This is an example of the Block Webview widget for using Merman to embed snippets of code in a website.
Merman is an AST viewing/editing solution. It uses a syntax definition to provide a traditional source-like representation of an AST, but maintaining all of the structure under-the-hood. This is a shift from most editors which operate on linear text, and where the syntax is built into the compiler which uses it to translate the text into an AST internally.
One of the benefits of shifting the responsibility of syntax definition to the client is that users can modify the syntax to their liking and stay source-compatible with all other users. This example shows this feature off by casting a single ESTree (Javascript) snippet in Javascript clothes (looks nearly the same), Python clothes, and a couple others.
Some final notes before the demo:
I used Acorn to translate a small Javascript program into a JSON ESTree AST. The program I used as input is:
for (let i = 1; i <= 100; ++i) {
let out = ""
if (i % 3 === 0) {
out += "Fizz"
}
if (i % 5 === 0) {
out += "Buzz"
}
if (out.length === 0) {
out += i
}
console.log(out + " ")
}
(this is plain text)
The ESTree AST output is listed at the end of this page because it's huge.
The AST gets fed directly into the Webview widget along with the syntax. Here I used the Javascript-like syntax. As you can see it produced a representation similar to the input source above. Highlighting is defined in the syntax and is based on the AST structure (no regexes).
This is mostly a demonstration of an indentation-based syntax, rather than an attempt to make it look exactly like Python.
Python doesn't have any c-style for loop. I could have introduced a sugar to make "c-style for loops with integer bounds, 1-unit increment, less than condition" look like "enumerate(x)" but I thought that would be a bit awkward...
Prodel is a Japanese literate programming language. This is unfortunately a poor immitation of Prodel's syntax. The for loop keywords don't make a ton of sense, also the mixture of full-width characters and space-less ascii identifiers is pretty ugly so I added some unnecessary spaces. I wanted to try vertical text but hit a number of browser/w3c spec issues - no way to get vertical text metrics, 「」 and ー don't get rotated 90 degrees, etc. so I gave up on that.
Finally, this is the AST used as input to the Webview code widgets. It's the full AST translation of the original source, and you'll get chunks of this in your clipboard if you try to copy parts of the above snippets.


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CORKY ROMANO (2001). 1/4 star out of 4. Starring Chris Kattan, Vinessa Shaw, Peter Falk, Peter Berg, Chris Penn, Fred Ward, Richard Roundtree, Matthrew Glave, Roger Fan and David Sheridan. Written by David Garrett & Jason Ward. Directed by Rob Pritts. Rated PG-13. Approx. 88 minutes.
It's too bad. I was all set to blame Lorne Michaels for another comedic disaster starring a Saturday Night Live cast member when I noticed Michaels name does not appear anywhere in the credits.
OK, Lorne, you're off the hook for this one.
But someone needs to take the blame for foisting Corky Romano on an unsuspecting public.
Corky Romano stars Chris Kattan, one of the less-than-funny SNL cast members, in a movie that hardly qualifies as a comedy. Heck, it hardly qualifies as a motion picture.
Corky Romano is an embarrassment, a sloppy, sophomoric feature.
 He is an assistant veterinarian as well as the outcast, youngest son of a reputed crime lord, "Pops" Romano (Peter Falk).
Corky is drafted by the family to infiltrate the FBI and retrieve whatever evidence the bureau has on his dad.
Of course it is all implausible nonsense, made moreso by the incompetence of Kattan's Corky, who acts as if he can't even tie his shoelaces.
But, only in the movies, through a crooked computer hacker Corky is renamed Corky Pissant and is a full-fledged FBI operative, skilled in five languages, an Olympic marksman and just a superman among crimefighters.
It numbs the mind to think that screenwriters David Garrett and Jason Ward have such contempt for their audience that they believe any intelligent FBI official would believe a klutzy, nerd such as Corky is a special agent. It's insulting and contemptible.
The screenwriters' plot is predictable; everything can be foretold a reel or three before it happens. They don't create any characters, just throw us familiar types. Illogical and implausible situations abound throughout.
Corky Romano is not funny and lacks any comedic pacing.
Plus Kattan can't carry the movie. He is funny in small spurts, but he does not have the presence or weight to bolster a feature-length venture.
It is sad to see a great actor such as Falk reduced to playing such a stereotypical character, nor is there anything funny about illiteracy nor homosexuality, two areas the writers unsuccessfully try to mine for humor, but come up with only pyrite.
The only good that may come from this entire folly is to give Lorne Michaels second thoughts about mounting any features based on some of Kattan's SNL characters.
Corky Romano is for the dogs, it stinks. It's about as funny as road kill. So, I'd advise you to swerve around it.
Bob Bloom is the film critic at the Journal and Courier in Lafayette, IN. He can be reached by e-mail at<EMAIL_ADDRESS>or at<EMAIL_ADDRESS>Other reviews by Bloom can be found at www.jconline.com by clicking on golafayette. Bloom's reviews also can be found on the Web at the Internet Movie Database: http://www.imdb.com/M/reviews_by?Bob+Bloom
========== X-RAMR-ID: 29815 X-Language: en X-RT-ReviewID: 254476 X-RT-TitleID: 1110376 X-RT-SourceID: 872 X-RT-AuthorID: 1363 X-RT-RatingText: .25/4
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


Acknowledgments
It's a pleasure to acknowledge my debt to the many people involved, directly or indirectly, in the production of this book. In particular, I'd like to mention my reviewers Stephane Faroult, Jonathan Gennick, Lex de Haan, Anthony Molinaro, Peter Robson, and Michael Wener for their helpful comments on earlier drafts of the manuscript. I'd also like to thank Nagraj Alur and Hugh Darwen for various technical discussions. Next, I'd like to thank my wife Lindy (as always) for her support throughout this and all of my other database projects over the years. Finally, I'm grateful to everyone at O'Reilly—especially Jonathan Gennick and Genevieve d'Entremont—for their encouragement, contributions, and support throughout the production of this book.
—C. J. Date, Healdsburg, California, 2005
|


Historically the United States has led the world in refugee admissions, resettling an estimated third-to-half of the world’s refugees since World War II. However, the Trump administration has changed that. For the first time since the adoption of the 1980 Refugee Act the United States has resettled fewer refugees than the rest of the world. Given President Trump’s discriminatory rhetoric towards members of the Islamic faith, this decrease in refugees appears to particularly disadvantage refugees from Muslim-majority countries.
Admission as a refugee is the most challenging way for someone to enter the United States. To be placed in the United States a refugee must go through a 20-step vetting process, involving screenings from the United Nations and multiple U.S. federal agencies.
The process from application to resettlement takes eighteen months at a minimum, but can stretch up to three years.
Since 1980, the refugee resettlement process has largely been controlled by the presidency. Every year in October the Executive Branch sets a cap or “ceiling” on the number of refugees admitted into the United States in the next fiscal year.
Historically, this upper limit on refugees entering the United States has averaged around 96,000, but the actual number of refugees settled in the U.S. often falls short of this cap. In response to the Syrian Civil War and the growing refugee crisis across the globe, the Obama administration increased the refugee cap from 85,000 in FY 2016 to 110,000 in FY 2017.
One of the first policy decisions made by the Trump administration was to halt refugee settlement in the United States. On January 27, 2017, President Trump signed Executive Order 13769, commonly known as the Muslim Ban, which barred entry from seven Muslim-majority nations and
imposed a 120-day ban on all refugees entering the United States. While the courts intervened to dismantle portions of the ban, in October, 2017 the administration passed new vetting policies that further slowed resettlement processes and imposed a new 90-day ban on 11 countries, including nine Muslim-Majority countries.
These federal actions resulted in a dramatic slowdown in domestic refugee resettlement. Despite the 110,000 ceiling in 2017, the United States only resettled 53,716 refugees. In 2018, the Trump administration further reduced the cap to a nearly 40-year low of 45,000, and, over the course of the year, resettled less
than half of that target (22,491). In 2019, the Trump Administration announced it would further reduce the cap to 30,000 refugees and, as of May 2019, the country is well short of reaching that limit.
These reductions in United States refugee resettlement are coming at a time when the number of refugees worldwide is growing. According to the UN High Commissioner for Refugees (UNCHR), the number of refugees globally nearly doubled between 2012 and 2017, from 10.4 million to 19.9 million over the five years. As a result the United States is further exacerbating the global refugee crisis.


odgi position¶
SYNOPSIS¶
odgi position [-i, –target=FILE] [OPTION]…
DESCRIPTION¶
The odgi position(1) command translates positions and coordinate ranges
between nodes and embedded paths. It provides liftover functionality,
allowing us to translate a position between any reference paths embedded
in the -i, --target
graph. We can additionally project coordinates
and annotations from a source graph -x, --source
into the
target
. When completing this “graph lift”, the intersecting set of
paths in the two graphs are used to complete the coordinate projection.
OPTIONS¶
Graph Files IO¶
-i, –target=FILE
Describe positions in this graph.
-x, –source=FILE
Translate positions from this graph into the target graph using common
--lift-paths
shared between both graphs [default: use the same
source/target graph]Position Options¶
-r, –ref-paths=STRING
Translate the given positions into positions relative to this
reference path.
-R, –ref-paths=FILE
Use the ref-paths in FILE.
-l, –lift-path=STRING
Lift positions from
--source
to --target
via coordinates in
this path common to both graphs [default: all common paths between
--source
and --target
].-g, –graph-pos=[[node_id][,offset[,(+|-)]**]**]
A graph position, e.g. 42,10,+ or 302,0,-.
-F, –path-pos-file=FILE
A file with one path position per line.
-b, –bed-input=FILE
A BED file of ranges in paths in the graph to lift into the target
graph
-v
, --give-graph-pos
emit graph positions.-v, –give-graph-pos
Emit graph positions (node,offset,strand) rather than path positions.
-I, –all-immediate
Emit all positions immediately at the given graph/path position.
-d, –search-radius=STRING
Limit coordinate conversion breadth-first search up to DISTANCE bp
from each given position [default: 10000].
Threading¶
-t, –threads=N
Number of threads to use.
Program Information¶
-h, –help
Print a help message for odgi position.
EXIT STATUS¶
0
Success.
1
Failure (syntax or usage error; parameter error; file processing
failure; unexpected error).
BUGS¶
Refer to the odgi issue tracker at https://github.com/pangenome/odgi/issues.


