems, is too colourful, that it probably needs no introduction or elaboration. When it comes to misbehaving, the finger is conveniently pointed at us. In so many National Day rallies, our leaders often give special attention to address our “Malay problems”.
Today, there are some Malays that do not wish to associate themselves as Malays. They are successful, educated, and proud. Yes, they have broken away from the vicious cycle of the “Malay problem” that it would probably be apt to no longer call themselves Malay. Afterall, what is a Malay without problems?
Former Malaysian Prime Minister, Tun Dr Mahathir, wrote a book in 1969, titled “The Malay Dilemma”. In it, he posits that:
The dilemma was whether the Malays should accept this governmental aid, and to Dr Mahathir, they should.
If one were to compare his basic positions to the realities of Singapore, and superimpose them over to Singapore’s conditions, much similarities can be noticed on the fundamental and economic condition of the Malays here. We are the indigenous people of Singapore. Malay is the sole national language of Singapore. Our own nature has allowed us to be controlled by others. And it is no surprise who controls the economy.
So this, on top of our other problems like drugs, pre-adult marriage, delinquency, broken families, poverty and poor educational performance constitutes a dilemma. To any Malay, just staring at these issues is depressing. How then would we have not venerated a 12 year old girl for achieving the highest PSLE score ever? We desperately needed a hero. We needed a success story, and how sad is that?
What we Malays forget is the potential of our own success. That whether or not we are educated, broke records, or played a musical instrument, we have always had the potential to succeed. It is not the barriers that have been placed before us that prevents us from this success. It is only our lack of desire that stops us.
If a job requires Mandarin, then one should seek to learn it. Not complain about the inequality that persists. Personally, I agree that some of these Mandro-phile job requirements are just like a cow’s manure. But if we just sit there complaining, we’ll still be jobless tomorrow, and we will not get out of our poverty. Prophet Muhammad said, “Find knowledge even if it means going to China”. We should count ourselves lucky that China has decided to come to us.
If we are poor in Math, then we should seek to get better at it. I myself was a top class failure in Math. I kept scoring F9s consistently in secondary school. Until one day, I was inspired by the many Muslim mathematicians and scientists that created the modern number system and many complex Mathematical theories. I took 2 months away from my secondary 3 holidays, to do 1 ten year series each day. Eventually, I scored distinctions in my secondary 4 year and I passed my O levels with nothing less than B3 for all subjects. Success was attained with much sacrifice, and this is what we Malays lack sometimes.
Fandi Ahmad didn’t become a great footballer because he was born one. If you read his biography, he stayed back 1 hour each practice session to shoot at goal. He sacrificed 1 hour every day, when he could be enjoying himself, so that he could become the best, and indeed he still is.
Desire. Hunger. Sacrifice. Action. These are the keywords that will be provide impetus to Melayu 2.0, Forget the misgivings of the past. We shall not harp on it. Pondering on the Malay Dilemma will serve us no good. What we need is to create more success stories and the only way to do that is to believe in ourselves.
If I may borrow the words of President Barack Obama, “We, are the change we’ve been waiting for”. And that’s the difference of the Singapore Malay. We, wait for no one, and no government to help us. Self-help is a pillar in the Singapore Malay community, and we must help ourselves, not because there is no affirmative action, but because this betterment is what we seek for ourselves.
This cannot be done by me alone, nor can it be done by the good friends I have in the core team. This can only be done as a community, as one people, and that is why you matter. We want change. And your contribution towards this movement is critical. I’m sure like me, you’ve had enough. So I ask you to stand up and be counted. Because we are the change we’ve been looking for.
©2019 Hazrul Azhar - Split Template by One Page Love


Some quick example text to build on the card title and make up the bulk of the card's content.
(Please let us know any additional customization you want & we will let you about the price impact)
Cake Size: 6” Inch diameter (14 finger slices)
Toppers & Toys: Gold Candle ($2.50) $2.50
$57.30
Quantity : 1