(out of ****)
_A_Simple_Plan_ (R) **** _Very_Bad_Things_ (R) **** _A_Simple_Plan_ and _Very_Bad_Things_ are films of two opposing genres--drama and comedy--but both are actually so similar that their titles could very well be interchangeable. Both are about botched secret schemes that lead to downward spirals of transgression; both are bound to leave audiences unsettled--and both are among the most memorable films of the year. Although his filmmaking career has spanned twenty years, Sam Raimi has always remained on the fringes of Hollywood, scoring no big box office hits but amassing a fiercely devoted cult following and with his trademark brand of dark humor (more often than not tinged with gore) and wildly kinetic camera work. More than a few Raimi cultists weaned on the likes of his _Evil_Dead_ trilogy will undoubtedly cry "sellout" after seeing _A_Simple_Plan_, which neither looks nor feels like a traditional Raimi film. Instead, it looks and feels like a simply "traditional" film: no flashy camera work, no excessive violence, no macabre humor. Thematically, on the other hand, this adaptation of Scott B. Smith's bestselling novel is exactly what one would expect from the auteur.  Their plan, as the title states, is simple: split the money between them, but only after the plane is discovered and it is determined that the authorities are not tracing the cash. As they say, "the best laid plans of mice and men often go awry," and that's exactly what happens. As jealousy, greed, and suspicion enter the picture, a tense and ever-twisting turn of events follows, in which the most innocent characters reveal their more sinister tendencies--and vice versa. This theme of the ever-shifting tides of evil within people is a perfect fit for the dark sensibilities of Raimi, and he made a wise decision in keeping his showy visual tendencies in check. Any of Raimi's usual visual theatrics would have detracted from Smith's tightly-wound script, and his restrained approach intensifies the suspense of the story. Adding to the complexity and power of the story are the actors, whose multidimensional performances create complex characters the audience sometimes hates yet maintains a certain empathy for. Thornton is likely to receive the most attention for his heartwrenching turn as the sad sack Jacob, who may be slow-witted but is nobody's fool. Equally as impressive though certain to be overlooked in Thornton's shadow is Paxton's subtle, slow burn as the often-conflicted Hank. Bridget Fonda's role as Hank's wife Sarah seems simple at the start, but as the character gradually takes on sharper edges, so does Fonda's performance. The film's richness of character lends its conclusion a poignant and haunting impact. As badly as the characters in _A_Simple_Plan_ behave, nothing they do comes off quite as reprehensible as the deeds perpetrated by the characters inhabiting _Very_Bad_Things_, the audacious writing/directing debut of actor Peter Berg. Stuffed with scenes of stylishly shot splatter, this film is as violent as any that has been released as this or any year--and it's all played for _laughs_ (coincidentally, much like Raimi's earlier work). That shameless, eager-to-shock energy, with a crafty script and a flawless ensemble cast to match, make this beyond-black comedy a very good thing indeed. A few days before his wedding to Laura Garrity (Cameron Diaz), Kyle Fisher (Jon Favreau) heads to Las Vegas for a big bachelor blowout with his buddies: self-improvement-obsessed realtor Robert Boyd (Christian Slater), quiet auto mechanic Charles Moore (Leland Orser), straightlaced family man Adam Berkow (Daniel Stern), and Adam's boorish younger brother Michael (Jeremy Piven). Mix these five men, gallons of booze, pounds of cocaine and marijuana, and a stripper into a hotel room and something bad is bound to happen--and it does. A rather grisly "complication" during sex with Michael leaves the stripper dead, and the ever-cunning Boyd comes up with, yes, a simple plan to correct, as he calls it, the "105-pound problem"--bury her body in the desert. Predictably, this rash decision just leads to more trouble. What isn't so predictable, however, is the severity of the troubling situations Berg puts his characters in. These developments will undoubtedly offend some, but most people would be laughing too hard to be offended. An obvious comparison would be to the Farrelly Brothers' surprise sensation _There's_Something_About_Mary_, but the brands of humor are distinctly different; whereas the Farrellys dabbled in "gross-out" bodily function humor, Berg's violent variety of comedy can best be described as "shock" humor. But however different their specific sensibilities are, the Farrellys and Berg share the same go-for-broke attitude when it comes to generating laughs, going so far as to seem to dare the audience not to laugh. "Shock" gags would not mean anything if they didn't organically emerge from the story, and like _Mary_, the very bad things of the title are firmly rooted in the script. But there's more to Berg's assured writing than his ability to jolt the audience into laughter; there are also some juicy roles, and each cast member tackles their respective job with aplomb. The characters truly take shape, and the actors achieve liftoff, after the stripper incident, when everyone experiences different types of emotional fallout. The fact that Kyle's increasing anxiety can be palpably felt while not exactly seen is a tribute to Favreau's firm grasp of the character, who tries to maintain a veneer of composure throughout. Adam becomes mad with paranoia, leading to some effectively hammy hysterics by Stern. Nicely playing off of him is Piven, whose all-attitude Michael undergoes the most dramatic arc in the film. Slater's often irksome Nicholson-channelling works like a charm for Boyd. As his self-improvement philosophy becomes increasingly, shall we say, dark, Slater's devilish Jack-like grin and swagger could not be more perfect; it's his best performance since _True_Romance_. As the wedding date nears and the tension mounts, the chirpy Laura seems less like herself--or is that _more_?--and Diaz obviously has a blast. Even a relatively peripheral player like Adam's wife Lois (Jeanne Tripplehorn) takes on greater depth as things get more and more horrifying; only Orser's barely-heard Moore remains an enigma, but I believe that was the point. Berg falls a little short at the end; his ultimate resolution doesn't quite live up to the raucous build up, but it closes the film with an appropriately acidic sting. (_A_Simple_Plan_ opens December 4; _Very_Bad_Things_ opens November 25)
Michael Dequina
<EMAIL_ADDRESS>|<EMAIL_ADDRESS>Mr. Brown's Movie Site: http://welcome.to/mrbrown
CompuServe Hollywood Hotline: http://www.HollywoodHotline.com
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


Do not send real Ether!!!
This is a demo page, use only Rinkeby test network.
{{funding.contract}}
{{selectedDoctor.bio}}


Full
Longer parameter versions of System.Linq.Enumerable
methods
Functions and values
| Function or value | Description |
aggregate (...)
Signature: seed:'TAccumulate -> func:('TAccumulate -> 'TSource -> 'TAccumulate) -> resultSelector:('TAccumulate -> 'TResult) -> source:(type) -> 'TResult
Type parameters: 'TAccumulate, 'TSource, 'TResult |
Go to GitHub source |
any predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> bool
Type parameters: 'TSource |
Calls |
contains value comparer source
Signature: value:'?8194 -> comparer:(type) -> source:(type) -> bool
Type parameters: '?8194 |
Calls |
count predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> int
Type parameters: 'TSource |
Calls |
defaultIfEmpty defaultValue source
Signature: defaultValue:'?8198 -> source:(type) -> (type)
Type parameters: '?8198 |
Calls |
distinct comparer source
Signature: comparer:(type) -> source:(type) -> (type)
Type parameters: '?8200 |
Calls |
except second comparer first
Signature: second:(type) -> comparer:(type) -> first:(type) -> (type)
Type parameters: '?8202 |
Calls |
first predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
firstOrDefault predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
groupBy (...)
Signature: keySelector:('TSource -> 'TKey) -> elementSelector:('TSource -> 'TElement) -> resultSelector:('TKey -> (type) -> 'TResult) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey, 'TElement, 'TResult |
Go to GitHub source |
groupJoin (...)
Signature: outerKeySelector:('TOuter -> 'TKey) -> innerKeySelector:('TInner -> 'TKey) -> resultSelector:('TOuter -> (type) -> 'TResult) -> comparer:(type) -> outer:(type) -> inner:(type) -> (type)
Type parameters: 'TOuter, 'TKey, 'TInner, 'TResult |
Go to GitHub source |
intersect comparer first second
Signature: comparer:(type) -> first:(type) -> second:(type) -> (type)
Type parameters: '?8218 |
Calls |
join (...)
Signature: outerKeySelector:('TOuter -> 'TKey) -> innerKeySelector:('TInner -> 'TKey) -> resultSelector:('TOuter -> 'TInner -> 'TResult) -> comparer:(type) -> outer:(type) -> inner:(type) -> (type)
Type parameters: 'TOuter, 'TKey, 'TInner, 'TResult |
Go to GitHub source |
last predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
lastOrDefault predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
longCount predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> int64
Type parameters: 'TSource |
Calls |
orderBy keySelector comparer source
Signature: keySelector:('TSource -> 'TKey) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey |
Calls |
orderByDescending (...)
Signature: keySelector:('TSource -> 'TKey) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey |
Calls |
select selector source
Signature: selector:('TSource -> (type) -> 'TResult) -> source:(type) -> (type)
Type parameters: 'TSource, 'TResult |
Calls |
selectMany (...)
Signature: collectionSelector:('TSource -> (type) -> (type)) -> resultSelector:('TSource -> 'TCollection -> 'TResult) -> source:(type) -> (type)
Type parameters: 'TSource, 'TCollection, 'TResult |
Go to GitHub source |
sequenceEqual comparer first second
Signature: comparer:(type) -> first:(type) -> second:(type) -> bool
Type parameters: '?8244 |
Calls |
single predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
singleOrDefault predicate source
Signature: predicate:('TSource -> (type)) -> source:(type) -> 'TSource
Type parameters: 'TSource |
Calls |
skipWhile predicate source
Signature: predicate:('TSource -> (type) -> (type)) -> source:(type) -> (type)
Type parameters: 'TSource |
Calls |
takeWhile predicate source
Signature: predicate:('TSource -> (type) -> (type)) -> source:(type) -> (type)
Type parameters: 'TSource |
Calls |
thenBy keySelector comparer source
Signature: keySelector:('TSource -> 'TKey) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey |
Calls |
thenByDescending (...)
Signature: keySelector:('TSource -> 'TKey) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey |
Calls |
toDictionary (...)
Signature: keySelector:('TSource -> 'TKey) -> elementSelector:('TSource -> 'TElement) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey, 'TElement |
Go to GitHub source |
toLookup (...)
Signature: keySelector:('TSource -> 'TKey) -> elementSelector:('TSource -> 'TElement) -> comparer:(type) -> source:(type) -> (type)
Type parameters: 'TSource, 'TKey, 'TElement |
Go to GitHub source |
union comparer first second
Signature: comparer:(type) -> first:(type) -> second:(type) -> (type)
Type parameters: '?8268 |
Calls |
where predicate source
Signature: predicate:('TSource -> (type) -> (type)) -> source:(type) -> (type)
Type parameters: 'TSource |
Calls |