{{ 'APP.ORGANIZATION' | translate }}
We at TOGA believe that fashion, first and foremost, should be something useful and functional. Second, purposeful fashion should not require a supreme effort in deciding what to wear. Clothing should follow the design path of any object we consider to be functional and that supports our way of living. We at TOGA strive to give impulse to a new fashion era, one that addresses the functionality of the notion, but that is at the service of the customer. We see clothing always as functional, modular, the only straight way to improve the overall quality of life.
For all the people who think, dream, create: stop wasting time with choosing a garderobe. Our TOGA garment pieces serve a purpose of extreme functionality. The customers feel that our uniforms make them more important while wearing them. But it also saves them so much time, time that can be reinvested with family, friends, hobbies.  And lastly, choose TOGA to keep your true self throughout the day, by only wearing purposeful clothing.
TOGA Imperial UG haftungsbeschränkt (TOGA for short), is a company in the fashion clothing industry, dedicated to corporate uniforms niche. We analyse the corporate environment and choose the appropriate design. We develop high quality 3D designs to fit any corporate identity. We produce TOGA uniform pieces like: jackets, coats, dresses, shirts, blouses, pants, skirts (also in collaboration with 3rd party suppliers).
Uniform Design consultation;
Corporate Environment & Individual Lifestyle analysis;
3D fashion designs ready for production;
Prototype development of fashion garments.
Wear a personalized Uniform.
Try useful clothing for a change.
Enjoy fashion with a defined purpose.
Live a functional & minimalistic life.


| DOSE: |
166 mg |
insufflated |
DPT |
(powder / crystals) |
It was a warm summer day. I had recently walked home from my research job to find my roomate in the living room. 'A package came today,' he said with a certain gleam in his eye. The package was of dipropyltryptamine, the HCl salt to be exact, and we were both quite anxious to let the stuff enter our bodies.
My roomate called in sick for work, and I proceeded to cut the powder into finer grains for insufflation. After we finished our ingestion we just sat upstairs in a living-room type area. Almost immediately, my roomate, who had just recently eaten, was quite struck by nausea. I hadn't eaten yet that day and felt no nausea whatsoever. I began to feel the effects approximately 30 minutes later. It consisted of an amphetamine like rush, something I had not anticipated. I imagined that this substance would be similar in experience to DMT, but I would have to say that little similarity exists for those who have experienced DMT.
By this time I could no longer stay contained within the house, so I wandered outside. I was not tripping in any sense, just incredibly uplifted and wired. I circled my house several times, finally convincing myself to stop after around the seventh lap to keep from receiving unneeded attention from the neighborhood. So I sat down on the porch. Within a minute I began circling again. I felt like I was spiinning deeper and deeper into the experience, although I never lost coherency. Things began to sparkle with a psylocybian quality and became 'wavey'. My teeth began to chatter, though I wasn't cold. I decided it was time to enter the house again.
It was after I entered the house that some disturbing physiological side effects manifested themselves. The teeth chattering gave way to full body shudders. I couldn't quite say that they were as violent as convulsions but they were definitely unwelcome and uncontrollable. I began to moan, and due to my violent shaking it came out as 'Ah-yah-yah-yah-yah!' My roomate, who was experiencing none of these tremors, then turned to look at me and dub me 'a human vibrator'. It was soon after these tremors began that I began to trip balls.
The trip seemed to have no subjective baggage associated with it. It didn't have the 'Wow!' of LSD or the religiousness of shrooms. I remained entirely coherent, but lost total control of my body, speech was difficult. I remained shaking on the bed, my hands contracted into useless claws while I watched some of the most extreme visuals of my life. This probably lasted for a half hour, after which I could then get up. I was still mildly tripping, like a low dose of LSD, and had severely hindered motor control. We decided to go for a walk.
The effects seemed to have tapered off to this low-level trip and then continue on this plateau. Visuals were faint and would unexpectedly come and go. One of the most disturbing aspects of this experience, besides the tremors, was that my hands became numbed, particularly my dominant hand, and remained so for a few hours. This happened to my roomate as well, although he did not have the tremors I experienced. The effects seemed to trail on for hours, the after-effects about the same magnitude of the trip itself. A dull throbbing headache appeared before I went to bed, which was around six hours after injestion. I slept soundly and awoke with much energy, but I believed that my nerves, especially in my hands, were still agitated by the experience.
The experience was very fun and intense, but due to the intensity and nature of the physiological side effects, I will most likely never do this drug again.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