WITNESS LIST
Culture, Recreation & Tourism Committee
October 18, 2012 - 10:00 AM
Interim Charge #1, Invasive Aquatic Species
On:
Chilton, Earl (Texas Parks and Wildlife Department)
Cook, Jerry (Institute for the Study of Invasive Species, Sam Houston State University)
Rickman, Mike (North Texas Municipal Water District)
Stephens, V.A. (Caddo Lake Institute)
Interim Charge #4, Drought and Wildfire
On:
Huber, Karen (Travis County)
Lindsay, David (Central Texas Water Coalition)
Tedder, Jo (Central Texas Water Coalition, Burnet County Commissioners Court, and Llano
County Commissioners Court)
Interim Charge #5, Agency Oversight
On:
Boruff, Scott (Texas Parks and Wildlife Department)
Gibbs, Gary (Texas Commission on the Arts)
Laine, Larry (General Land Office)
Leisure, Brent (Texas Parks and Wildlife Department)
Rudd, Peggy (Texas State Library and Archives Commission)
Sneed, John (State Preservation Board)
Tucker, Kaye (General Land Office)
Waters, Michael (Texas State Library and Archives Commission)
1


Tools that analyze read coverage to detect copy number variants.
| Name | Summary |
|---|---|
| AnnotateIntervals | Annotates intervals with GC content, mappability, and segmental-duplication content |
| CallCopyRatioSegments | Calls copy-ratio segments as amplified, deleted, or copy-number neutral |
| CreateReadCountPanelOfNormals | Creates a panel of normals for read-count denoising |
| DenoiseReadCounts | Denoises read counts to produce denoised copy ratios |
| DetermineGermlineContigPloidy | Determines the baseline contig ploidy for germline samples given counts data |
| FilterIntervals | Filters intervals based on annotations and/or count statistics |
| GermlineCNVCaller | Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy |
| ModelSegments | Models segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts |
| PlotDenoisedCopyRatios | Creates plots of denoised copy ratios |
| PlotModeledSegments | Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates |
| PostprocessGermlineCNVCalls | Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios |
Tools that count coverage, e.g. depth per allele
| Name | Summary |
|---|---|
| ASEReadCounter | Generates table of filtered base counts at het sites for allele specific expression |
| AnalyzeSaturationMutagenesis | **BETA** (EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment. |
| CollectAllelicCounts | Collects reference and alternate allele counts at specified sites |
| CollectReadCounts | Collects read counts at specified intervals |
| CountBases | Count bases in a SAM/BAM/CRAM file |
| CountBasesSpark | Counts bases in the input SAM/BAM |
| CountReads | Count reads in a SAM/BAM/CRAM file |
| CountReadsSpark | Counts reads in the input SAM/BAM |
| DepthOfCoverage | **BETA** Generate coverage summary information for reads data |
| GeneExpressionEvaluation | **BETA** Evaluate gene expression from RNA-seq reads aligned to genome. |
| GetPileupSummaries | Tabulates pileup metrics for inferring contamination |
| LocalAssembler | **BETA** Local assembler for SVs |
| Pileup | Prints read alignments in samtools pileup format |
| PileupSpark | **BETA** Prints read alignments in samtools pileup format |
Tools that collect sequencing quality related and comparative metrics
| Name | Summary |
|---|---|
| AccumulateVariantCallingMetrics (Picard) | Combines multiple Variant Calling Metrics files into a single file |
| AnalyzeCovariates | Evaluate and compare base quality score recalibration (BQSR) tables |
| BamIndexStats (Picard) | Generate index statistics from a BAM file |
| CalcMetadataSpark | **BETA** (Internal) Collects read metrics relevant to structural variant discovery |
| CalculateContamination | Calculate the fraction of reads coming from cross-sample contamination |
| CalculateFingerprintMetrics (Picard) | Calculate statistics on fingerprints, checking their viability |
| CalculateReadGroupChecksum (Picard) | Creates a hash code based on the read groups (RG). |
| CheckFingerprint (Picard) | Computes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes |
| CheckPileup | Compare GATK's internal pileup to a reference Samtools mpileup |
| CheckTerminatorBlock (Picard) | Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise |
| ClusterCrosscheckMetrics (Picard) | Clusters the results of a CrosscheckFingerprints run by LOD score |
| CollectAlignmentSummaryMetrics (Picard) | Produces a summary of alignment metrics from a SAM or BAM file. |
| CollectArraysVariantCallingMetrics (Picard) | Collects summary and per-sample from the provided arrays VCF file |
| CollectBaseDistributionByCycle (Picard) | Chart the nucleotide distribution per cycle in a SAM or BAM file |
| CollectBaseDistributionByCycleSpark | **BETA** Collects base distribution per cycle in SAM/BAM/CRAM file(s). |
| CollectGcBiasMetrics (Picard) | Collect metrics regarding GC bias. |
| CollectHiSeqXPfFailMetrics (Picard) | Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories. |
| CollectHsMetrics (Picard) | Collects hybrid-selection (HS) metrics for a SAM or BAM file. |
| CollectIndependentReplicateMetrics (Picard) | **EXPERIMENTAL** Estimates the rate of independent replication rate of reads within a bam. |
| CollectInsertSizeMetrics (Picard) | Collect metrics about the insert size distribution of a paired-end library. |
| CollectInsertSizeMetricsSpark | **BETA** Collects insert size distribution information on alignment data |
| CollectJumpingLibraryMetrics (Picard) | Collect jumping library metrics. |
| CollectMultipleMetrics (Picard) | Collect multiple classes of metrics. |
| CollectMultipleMetricsSpark | **BETA** Runs multiple metrics collection modules for a given alignment file |
| CollectOxoGMetrics (Picard) | Collect metrics to assess oxidative artifacts. |
| CollectQualityYieldMetrics (Picard) | Collect metrics about reads that pass quality thresholds and Illumina-specific filters. |
| CollectQualityYieldMetricsSpark | **BETA** Collects quality yield metrics from SAM/BAM/CRAM file(s). |
| CollectRawWgsMetrics (Picard) | Collect whole genome sequencing-related metrics. |
| CollectRnaSeqMetrics (Picard) | Produces RNA alignment metrics for a SAM or BAM file. |
| CollectRrbsMetrics (Picard) | Collects metrics from reduced representation bisulfite sequencing (Rrbs) data. |
| CollectSamErrorMetrics (Picard) | Program to collect error metrics on bases stratified in various ways. |
| CollectSequencingArtifactMetrics (Picard) | Collect metrics to quantify single-base sequencing artifacts. |
| CollectTargetedPcrMetrics (Picard) | Calculate PCR-related metrics from targeted sequencing data. |
| CollectVariantCallingMetrics (Picard) | Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file |
| CollectWgsMetrics (Picard) | Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. |
| CollectWgsMetricsWithNonZeroCoverage (Picard) | **EXPERIMENTAL** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. |
| CompareBaseQualities | Compares the base qualities of two SAM/BAM/CRAM files |
| CompareDuplicatesSpark | **BETA** Determine if two potentially identical BAMs have the same duplicate reads |
| CompareMetrics (Picard) | Compare two metrics files. |
| CompareSAMs (Picard) | Compare two input ".sam" or ".bam" files. |
| ConvertSequencingArtifactToOxoG (Picard) | Extract OxoG metrics from generalized artifacts metrics. |
| CrosscheckFingerprints (Picard) | Checks that all data in the input files appear to have come from the same individual |
| EstimateLibraryComplexity (Picard) | Estimates the numbers of unique molecules in a sequencing library. |
| FlagStat | Accumulate flag statistics given a BAM file |
| FlagStatSpark | Spark tool to accumulate flag statistics |
| GetSampleName | Emit a single sample name |
| MeanQualityByCycle (Picard) | Collect mean quality by cycle. |
| MeanQualityByCycleSpark | **BETA** MeanQualityByCycle on Spark |
| QualityScoreDistribution (Picard) | Chart the distribution of quality scores. |
| QualityScoreDistributionSpark | **BETA** QualityScoreDistribution on Spark |
| ValidateSamFile (Picard) | Validates a SAM or BAM file. |
| ViewSam (Picard) | Prints a SAM or BAM file to the screen |
Tools that process genomic intervals in various formats
| Name | Summary |
|---|---|
| BedToIntervalList (Picard) | Converts a BED file to a Picard Interval List. |
| IntervalListToBed (Picard) | Converts an Picard IntervalList file to a BED file. |
| IntervalListTools (Picard) | A tool for performing various IntervalList manipulations |
| LiftOverIntervalList (Picard) | Lifts over an interval list from one reference build to another. |
| PreprocessIntervals | Prepares bins for coverage collection |
| SplitIntervals | Split intervals into sub-interval files. |
Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection
| Name | Summary |
|---|---|
| PathSeqBuildKmers | Builds set of host reference k-mers |
| PathSeqBuildReferenceTaxonomy | Builds a taxonomy datafile of the microbe reference |
| PathSeqBwaSpark | Step 2: Aligns reads to the microbe reference |
| PathSeqFilterSpark | Step 1: Filters low quality, low complexity, duplicate, and host reads |
| PathSeqPipelineSpark | Combined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring |
| PathSeqScoreSpark | Step 3: Classifies pathogen-aligned reads and generates abundance scores |
Miscellaneous tools, e.g. those that aid in data streaming
| Name | Summary |
|---|---|
| CreateHadoopBamSplittingIndex | **BETA** Create a Hadoop BAM splitting index |
| FifoBuffer (Picard) | Provides a large, FIFO buffer that can be used to buffer input and output streams between programs. |
| GatherBQSRReports | Gathers scattered BQSR recalibration reports into a single file |
| GatherTranches | **BETA** Gathers scattered VQSLOD tranches into a single file |
| IndexFeatureFile | Creates an index for a feature file, e.g. VCF or BED file. |
| ParallelCopyGCSDirectoryIntoHDFSSpark | **BETA** Parallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark |
| ReadAnonymizer | **EXPERIMENTAL** Replace bases in reads with reference bases. |
| ReblockGVCF | Condenses homRef blocks in a single-sample GVCF |
Tools that manipulate read data in SAM, BAM or CRAM format
| Name | Summary |
|---|---|
| AddCommentsToBam (Picard) | Adds comments to the header of a BAM file. |
| AddOATag (Picard) | Record current alignment information to OA tag. |
| AddOrReplaceReadGroups (Picard) | Assigns all the reads in a file to a single new read-group. |
| ApplyBQSR | Apply base quality score recalibration |
| ApplyBQSRSpark | **BETA** Apply base quality score recalibration on Spark |
| BQSRPipelineSpark | **BETA** Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark |
| BamToBfq (Picard) | Converts a BAM file into a BFQ (binary fastq formatted) file |
| BaseRecalibrator | Generates recalibration table for Base Quality Score Recalibration (BQSR) |
| BaseRecalibratorSpark | **BETA** Generate recalibration table for Base Quality Score Recalibration (BQSR) on Spark |
| BuildBamIndex (Picard) | Generates a BAM index ".bai" file. |
| BwaAndMarkDuplicatesPipelineSpark | **BETA** Takes name-sorted file and runs BWA and MarkDuplicates. |
| BwaSpark | **BETA** Align reads to a given reference using BWA on Spark |
| CleanSam (Picard) | Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads |
| ClipReads | Clip reads in a SAM/BAM/CRAM file |
| CollectDuplicateMetrics (Picard) | Collect Duplicate metrics from marked file. |
| ConvertHeaderlessHadoopBamShardToBam | **BETA** Convert a headerless BAM shard into a readable BAM |
| DownsampleSam (Picard) | Downsample a SAM or BAM file. |
| ExtractOriginalAlignmentRecordsByNameSpark | **BETA** Subsets reads by name |
| FastqToSam (Picard) | Converts a FASTQ file to an unaligned BAM or SAM file |
| FilterSamReads (Picard) | Subsets reads from a SAM or BAM file by applying one of several filters. |
| FixMateInformation (Picard) | Verify mate-pair information between mates and fix if needed. |
| FixMisencodedBaseQualityReads | Fix Illumina base quality scores in a SAM/BAM/CRAM file |
| GatherBamFiles (Picard) | Concatenate efficiently BAM files that resulted from a scattered parallel analysis |
| LeftAlignIndels | Left-aligns indels from reads in a SAM/BAM/CRAM file |
| MarkDuplicates (Picard) | Identifies duplicate reads. |
| MarkDuplicatesSpark | MarkDuplicates on Spark |
| MarkDuplicatesWithMateCigar (Picard) | Identifies duplicate reads, accounting for mate CIGAR. |
| MergeBamAlignment (Picard) | Merge alignment data from a SAM or BAM with data in an unmapped BAM file. |
| MergeSamFiles (Picard) | Merges multiple SAM and/or BAM files into a single file. |
| PositionBasedDownsampleSam (Picard) | Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell. |
| PrintDistantMates | Unmaps reads with distant mates. |
| PrintReads | Print reads in the SAM/BAM/CRAM file |
| PrintReadsHeader | Print the header from a SAM/BAM/CRAM file |
| PrintReadsSpark | PrintReads on Spark |
| ReorderSam (Picard) | Reorders reads in a SAM or BAM file to match ordering in a second reference file. |
| ReplaceSamHeader (Picard) | Replaces the SAMFileHeader in a SAM or BAM file. |
| RevertBaseQualityScores | Revert Quality Scores in a SAM/BAM/CRAM file |
| RevertOriginalBaseQualitiesAndAddMateCigar (Picard) | Reverts the original base qualities and adds the mate cigar tag to read-group BAMs |
| RevertSam (Picard) | Reverts SAM or BAM files to a previous state. |
| RevertSamSpark | **BETA** Reverts SAM, BAM or CRAM files to a previous state. |
| SamFormatConverter (Picard) | Convert a BAM file to a SAM file, or a SAM to a BAM |
| SamToFastq (Picard) | Converts a SAM or BAM file to FASTQ. |
| SetNmAndUqTags (Picard) | DEPRECATED: Use SetNmMdAndUqTags instead. |
| SetNmMdAndUqTags (Picard) | Fixes the NM, MD, and UQ tags in a SAM file |
| SimpleMarkDuplicatesWithMateCigar (Picard) | **EXPERIMENTAL** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. |
| SortSam (Picard) | Sorts a SAM or BAM file |
| SortSamSpark | **BETA** SortSam on Spark (works on SAM/BAM/CRAM) |
| SplitNCigarReads | Split Reads with N in Cigar |
| SplitReads | Outputs reads from a SAM/BAM/CRAM by read group, sample and library name |
| SplitSamByLibrary (Picard) | Splits a SAM or BAM file into individual files by library |
| SplitSamByNumberOfReads (Picard) | Splits a SAM or BAM file to multiple BAMs. |
| UmiAwareMarkDuplicatesWithMateCigar (Picard) | **EXPERIMENTAL** Identifies duplicate reads using information from read positions and UMIs. |
| UnmarkDuplicates | Clears the 0x400 duplicate SAM flag |
Tools that analyze and manipulate FASTA format references
| Name | Summary |
|---|---|
| BaitDesigner (Picard) | Designs oligonucleotide baits for hybrid selection reactions. |
| BwaMemIndexImageCreator | Create a BWA-MEM index image file for use with GATK BWA tools |
| ComposeSTRTableFile | Composes a genome-wide STR location table used for DragSTR model auto-calibration |
| CountBasesInReference | Count the numbers of each base in a reference file |
| CreateSequenceDictionary (Picard) | Creates a sequence dictionary for a reference sequence. |
| ExtractSequences (Picard) | Subsets intervals from a reference sequence to a new FASTA file. |
| FastaAlternateReferenceMaker | Create an alternative reference by combining a fasta with a vcf. |
| FastaReferenceMaker | Create snippets of a fasta file |
| FindBadGenomicKmersSpark | **BETA** Identifies sequences that occur at high frequency in a reference |
| NonNFastaSize (Picard) | Counts the number of non-N bases in a fasta file. |
| NormalizeFasta (Picard) | Normalizes lines of sequence in a FASTA file to be of the same length. |
| ScatterIntervalsByNs (Picard) | Writes an interval list created by splitting a reference at Ns. |
| ShiftFasta | **BETA** Creates a shifted fasta file and shift_back file |
Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)
| Name | Summary |
|---|---|
| CalibrateDragstrModel | estimates the parameters for the DRAGstr model |
| CombineGVCFs | Merges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations |
| GenomicsDBImport | Import VCFs to GenomicsDB |
| GenotypeGVCFs | Perform joint genotyping on one or more samples pre-called with HaplotypeCaller |
| GnarlyGenotyper | **BETA** Perform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller |
| HaplotypeCaller | Call germline SNPs and indels via local re-assembly of haplotypes |
| HaplotypeCallerSpark | **BETA** HaplotypeCaller on Spark |
| LearnReadOrientationModel | Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter |
| Mutect2 | Call somatic SNVs and indels via local assembly of haplotypes |
| ReadsPipelineSpark | **BETA** Runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF. |
Tools that detect structural variants
| Name | Summary |
|---|---|
| CpxVariantReInterpreterSpark | **BETA** (Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf |
| DiscoverVariantsFromContigAlignmentsSAMSpark | **BETA** (Internal) Examines aligned contigs from local assemblies and calls structural variants |
| ExtractSVEvidenceSpark | **BETA** (Internal) Extracts evidence of structural variations from reads |
| FindBreakpointEvidenceSpark | **BETA** (Internal) Produces local assemblies of genomic regions that may harbor structural variants |
| PrintSVEvidence | **EXPERIMENTAL** Prints SV evidence records |
| StructuralVariationDiscoveryPipelineSpark | **BETA** Runs the structural variation discovery workflow on a single sample |
| SvDiscoverFromLocalAssemblyContigAlignmentsSpark | **BETA** (Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints |
Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine
| Name | Summary |
|---|---|
| AnnotateVcfWithBamDepth | (Internal) Annotate a vcf with a bam's read depth at each variant locus |
| AnnotateVcfWithExpectedAlleleFraction | (Internal) Annotate a vcf with expected allele fractions in pooled sequencing |
| CalculateGenotypePosteriors | Calculate genotype posterior probabilities given family and/or known population genotypes |
| CalculateMixingFractions | (Internal) Calculate proportions of different samples in a pooled bam |
| Concordance | Evaluate concordance of an input VCF against a validated truth VCF |
| CountFalsePositives | **BETA** Count PASS variants |
| CountVariants | Counts variant records in a VCF file, regardless of filter status. |
| CountVariantsSpark | CountVariants on Spark |
| EvaluateInfoFieldConcordance | **BETA** Evaluate concordance of info fields in an input VCF against a validated truth VCF |
| FilterFuncotations | **EXPERIMENTAL** Filter variants based on clinically-significant Funcotations. |
| FindMendelianViolations (Picard) | Finds mendelian violations of all types within a VCF |
| FuncotateSegments | **BETA** Functional annotation for segment files. The output formats are not well-defined and subject to change. |
| Funcotator | Functional Annotator |
| FuncotatorDataSourceDownloader | Data source downloader for Funcotator. |
| GenotypeConcordance (Picard) | Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls. |
| ValidateBasicSomaticShortMutations | **EXPERIMENTAL** Check variants against tumor-normal bams representing the same samples, though not the ones from the actual calls. |
| ValidateVariants | Validate VCF |
| VariantEval | **BETA** General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) |
| VariantsToTable | Extract fields from a VCF file to a tab-delimited table |
Tools that filter variants by annotating the FILTER column
| Name | Summary |
|---|---|
| ApplyVQSR | Apply a score cutoff to filter variants based on a recalibration table |
| CNNScoreVariants | Apply a Convolutional Neural Net to filter annotated variants |
| CNNVariantTrain | **EXPERIMENTAL** Train a CNN model for filtering variants |
| CNNVariantWriteTensors | **EXPERIMENTAL** Write variant tensors for training a CNN to filter variants |
| CreateSomaticPanelOfNormals | **BETA** Make a panel of normals for use with Mutect2 |
| FilterAlignmentArtifacts | **EXPERIMENTAL** Filter alignment artifacts from a vcf callset. |
| FilterMutectCalls | Filter somatic SNVs and indels called by Mutect2 |
| FilterVariantTranches | Apply tranche filtering |
| FilterVcf (Picard) | Hard filters a VCF. |
| VariantFiltration | Filter variant calls based on INFO and/or FORMAT annotations |
| VariantRecalibrator | Build a recalibration model to score variant quality for filtering purposes |
Tools that manipulate variant call format (VCF) data
| Name | Summary |
|---|---|
| FixVcfHeader (Picard) | Replaces or fixes a VCF header. |
| GatherVcfs (Picard) | Gathers multiple VCF files from a scatter operation into a single VCF file |
| GatherVcfsCloud | **BETA** Gathers multiple VCF files from a scatter operation into a single VCF file |
| LeftAlignAndTrimVariants | Left align and trim vairants |
| LiftoverVcf (Picard) | Lifts over a VCF file from one reference build to another. |
| MakeSitesOnlyVcf (Picard) | Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information. |
| MergeVcfs (Picard) | Combines multiple variant files into a single variant file |
| PrintVariantsSpark | Prints out variants from the input VCF. |
| RemoveNearbyIndels | (Internal) Remove indels from the VCF file that are close to each other. |
| RenameSampleInVcf (Picard) | Renames a sample within a VCF or BCF. |
| SelectVariants | Select a subset of variants from a VCF file |
| SortVcf (Picard) | Sorts one or more VCF files. |
| SplitVcfs (Picard) | Splits SNPs and INDELs into separate files. |
| UpdateVCFSequenceDictionary | Updates the sequence dictionary in a variant file. |
| UpdateVcfSequenceDictionary (Picard) | Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary. |
| VariantAnnotator | Tool for adding annotations to VCF files |
| VcfFormatConverter (Picard) | Converts VCF to BCF or BCF to VCF. |
| VcfToIntervalList (Picard) | Converts a VCF or BCF file to a Picard Interval List |
Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters
| Name | Summary |
|---|---|
| CheckIlluminaDirectory (Picard) | Asserts the validity for specified Illumina basecalling data. |
| CollectIlluminaBasecallingMetrics (Picard) | Collects Illumina Basecalling metrics for a sequencing run. |
| CollectIlluminaLaneMetrics (Picard) | Collects Illumina lane metrics for the given BaseCalling analysis directory. |
| ExtractIlluminaBarcodes (Picard) | Tool determines the barcode for each read in an Illumina lane. |
| IlluminaBasecallsToFastq (Picard) | Generate FASTQ file(s) from Illumina basecall read data. |
| IlluminaBasecallsToSam (Picard) | Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. |
| MarkIlluminaAdapters (Picard) | Reads a SAM or BAM file and rewrites it with new adapter-trimming tags. |
Tools that manipulate data generated by Genotyping arrays
| Name | Summary |
|---|---|
| BpmToNormalizationManifestCsv (Picard) | Program to convert an Illumina bpm file into a bpm.csv file. |
| CombineGenotypingArrayVcfs (Picard) | Program to combine multiple genotyping array VCF files into one VCF. |
| CreateBafRegressMetricsFile (Picard) | Program to generate a picard metrics file from the output of the bafRegress tool. |
| CreateVerifyIDIntensityContaminationMetricsFile (Picard) | Program to generate a picard metrics file from the output of the VerifyIDIntensity tool. |
| GtcToVcf (Picard) | Program to convert an Illumina GTC file to a VCF |
| MergePedIntoVcf (Picard) | Program to merge a single-sample ped file from zCall into a single-sample VCF. |
| VcfToAdpc (Picard) | Program to convert an Arrays VCF to an ADPC file. |
Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM
| Name | Summary |
|---|---|
| MethylationTypeCaller | **EXPERIMENTAL** Identify methylated bases from bisulfite sequenced, methylation-aware BAMs |
Applied by engine to select reads for analysis
| Name | Summary |
|---|---|
| AlignmentAgreesWithHeaderReadFilter | Filters out reads where the alignment does not match the contents of the header |
| AllowAllReadsReadFilter | Do not filter out any read |
| AmbiguousBaseReadFilter | Filters out reads that have greater than the threshold number of N bases |
| CigarContainsNoNOperator | Filter out reads with CIGAR containing N operator |
| FirstOfPairReadFilter | Keep only reads that are first of pair |
| FragmentLengthReadFilter | Keep only read pairs with insert length less than or equal to the given value |
| GoodCigarReadFilter | Keep only reads containing good CIGAR string |
| HasReadGroupReadFilter | Filter out reads without Read Group |
| IntervalOverlapReadFilter | Filters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L on an indexed bam file. |
| LibraryReadFilter | Keep only reads from the specified library |
| MappedReadFilter | Filter out unmapped reads |
| MappingQualityAvailableReadFilter | Filter out reads without available mapping quality |
| MappingQualityNotZeroReadFilter | Filter out reads with mapping quality equal to zero |
| MappingQualityReadFilter | Keep only reads with mapping qualities within a specified range |
| MatchingBasesAndQualsReadFilter | Filter out reads where the bases and qualities do not match |
| MateDifferentStrandReadFilter | Keep only reads with mates mapped on the different strand |
| MateDistantReadFilter | Keep only paired reads with mates mapped >= mate-too-distant-length (default 1KB) apart or on different contigs |
| MateOnSameContigOrNoMappedMateReadFilter | Keep only reads whose mate maps to the same contig or is unmapped |
| MateUnmappedAndUnmappedReadFilter | Filters reads whose mate is unmapped as well as unmapped reads. |
| MetricsReadFilter | Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments |
| NonChimericOriginalAlignmentReadFilter | Filters reads whose original alignment was chimeric. |
| NonZeroFragmentLengthReadFilter | Filter out reads with fragment length different from zero |
| NonZeroReferenceLengthAlignmentReadFilter | Filter out reads that do not align to the reference |
| NotDuplicateReadFilter | Filter out reads marked as duplicate |
| NotProperlyPairedReadFilter | Keep only paired reads that are not properly paired |
| NotSecondaryAlignmentReadFilter | Filter out reads representing secondary alignments |
| NotSupplementaryAlignmentReadFilter | Filter out reads representing supplementary alignments |
| OverclippedReadFilter | Filter out reads that are over-soft-clipped |
| PairedReadFilter | Filter out unpaired reads |
| PassesVendorQualityCheckReadFilter | Filter out reads failing platfor/vendor quality checks |
| PlatformReadFilter | Keep only reads with matching Read Group platform |
| PlatformUnitReadFilter | Filter out reads with matching platform unit attribute |
| PrimaryLineReadFilter | Keep only reads representing primary alignments (those that satisfy both the NotSecondaryAlignment and NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or 0x800 flags set). |
| ProperlyPairedReadFilter | Keep only reads that are properly paired |
| ReadGroupBlackListReadFilter | Keep records that don't match the specified filter string(s). |
| ReadGroupReadFilter | Keep only reads from the specified read group |
| ReadLengthEqualsCigarLengthReadFilter | Filter out reads where the read and CIGAR do not match in length |
| ReadLengthReadFilter | Keep only reads whose length is within a certain range |
| ReadNameReadFilter | Keep only reads with this read name |
| ReadStrandFilter | Keep only reads whose strand is as specified |
| SampleReadFilter | Keep only reads for a given sample |
| SecondOfPairReadFilter | Keep only paired reads that are second of pair |
| SeqIsStoredReadFilter | Keep only reads with sequenced bases |
| SoftClippedReadFilter | Filter out reads that are over-soft-clipped |
| ValidAlignmentEndReadFilter | Keep only reads where the read end is properly aligned |
| ValidAlignmentStartReadFilter | Keep only reads with a valid alignment start |
| WellformedReadFilter | Keep only reads that are well-formed |
Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836
| Name | Summary |
|---|---|
| AS_BaseQualityRankSumTest | Allele-specific rank sum test of REF versus ALT base quality scores (AS_BaseQRankSum) |
| AS_FisherStrand | Allele-specific strand bias estimated using Fisher's exact test (AS_FS) |
| AS_InbreedingCoeff | Allele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff) |
| AS_MappingQualityRankSumTest | Allele-specific rank sum test for mapping qualities of REF versus ALT reads (AS_MQRankSum) |
| AS_QualByDepth | Allele-specific call confidence normalized by depth of sample reads supporting the allele (AS_QD) |
| AS_RMSMappingQuality | Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ) |
| AS_ReadPosRankSumTest | Allele-specific rank sum test for relative positioning of REF versus ALT allele within reads (AS_ReadPosRankSum) |
| AS_StrandOddsRatio | Allele-specific strand bias estimated by the symmetric odds ratio test (AS_SOR) |
| AlleleFraction | Variant allele fraction for a genotype |
| AllelePseudoDepth | Total depth of coverage per sample and over all samples (DP) |
| AssemblyComplexity | Describe the complexity of an assembly region |
| BaseQuality | Median base quality of bases supporting each allele (MBQ) |
| BaseQualityRankSumTest | Rank sum test of REF versus ALT base quality scores (BaseQRankSum) |
| ChromosomeCounts | Counts and frequency of alleles in called genotypes (AC, AF, AN) |
| ClippingRankSumTest | Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingRankSum) |
| CountNs | Number of Ns at the pileup |
| Coverage | Total depth of coverage per sample and over all samples (DP) |
| DepthPerAlleleBySample | Depth of coverage of each allele per sample (AD) |
| DepthPerSampleHC | Depth of informative coverage for each sample (DP) |
| ExcessHet | Phred-scaled p-value for exact test of excess heterozygosity (ExcessHet) |
| FeaturizedReadSets | Featurized read sets for Mutect3 training data |
| FisherStrand | Strand bias estimated using Fisher's exact test (FS) |
| FragmentLength | Median fragment length of reads supporting each allele (MFRL) |
| GenotypeSummaries | Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDEV) |
| InbreedingCoeff | Likelihood-based test for the consanguinity among samples (InbreedingCoeff) |
| LikelihoodRankSumTest | Rank sum test of per-read likelihoods of REF versus ALT reads (LikelihoodRankSum) |
| MappingQuality | Median mapping quality of reads supporting each allele (MMQ) |
| MappingQualityRankSumTest | Rank sum test for mapping qualities of REF versus ALT reads (MQRankSum) |
| MappingQualityZero | Count of all reads with MAPQ = 0 across all samples (MQ0) |
| OrientationBiasReadCounts | Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1) |
| OriginalAlignment | Number of alt reads with an OA tag that doesn't match the current alignment contig. |
| PossibleDeNovo | Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo) |
| QualByDepth | Variant confidence normalized by unfiltered depth of variant samples (QD) |
| RMSMappingQuality | Root mean square of the mapping quality of reads across all samples (MQ) |
| ReadPosRankSumTest | Rank sum test for relative positioning of REF versus ALT alleles within reads (ReadPosRankSum) |
| ReadPosition | Median distance of variant starts from ends of reads supporting each allele (MPOS) |
| ReferenceBases | Annotate with local reference bases (REF_BASES) |
| SampleList | List of samples that are not homozygous reference at a variant site (Samples) |
| StrandBiasBySample | Number of forward and reverse reads that support REF and ALT alleles (SB) |
| StrandOddsRatio | Strand bias estimated by the symmetric odds ratio test (SOR) |
| TandemRepeat | Tandem repeat unit composition and counts per allele (STR, RU, RPA) |
| UniqueAltReadCount | Number of non-duplicate-insert ALT reads (AS_UNIQ_ALT_READ_COUNT) |
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version <IP_ADDRESS> built at Wed, 18 Aug 2021 19:58:25 -0400.