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| DOSE: |
9.4 g |
oral |
Morning Glory |
(cookie / food) |
| |
2.0 g |
oral |
Vitamin C |
(pill / tablet) |
I have had some previous experience with Morning Glory seeds (2 or 3 decent trips), but never Heavenly Blues. My friend recently acquired some Heavenly Blues, so one day I decided to try them out with him.
An hour or so before ingesting the seeds, my friend and I each took 2 1000mg vitamin C tablets, which supposedly makes for a more intense trip, while decreasing paranoia. We then made some milkshakes, milk, vanilla ice cream and bananas. Then we ground up the seeds with a food processor (app. 250 each) and blended them into the shakes. We devoured the milshakes around noon. At the time, this was a delicious alternative to Morning Glory tea (anyone who has tried this knows how horrid it tastes). However, in retrospect, the thought of the milkshake makes me nauseous.
About 20 minutes after ingestion, the nausea set in. We began to eat Tums, which we had on hand from previously gained knowledge. We plowed through the Tums, and then went our seperate ways. I lay down in my bed and tried to combat the sickness that way for a while, while my friend wandered off. I saw him infrequently throughout the rest of the day, so at this point I may as well leave him out of the account.
Maybe about an hour into the trip the nausea began to get worse. I knew I should keep it in my system as long as possible, so I forced myself not to throw up. At this point I began to come up, and was enjoying minor body rushes and a feeling very similar to a Cannabis high.
The nausea continued to plague my thoughts though, and easily overpowered any euphoria I may have had at this time. After about an hour and half of terrible terrible nausea I decided to go for a walk. I saw some very cool visuals within the trees, which I always do when tripping. I was also listening to music the whole time, and was experiencing some minor audio benefits. The music seemed to be speaking to me, and I felt like I was having a conversation with the singers. Very cool.
After an hour or so of this I returned to my room. It was soon getting dark and cold outside, and I decided to stay around indoors for a while. At this point I really began to trip hard.
I became unfunctional, and paranoid. I thought that everything I was doing was wrong, and that if someone walked in on me they would have been disgusted. I was only listening to music and lying down. My other friend who knew I was tripping made me some chunky's soup, which I was very grateful for. He told me later that I was basically unable to function. I couldn't open doors without help, I thought everything that was said to me was a personal attack, and I grew afraid of handshakes and high-fives. I have no real recollection of this time, but everyone who saw me throughout this time said I was fairly out of sorts.
In my fairly paranoid sense, my friends decided it would be best to leave me alone, I guess. I sat alone in my room, curled into a ball in the corner of my bed. I was istening to Crosby Stills Nash and Young, live version. I felt at this time that I became the song, and taking my pulse, I realized that it matched flawlessly with the beat. I felt every note going through my body, out to my limbs, and into my fingers and toes. It was incredible. At one point I realized I had been holding my breath, so I let it out in a long content exhalation. As my breath ended, I realized in the back of my mind that CSNY hit their last note and let it out. My breath and their note ended at the same instant.
I had heard before thet morning glories were a very audial drug, but had never experienced it before this. It was simply incredible.
While I may have had an amazing trip by the end, I won't be doing Heavenly Blues again, probably ever. Though I was somehow able to not vomit, the nausea was the worst I have ever had from a drug, and lasted over 2 and a half hours. I won't say I recommend anything I did, but if you're looking for such an audial experience, this may be it. At least, its the only such experience I've had.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