Seam Erasure
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Type of Value Preserving Energy:
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Linear Interpolation
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Global minimization
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Padding in computer terms is not that cool
Starting websites from scratch is like running a tech marathon
March 29, 2015
I usually feel pretty drained when I reach time to do my tech blog. Mosly after sitting here for hours battling with CSS and finding syntax errors, I'd like a break. However, my tech thoughts must be brought to the world. I did learn a lot this week.
I would like to learn even more about positioning: absolute, static, fixed, sticky, relative. I understand it. Slightly Do you ever have a few topics where it just seems to take awhile to sink in? These are definitely one of them for me. They are basically trying to position different blocks of color or content on site, but each category has different properties. Those properties can then mess with everything else around it, thus creating sometimes a frustrating situation.
I can tell you, however, about margins, padding, and borders. Like positioning, they're very good things to know. Dev tools in Chrome has given me a better idea about it, so I'm feel pretty cool right now. A MARGIN - is kind of what you think it would be. Like in Word or other text editors, your margins are on the side of your text. Now think of your text is in a invisible block. A Border would be directly around that block. In most designs, we put it at 0 pixels so it won't even show up. Padding, on the other hand, is the weird sister of the bunch. Take that pretend border around your Word document text and increase the space. Say you had 10 pixels of padding. This would add space INSIDE the border and push the text more into the middle. There are great diagrams out there. Here is a great one from W3 schools.


The <md-radio-group>
directive identifies a grouping
container for the 1..n grouped radio buttons; specified using nested
<md-radio-button>
elements.
The radio button uses the accent color by default. The primary color palette may be used with
the md-primary
class.
Note: <md-radio-group>
and <md-radio-button>
handle tabindex
differently
than the native <input type="radio">
controls. Whereas the native controls
force the user to tab through all the radio buttons, <md-radio-group>
is focusable and by default the <md-radio-button>
s are not.
| Parameter | Type | Description |
|---|---|---|
* ng-model
string
|
string |
Assignable angular expression to data-bind to. |
ng-change
string
|
string |
AngularJS expression to be executed when input changes due to user interaction. |
md-no-ink
boolean
|
boolean |
If present, disables ink ripple effects. |


All requests can take an optional parameter request_id, which will appear in the response.
We will use device IDs based on client certificates. But for now, a request parameter x-id can be used. Using a new device ID automatically creates a new profile (with no name etc).
In all cases GET and POST are interchangeable. GET is shown here due to laziness but devices should probably POST.
The synchronisation mechanism is based on feeding
server-generated SQL directly to a local Sqlite3 database, using
the schema from client/db/create.sql
. (Soon the
schema will be auto-magically recreated by the server, watch this
space...)
timeline
and sequence
parameters are optional, and should be loaded from the Sqlite
table 'control' if it contains a row (it should contain one row
if it's every been synchronised successfully, and no rows if it
is a newly created schema); this returns a JSON document
containing a top level dictionary with the following members:
{ "operation" : "refresh" }
if the server
has determined that it needs to send a complete data
transfusion, deleting and reinserting all replicated state
(because the sequence number is too old for an incremental
update, or the timeline number has changed due to a major
data loss event on the server); or { "operation" :
"incremental" }
if it is possible to send a series of
changesmetadata
is a list of dictionaries like these:
{ "INSERT" : "uri" }
-- to indicate that the object identified by uri has been inserted{ "UPDATE" : "uri" }
-- ... updated{ "DELETE" : "uri" }
-- ... deleted{ "more" : true }
-- an incremental
synchronisation hit the configured maximum size, and
the client should rince and repeat to see if more
changes are available{ "sql" : [ "INSERT ..." ... ] }
contains a
list of SQL statements to be executed, as one transaction,
by the client.INSERT
, UPDATE
, DELETE
instructions are as follows:
match/12345678-1234-1234-1234-123456789012
-- a match (this is actually the ID of the search on the
other side, but in the client database it is the primary key
for a match record; it is a UUID in 8-4-4-4-12 format)search/12345678-1234-1234-1234-123456789012
-- a search belonging to the usercurl --upload-file foo.jpg -u captain:cook https://dev.speedycrew.com/api/1/media/1234/foo?x-id=1234
to PUT a new media filecurl -X DELETE -u captain:cook https://dev.speedycrew.com/api/1/media/1234/foo?x-id=1234
to DELETE a new media file


Functions for calculating the OPTICS Cordillera. The OPTICS Cordillera measures the amount of 'clusteredness' in a numeric data matrix within a distance-density based framework for a given minimum number of points comprising a cluster, as described in Rusch, Hornik, Mair (2017) <doi:10.1080/10618600.2017.1349664>. There is an R native version and a version that uses 'ELKI', with methods for printing, summarizing, and plotting the result. There also is an interface to the reference implementation of OPTICS in 'ELKI'.
| Version: | 0.8-0 |
| Depends: | R (≥ 3.1.2) |
| Imports: | dbscan, yesno |
| Suggests: | cluster, scatterplot3d, MASS |
| Published: | 2018-01-14 |
| Author: | Thomas Rusch [aut, cre], Patrick Mair [ctb], Kurt Hornik [ctb] |
| Maintainer: | Thomas Rusch <thomas.rusch at wu.ac.at> |
| License: | GPL-2 | GPL-3 |
| URL: | http://r-forge.r-project.org/projects/stops/ |
| NeedsCompilation: | no |
| SystemRequirements: | ELKI (>=0.6.0 if used) |
| Citation: | cordillera citation info |
| Materials: | NEWS |
| CRAN checks: | cordillera results |
| Reference manual: | cordillera.pdf |
| Package source: | cordillera_0.8-0.tar.gz |
| Windows binaries: | r-devel: cordillera_0.8-0.zip, r-release: cordillera_0.8-0.zip, r-oldrel: cordillera_0.8-0.zip |
| OS X binaries: | r-release: cordillera_0.8-0.tgz, r-oldrel: cordillera_0.8-0.tgz |
| Old sources: | cordillera archive |
Please use the canonical form https://CRAN.R-project.org/package=cordillera to link to this page.


Cpmm: cross-product matrix multiplication operation (distributed matrix multiply
by join over common dimension and subsequent aggregation of partial results).
This function pre-aggregates distinct values of recoded columns per partition (part of distributed recode map
construction, used for recoding, binning and dummy coding).


Want to Visit:
New York, Shanghai, Sydney
I can take you around to the fantastic food markets London has to offer!
Want to Visit:
London, Tokyo, Barcelona
New York is the city that never sleeps! If you want to party like a king in NYC, I can show you the ropes.
Want to Visit:
New York, Milan
Let's go shopping!
Want to Visit:
New York, Shanghai, Sydney
I can take you around to the fantastic food markets London has to offer!
Want to Visit:
London, Tokyo, Barcelona
New York is the city that never sleeps! If you want to party like a king in NYC, I can show you the ropes.
Want to Visit:
New York, Milan
Let's go shopping!