@vndmtrx 整理
Awesome Node.js
A curated list of astonishing Node.js frameworks, libraries and resources. Inspired by awesome-php and awesome-python.
Your pull requests are very welcome! Let's make this the awesomest resource for Node!
Environment Management
Libraries for Node version and environment management.
- nodeenv - Virtual environment for Node.js & integrator with virtualenv.
- nave - Virtual Environments for Node.
- n - Node version management.
- nvm - Node Version Manager (does not require prior installation of node).
Integrated Development Environments
IDEs and Editors for development
- Enide - Node Eclipse IDE with Nodeclipse plugin.
- InteliJIDEA - Fast Node plugin for InteliJ.
- Webstorm - "Create great websites and applications in a great IDE. The best JavaScript IDE and HTML editor is at your service."
- Visual Studio - With Node.js Tools for Visual Studio (Supports editing, IntelliSense, profiling, npm, TypeScript, debugging locally and remotely on Windows/MacOS/Linux)
- Atom - The hackable editor by GitHub
- Brackets - An open source code editor for the web, written in JavaScript, HTML and CSS.
- Cloud9 - Web editor with collaboration tools.
- Notepad++ - Notepad++ is a free source code editor and Notepad replacement that supports several languages.
- CmdEr - Not really and IDE, but a great "lovely console emulator package for Windows"
- Cloud Commander - Web file manager. Has editor and console. Allows you to develop web applications, sites etc.
Documentation
Libraries for generating project documentation.
- Docco - Docco is a quick-and-dirty documentation generator, written in Literate CoffeeScript.
- Groc - Documentation generation, in the spirit of literate programming.
- dox - JavaScript documentation generator for node using markdown and jsdoc.
Package Management
Libraries for package and dependency management.
- npm - Default package manager. Installs, publishes and manages node programs.
Libraries for building and task running
- Gulp.js - A streaming build system which use of streams and code-over-configuration.
- Grunt.js - A task runner to ease epetitive tasks like unit testing, compilation and so on.
- Nodemon - A dev utility that monitor any changes in source and automatically restart server.
- Browserify - Browserify lets you require('modules') in the browser by bundling up all of your dependencies.
Communication
- Socket.IO - Websocket framework for Node and Javascript.
- SockJS - Websocket emulation.
- Primus - An abstraction layer for real-time frameworks to prevent module lock-in.
- BinaryJS - BinaryJS is bidrectional realtime binary data with binary websockets
Database Drivers
Libraries for connecting and operating databases
Tools for debugging Node applications
- node-inspector - Node.js debugger based on Blink Developer Tools.
- longjohn - Longer stack traces for Node.
- TypesJs - Easy type checking, for Node & browsers.
- Nodev - Tool for easier debugging based on nodemon and node-inspector.
- cf-node-debug - Proxy to aid in debugging node running on a PaaS.
Logging
Tools for generating and working with log files.
- caterpillar - A logging system that can log and pipe the output off to different locations.
- tracer - A powerful and customizable logging library for node.js.
- Log.io - Real time logging facility on the browser.
- Bunyan - A simple and fast JSON logging module for node.js services.
ORM
Libraries that implement Object-Relational Mapping or datamapping techniques.
- Sequelize - Sequelize library provides easy access to MySQL, MariaDB, SQLite or PostgreSQL databases.
- Node-orm2 - Another Relational Object Mapper.
- Mongoose - Almost an ORM for mongodb.
Web Frameworks
Web development frameworks.
- Express - A minimal and flexible node.js web application framework.
- Flatiron - An adaptable framework for building modern web applications.
- Koa - A framework which aims to be a smaller, more expressive, and more robust foundation for web applications.
- Totaljs - Friendly responsive design web application framework for node.
- Meteor - A platform that has strong features such as live page update, sync and hopt code pushes.
- Hapi - A rich framework for building applications and services.
Application Servers
Application Server is an environment to run and manage multiple applications.
- Impress - Impressive multipurpose scalable Application Server optimized for high load API and web applications.
Content Management System
- Calipso - Calipso is a simple CMS, built along similar themes to Drupal and Wordpress.
- KeystoneJS - Node.js CMS and web application platform built on Express and MongoDB.
RESTful API
Libraries for developing RESTful APIs.
- Sails - MVC framework which generates a RESTful JSON API.
- Node-restify - A node.js module built specifically to build correct REST web services.
- Heimdall - REST API Guardian for Express.
Libraries for deal with forms and form data
Files and MIME Type Manipulation
- PDFKit - A JavaScript PDF generation library for Node and browser.
Authentication and OAuth
Libraries for implementing authentications schemes.
- PassportJS - Simple authentication middleware framework.
- ldapjs - Pure JavaScript, from-scratch framework for implementing LDAP clients and servers.
Template Engine
Libraries and tools for templating and lexing.
- ECT - "Fastest JavaScript template engine with embedded CoffeeScript syntax" as they say (benchmark proof).
- Jade - Handful node template engine.
- Swig - A simple, powerful, and extendable JavaScript Template Engine.
Libraries and tools which support you by building Command-Line Interfaces.
- Inquirer - A collection of common interactive command line user interfaces. Ask questions, parsing, validating answers, managing hierarchical prompts and providing error feedback.
- commander.js - The complete solution for node.js command-line interfaces, inspired by Ruby's commander.
- cli - Rapidly build command line apps with node.
- cli-table - Pretty unicode tables for the CLI with Node.JS
- blessed - A curses-like library for node.js.
- chalk - Terminal string styling done right
- minimist - Simple module for command line arguments parsing.
- read - For reading user input from stdin.
- colors.js - get colors in your node.js console like what.
- configstore - Easily load and persist config without having to think about where and how.
- blessed - A curses-like library for node.js.
- log-symbols - Colored symbols for various log levels.https://github.com/sindresorhus/log-symbols
- terminal-menu - retro ansi terminal menus for serious 80s technicolor business.
- cli-spinner - A simple spinner for node cli.
- text-table - generate borderless text table strings suitable for printing to stdout.
Async Control Flow
Libraries, that help you manage asyncronous control flow and avoid callback hell.
- Callback-based:
- Async - Utility module which provides straight-forward, powerful functions for working with asynchronous JavaScript.
- Promise-based (Promises/A+):
- Q - Full-featured promise library with large API covering any situation you may encounter.
- RSVP.js - Lightweight, but still compliant, promise library.
- when.js - Rock solid, battle tested promise library.
- Bluebird - Bluebird is a fully featured promise library with focus on innovative features and performance.
- Fibers-base (node-fibers):
- asyncawait - Inspired by C# async/await feature, implementation of the same patter using fibers.
- Generator-based:
- Co - Generator based flow-control goodness for nodejs and the browser.
Testing
Testing frameworks.
- mocha - Mocha is a feature-rich JavaScript test framework running on node.js and the browser, making asynchronous testing simple and fun.
- tape - tap-producing test harness for node and browsers.
- should.js - BDD style assertions for node.js -- test framework agnostic.
- chai - BDD / TDD assertion framework for node.js and the browser that can be paired with any testing framework.
- sinon - Standalone test spies, stubs and mocks for JavaScript.
- Jasmine - Simple Behavioral tests for Node and Javascript.
- Expresso - TDD framework for Node.
- NodeUnit - Simple syntax unit test tool.
- Concrete - Continuous integration server.
- ready.js - Continuous javascript integration tool.
- Jezebel - A REPL and continuous test runner for Node.js Jasmine tests.
Miscellaneous
Miscellaneous Tools which doesn't fit to the other categories.
- Github Linker - Chrome extension that linkifies dependencies in package.json on GitHub.
Other Awesome Lists
Other amazingly awesome lists can be found in the awesome-awesome and awesome-awesomeness projects.