If We Won't who will.
We at ShareTheNeeds are trying to bridge the gap between the peoples who need help and those who are ready to help. Serving the community is the best way of returning the favour we owe to our mother earth. Using ShareTheNeeds Helping the needy is just a click away, You can organize camps and distribute the essential items to the needy people very easily.
As the name suggests sharing the essential items with needy is one of the best thing that a human could do for humanity. If any person is in urgent need of some essential items he could easily look for it. Using ShareTheNeeds we provide a service where the person in need can easily find the camps nearby and the items they are providing.
If you wanted to serve the community. Just organize the camps and share the details with all the other people in need through ShareTheNeeds.


[css:content/bootstrap.min.css]> <[css:content/stylish-portfolio.css]>
Use the Alba library in your testing projects to quickly write declarative specifications against the HTTP endpoint of an ASP.Net Core application by simulating an HTTP request in memory. Inspired by the "Scenario" testing mechanism in FubuMVC. Alba supports ASP.Net Core >2.1 and is tested against both netcoreapp2.1 and netcoreapp2.1.


This is a header element.
This is an address element.
This is a main element.
This is an ARIA application landmark.
This is an ARIA banner landmark.
This is an ARIA complementary landmark.
This is an ARIA contentinfo landmark.
This is an ARIA form landmark.
This is an ARIA main landmark.
This is an ARIA navigation landmark.
This is an ARIA search landmark.
This should NOT banner role.
This should NOT have banner role.
This should NOT have banner role.
This should NOT header role.
| This should NOT have banner role. |
This should NOT have banner role.
This should NOT banner role.
This should NOT have banner role.
This should NOT have banner role.
This should NOT header role.
This should NOT have banner role. |
This should NOT have banner role.
|
|


One Million Arab Coders
Profile
Member's list
Create new +
Title
Edit
Delete
{% for post in posts %}
{{post.title}}
edit
del
{% endfor %}


Dove Cameron's Fans Did The Sweetest Thing For Her During Her Date Night
Dove Cameron has the sweetest fans!

PHOTOS: Check out the latest pics of Dove Cameron
Dove took to her Twitter to open up about the very nice gesture.
“tommy & i went to the movies the other night & ate at @Cheesecake & apparently a table of young fans PAID FOR OUR MEAL before we could & then DIPPED,” Dove wrote.


@* * Copyright 2021 HM Revenue & Customs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. *@ @import uk.gov.hmrc.merchandiseinbaggage.config.AppConfig @import uk.gov.hmrc.merchandiseinbaggage.controllers.routes._ @import uk.gov.hmrc.merchandiseinbaggage.model.api._ @import uk.gov.hmrc.merchandiseinbaggage.model.api.DeclarationType.Export @this(layout: Layout, formHelper: FormWithCSRF, errorSummary: components.errorSummary, summaryList: includes.goodsSummary, button: components.button) @(form: Form[_], amendment: Amendment, isAgent: YesNo)(implicit request: Request[_], messages: Messages, appConfig: AppConfig) @agentOrTrader = @{if(YesNo.to(isAgent)) "agent" else "trader"} @layout(pageTitle = Some(title(form, "checkYourAnswers.amend.title")), maybeBackButtonUrl = None, maybeDeclarationType = Some(Export)) { @helper.form(action = CheckYourAnswersController.onSubmit()) { @helper.CSRF.formField @if(form.hasErrors) { @errorSummary(form.errors) }
@messages("checkYourAnswers.addMoreGoods")
@messages("checkYourAnswers.sendDeclaration.acknowledgement")
@messages("checkYourAnswers.sendDeclaration.confirm")


Add New Event
Event Name
Starting Date
Event Host
Finishing Date
Add Event
Today
OCT
4
2016
Starting UI
Hosted by Leoleo
Upcoming Events
The Next 7 Days
The Next 30 Days
the Next 90 Days
OCT
04
2016
EXO
Hosted by Leoleo
OCT
04
2016
OCT
04
2016
EXO
Hosted by Leoleo


Neptune
Purple Heart
The CPU godesses of Planeptune mostly Knoed as Purple Heart live with her sister being the most strong CPU godesses
Noire
Black Heart
Lady Noire are the CPU gooddesses and creator of the factory Nation Lastation most of her civilians dont know but by acting tsundere Lady Noire dont have friends
Blanc
white Heart
A Little Cute girl that will explode and attack anyone in front are a perfect descripiton of Lady Blanc the CPU Godesses and Leader of The Snow Nation Lowee
Vert
Green Heart
The Strongest NEET gamer of All Gamindustri are also The CPU Godesses and creator of The Nation Leanbox, Vert are also Knoed By wanting so much a Little Sister


Special Biriyani
34 votes
₹
195
[Served with 1 Gulab Jamun & Mint Raita] Adorned with fresh vegetables...
read more
Add +


Smart Lights
Lights & Groups
Scenes
Automation
Party
Settings
Light removed from group.
Group deleted.
All groups are included.
New RFID-Tag available.
Offline
Save Color
Groups
{{sharedScope.state.groups[groupId].name}}
Color of Light "{{sharedScope.state.lights[helpers.urlId].name}}"
Activate Colorloop
Color of Light "{{sharedScope.state.lights[helpers.urlId].name}}"
Activate Colorloop
Which color should be replaced?
Which color should be replaced?
Which groups should be added?
{{sharedScope.state.groups[groupId].name}}
done
Which groups should be added?
{{sharedScope.state.groups[groupId].name}}
done
Do you want to remove the light from group "{{sharedScope.state.groups[groups.selectedGroupId].name}}"?
YES
NO
Do you want to remove the light from group "{{sharedScope.state.groups[groups.selectedGroupId].name}}" ?
YES
NO
The group "{{sharedScope.state.groups[groups.selectedGroupId].name}}" will be deleted completely.
YES
NO
The group "{{sharedScope.state.groups[groups.selectedGroupId].name}}" will be deleted completely.
YES
NO


This API Lab is so much about cats...
Meet a cat!
Say:
Hello cat!
Then, say:
Meow!
Example 1
Example 2
Example 3
Example 4
Example 5
Example 6
Example 7


Paul McCartney to headline 50th Glastonbury music festival
Former Beatles singer to perform at legendary British music festival next June in Somerset, organisers confirm.
British musician Paul McCartney will take star billing at next year's Glastonbury, when the legendary UK music festival marks its 50th anniversary, organisers said.
Glastonbury coorganiser Emily Eavis said the former Beatles star would headline the Pyramid Stage on June 27 - the traditional highlight of the event in Somerset, southwest England.
"Having Paul McCartney coming back to headline the Pyramid next year is an absolute dream come true," she said in a statement on the festival's website on Monday.
"There really was no one that we wanted more for the 50th anniversary."
McCartney previously headlined Glastonbury in 2004. This year's headliner was grime star Stormzy.
He dropped hints on his Twitter feed before the announcement by posting photographs of composer Philip Glass, actress Emma Stone and musician Chuck Berry.
All 135,000 tickets for the 50th-anniversary festival went on sale last month and sold out in 34 minutes, organisers said.


What do you get if you multiply six by nine?
This is example 1a
This is example 1b
This is example 2a
This is example 2b
This is example 3a
This is example 3b


RedMatrix
Dream it. Do it.
The RedMatrix (aka "red") is an advanced social networking platform which was created by a
farmer in Australia - who grew disgusted by the lack of privacy and the increasing tendency of foreign corporations and governments to monitor and control the internet. This has strangled and subverted all that was once good about the web - and turned it into a "steaming pile of crap". (Aussies typically don't mince words.)
Working with a team of volunteers from six continents and over a period of several years, this has evolved into something quite spectacular, far removed from its humble beginnings as a tool to stay in contact with family members and friends that are separated by vast distances. It's an open source, decentralised identity and sharing system which brings back some semblance of privacy to a world that desperately needs it - today more than ever. It's a webserver platform not much more complicated than a WordPress blog and using the same technology, but thousands of times more capable in what it can do for your social communications and sharing needs.
Taking cues from life in the Aussie outback, the Red Matrix has no central authority. Each channel (or social profile) is independent and autonomous - controlling its own publishing privacy as desired. Some will want more privacy, some less. Unlike your typical social network - the matrix has no say in this decision and cannot subvert it. The NSA and all the other creepy voyeurs trying to find out what you and your friends are discussing can just bugger off. Server hubs are self-sufficient and the network will continue to function if any single node in the matrix goes offline. It also provides channel resilience. You can "clone" your channel (or social profile) to any hub in the network and carry on without interruption if your primary server chucks a wobbly for an hour - or a week. (No fail whale needed here.)
 Join us.
Welcome to the Matrix
Public Sites (sign up now!) | Project Home | Git | Developers
To be fair, this Aussie farmer knows more about electronic communications and web software than many professional developers. He's a somewhat respected internet pioneer who once worked for American corporate giants as a web communications and protocol wizard - and has returned from semi-retirement to try and save the net from what is has now become.


--- layout: post title: Encoding video for the NDS date: 2008-05-28 16:41:00.000000000 +02:00 categories: - Hows To tags: [nintendo, nds, video] status: publish type: post published: true meta: blogger_blog: psanxiao.blogspot.com blogger_author: Pablo<EMAIL_ADDRESS>blogger_permalink: /2008/05/encoding-video-for-nds.html author: login: psanxiao email<EMAIL_ADDRESS>display_name: psanxiao first_name: '' last_name: '' ---
I have had a nds since a couple of months. Of course its best quality is the gaming but it has more possibilities. There are many homebrew or applications that you can download from internet and they let you do many things like surf the web, check your email, you can use it like video and music player even install GNU/Linux.
The video player is a great feature, for example I use a video and music player for my nds called moonshell. The problem is that application uses a specific video format (dpg) so it is necessary to encode the videos before.
Recently I found this script in python, licensed under GPL2, that let you do it easily. You need also mpeg_stat, that analyze the streaming of a mpeg file. The use is as follow:
First you need to copy mpeg_stat to your /bin directory. Then you should copy the script to the same directory where you have the video/s to encode and then you can execute doing:
$ python dpgconv.py file_name.extension
It works perfectly with avi and mpeg videos, once it has done you can copy the video in your nds and to enjoy.
The moral of the post is: Is there anything that it cannot be made with python?