Fruit Images Search Engine
UPLOAD AN IMAGE
File Selected :
Query Image :
{% if query_path %}
{% endif %}
Searching Results :
{% for score in scores %}
{{ score[0] }}
{% endfor %}


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Portrait by Paul Delaroche
Here's the brief timeline of Peter's life:
You can find more information about one of the greatest rulers of Russia on his Wikipedia entry


T
- the generic typepublic interface ISentencePairProcessor<T extends HltContent>
| Modifier and Type | Method and Description |
|---|---|
T |
process(Sentence sentence1,
Sentence sentence2)
This definition of the process method takes two Sentence objects as input
and returns a list of HltContent objects which includes the results from
text processing..
|
long |
processAsync(Sentence sentence1,
Sentence sentence2)
This is asynchronous definition of the Process method.
|
Boolean |
tryGetResult(long requestId,
T hltContents)
This method is invoked multiple times as a polling mechanism to get the
output from the asynchronous process method for a requestId.
|
T process(Sentence sentence1, Sentence sentence2) throws AdeptModuleException
sentence1
- the sentence1sentence2
- the sentence2AdeptModuleException
- the adept module exceptionlong processAsync(Sentence sentence1, Sentence sentence2) throws AdeptModuleException
sentence1
- the sentence1sentence2
- the sentence2AdeptModuleException
- the adept module exceptionBoolean tryGetResult(long requestId, T hltContents) throws AdeptModuleException
requestId
- the request idhltContents
- the hlt contentsAdeptModuleException
- the adept module exceptionCopyright © 2015 Raytheon BBN Technologies. All rights reserved.


{car.vin}
@todo Was too lazy, move label to locallang.xml file
No images are defined for this car.
More information


Exceptions
CMIS 1.0 CMIS 1.1 Spec <IP_ADDRESS>
Exceptions are divided into three groups: general exceptions, specific exceptions, and implementation exceptions.
General exceptions and specific exceptions are defined in the CMIS specification.
Implementation exceptions are exceptions introduced by OpenCMIS and PortCMIS. Those exceptions handle connection and authentication problems.
General Exceptions
General exceptions may be returned by a repository in response to any CMIS service method call.
invalidArgument
One or more of the input parameters is missing or invalid.
notSupported
The CMIS operation is not supported by the repository.
objectNotFound
The object, or object type, or repository does not exist or the current user has no permission to see it.
permissionDenied
The user does not have sufficient permissions to perform the operation.
runtime
Any other cause not expressible by another CMIS exception.
Specific Exceptions
The following exceptions may be returned by a repository in response to one or more CMIS service methods calls.
constraint
The operation violates a repository- or object-level constraint defined in the CMIS domain model.
contentAlreadyExists
The operation attempts to set the content stream for a document that already has a content stream without explicitly specifying the “overwriteFlag” parameter.
filterNotValid
The property filter or rendition filter input to the operation is not valid.
nameConstraintViolation
The repository is not able to store the object that the user is creating/updating due to a name constraint violation. There could already be an object with the same name or the name contains a character that is not allowed.
storage
The repository is not able to store the object that the user is creating/updating due to an internal storage problem.
streamNotSupported
The operation is attempting to get or set a content stream for a document whose object type specifies that a content stream is not allowed for documents of that type.
updateConflict
The operation is attempting to update an object that is no longer current (as determined by the repository).
versioning
The operation is attempting to perform an action on a non-current version of a document that cannot be performed on a non-current version.
Implementation Exceptions
base
The OpenCMIS and PortCMIS exceptions are all derived from the CMIS base exception. If you want handle all CMIS exceptions at once, catch the CmisBaseException
.
connection
The client could not connect to the repository for some reason. Check if you need to configure a proxy server.
unauthorized
User authentication failed.
proxyAuthentication
Proxy authentication failed.
serviceUnavailable
The server reported that the CMIS service is currently not available.


Nodes Table
ID
Name
Node Type
Node Subtype
Node Cross Reference
Edges Table
ID
Name
Source
Interaction
Target
Source Receptor
Target Receptor
Immune Processes
Janeway References
Tools
New Network From Selected
Toggle Outgoing Edges
Toggle Incoming Edges
This app was made using
Cytoscape.js
.
Data reference
Node Types
Cell
Somatic
Lymphocyte
Myeloid
Precursor
APC
Blood
Cytokine
Chemokine
Colony-stimulating factors
Interferons
Interleukins
Tumor Necrosis Factors
Growth Factors
Antibody
Effector Molecule
Complement
Lipid Mediators
Toxic Mediators
Reactive Oxygen Species
Antimicrobial Peptides
Acute Phase Proteins
Cytotoxic Effectors
Metabolite
Enzymes
Vitamins
Antigen
Bacteria
Fungi
Virus
Self
Edge Types
Activate
Differentiate
Inhibit
Kill
Polarize
Recruit
Secrete
Survive