Reports problems with nesting decorators. The inspection highlights the cases when classmethod
or staticmethod
is applied before another decorator.
Example:
def innocent(f):
return f
class A:
@innocent # Decorator will not receive a callable it may expect
@classmethod
def f2(cls):
pass
@innocent # Decorator will not receive a callable it may expect
@staticmethod
def f1():
pass
As a quick-fix, the IDE offers to remove the decorator.


Queen Maxima arrives in Pakistan today
by News DeskQueen Máxima of the Netherlands will reach Pakistan on Monday (today) for a three-day visit in her capacity as the United Nations Secretary General’s Special Advocate for Inclusive Finance for Development.
According to Radio Pakistan, during the visit, the queen will call on the president and the prime minister, besides engagements with a range of stakeholders from the public and private sectors.
It may be added that inclusive finance for development is one of the key priorities of the Pakistan government for which it has taken a number of steps.
Queen Máxima will also attend the launch of the “Micro Payment Gateway,” an initiative of the State Bank of Pakistan aimed at “reducing cost of small payments and boosting digital transactions to benefit people and promote financial inclusion”.
The queen has been the UN Secretary General’s Special Advocate for Inclusive Finance for Development since 2009.
In this capacity, she is actively engaged worldwide in promoting access of individuals and enterprises to financial services at a reasonable cost, with the aim of improving economic and social development opportunities.
Queen Máxima had earlier visited Pakistan in February 2016.


ESP Stack Trace Decoder
An online ESP stack trace decoder that runs in your browser
.elf binary:
Stack trace:
Loading...
Output:


Cosmology Seminar
The next cosmology seminar takes place on Friday 2nd of December, seminar room E349 at 2pm. Our guest speaker will be Davide Dal Cin from SISSA (Trieste, Italy).
More …Cosmology Seminar
The next cosmology seminar takes place on Friday 2nd of December, seminar room E349 at 2pm. Our guest speaker will be Davide Dal Cin from SISSA (Trieste, Italy).
More …Mean-field approach to Random Apollonian Packing
Bubble nucleation is a phenomenon ubiquitous in physics, with applications ranging from the geometry of tree crowns, the structure of porous media and of sphere packing. Bubbles also find applications in cosmology such as the characterization of cosmic voids in the large scale structure and the signatures of cosmological phase transitions. In a new preprint, Pierre proposes a new method to determine the fractal properties of the so-called Random Apollonian Packing.
More …Cosmology Seminar
The next cosmology seminar takes place on Friday 30th of September, seminar room E349 at 2pm. Our guest speaker will be Nilanjandev Bhaumik from the Indian Institute of Science (Bangalore, India).
More …Slow-roll Inflation at N3LO
Cosmic Inflation, the most favoured scenario of the early Universe, implies that all forms of matter and radiation observed today are the outcome of quantum fluctuations occurring around the event horizon of a exponentially fast accelerating space-time. Clearing the ground for the incoming spatial and ground based cosmological observations, Pierre and Christophe have derived, at an unprecedented level of precision, the shape of the expected power spectra of both the quantum-generated gravitational waves and curvature perturbations.
More …BEL Center exhibition
Anticipating the opening of the Brout-Englert-Lemaître Center, a few aesthetic pictures associated with our researches will be on display during the “Walk in the Park” event, on Saturday the 25th at the Tournay Solvay Park (11am).
More …


Hey buddies, visited the Law Library at UCL the other day and couldn't find a single space to sit in. Looking for a quiet place, with lots of breathing space (I like big rooms) and natural light. Let me know if you find anything similar!
Hey Guys! New space found! It's called Tap Coffee. How do you find it? Just follow the numbers on the door. Literally. Each coffeeshop has a different number, to signify the number of the store #genius. Some are bigger than others and therefore more spacious, some smaller but cozier.
This place is filled with natural light and quirky furniture. The study space of the month is the Wellcome Library. Having spoken to our fellow students we also discovered that not many know about it. So you are bound to find space to study in there (for now). Go ahead and give it a visit!
What's Good?
Lighting, Space, Quiet
The minus?
You need to bring a clear bag to fill with the contents that you'll need - otherwise you can't bring anything else with you:/


Some stuff I do...
— Website —
Dalaine Flowershop is a local business of my friend located at La Paz, Tarlac City. It offers different services such as Balloons, Party Needs, Wedding Services, Funeral Services, Plants, Tables and Chairs, Special Events, Landscaping etc. This website is used for the promotion of the business and its services.
— Website —
Ellen's Flora Garden is a local Flowershop located at San Rafael, Tarlac City and it is also another business of my friend. This website is used for the promotion of the business and its services.
— Graphic Design —
These designs was a project during my NCIII:VGD Vocational course as a preparation for the upcoming assessment. Our teacher asked us to create our own logo, brochure, billboard, product packaging and website design for a sample business. I made these designs only in one day because our teacher gave us a deadline to create our own designs with added time pressure to test how quick can we do Graphic Design.
— Graphic Design —
Designs I made during my NCIII: Visual Graphic Design Vocational course
— Blog —
ON-J-T is my OJT blog that I created using Wordpress' Website and Blog creator. It is all about the different activities during my On-the-Job Training at ON Semiconductor SSMP Philippines Corporation.
Visit ON-J-T: jpjarin.wordpress.com
Call me:
0921-251-4153 / 0945-1465-176


Matrix Pencil Sparse Fourier Transform
Links
- Brief report describes how MPSFT works.
- PhD thesis contains some theory.
- Github page has the implementation details.
Introduction
SFT (sparse Fourier transform) algorithms aim to perform discrete Fourier transform in O(S) time, ignoring log factors, where S is the sparsity in frequency domain. In other words, the solution has a support of size S, plus some noise.
In MPSFT (Matrix Pencil Sparse Fourier Transform), we apply the matrix pencil method to improve the accuracy of mode identification and to reduce the chance of creating spurious modes (and having to correct them later). It makes SFT algorithms more feasible and practical. For N=2^22, we are faster than FFTW when S is less than around 1800. AAFFT is faster for a smaller range of S, say around <= 200. A more recent work DMSFT seems to be somewhat competitive with MPSFT.
Results
In the plot below, we fix N=2^22 and vary S (sparsity) and plot the running time. SFFT1 and SFFT2 are faster but they have a runtime of O(sqrt(NS)) ignoring log factors.
In the plot below, we fix K=50 and increase N. Here we see that MPSFT will be faster than SFFT1, SFFT2 for N being around 2^24.
Basic ingredients
We bin the signal in frequency domain by convolving with a smoothed boxcar filter. This can be achieved in time domain by multiplying with the corresponding window.
In each bin, we hope there is only one mode. Then using the matrix pencil method, we can identify each bit of the mode frequency and also detect if there is indeed exactly one mode.
We exploit some symmetry to roughly halve the computation cost of the matrix pencil method. We apply SIMD optimization to achieve >=2X speedup.


xAxis: {showMinLabel: null, showMaxLabel: null (auto)}. The last x label should not be displayed (overlap).
xAxis: {showMinLabel: null, showMaxLabel: null (auto)}. The last x label shoule be displayed (not overlap).
xAxis: {showMinLabel: true, showMaxLabel: true}, yAxis: {showMaxLabel: false}. The last x label should be displayed. 100 on y should not be displayed.


Cookie-Fish
Home
Sales
About us
Form Data
Shop Location
Max Number Of Custumer Per Hour
Mix Number Of Custumer Per Hour
Average Cookies Per Hour
Submit
Reset


68-year-old Man Celebrates 30 Children, 70 Grandchildren In Taraba
Loddo, who expressed appreciation to God for the gift, also said the celebration was an opportunity to show the right example on how to bring up children in both scholarship and character.
by SaharaReporters, New York
A Jalingo, Taraba State-based man, 68-year-old Adamu Loddo, has urged parents to ensure proper upbringing of children as he celebrated the gift of 30 surviving children and 70 grandchildren, according to the News Agency of Nigeria.
Loddo, who expressed appreciation to God for the gift, also said the celebration was an opportunity to show the right example on how to bring up children in both scholarship and character.
He said, “I am happy to say that at least 15 of my children and five grandchildren have obtained various degrees from different universities in Nigeria.
“I also derive joy and thank Allah for His favours as several of those children and grandchildren have also memorised the Holy Qur’an.
“I have to do this thanksgiving party (walima) while I am alive not to be silent and other people to do it on my behalf after my death.
“A child that is given appropriate training from home and brought up in the fear of God will not turn to social vices in his later years.
“Before blaming schools or society for anti-social behaviour of our wards, we should examine the type of home training we gave them.


Muslim League Discusses Ayodhya Verdict, NRC Issue With Sonia Gandhi
by Press Trust Of IndiaGeneral News
A delegation of Indian Union Muslim League (IUML) leaders met Congress president Sonia Gandhi on Wednesday and discussed various issues.
Written By Press Trust Of India | Mumbai | Updated On: November 21, 2019 06:31 IST
A delegation of Indian Union Muslim League (IUML) leaders met Congress president Sonia Gandhi on Wednesday and discussed various issues including the recent Supreme Court verdict on Ayodhya title dispute and NRC controversy in Assam. The delegation, led by party's national president KM Kader Mohideen, also took up the abrogation of Article 370 in Jammu and Kashmir and division of the state into two Union Territories -- Jammu and Kashmir and Ladakh, the sources said.
READ | CPI(M) slams Shah's nationwide NRC call, says it is "sectarian & devisive "
IUML, which is the second major ally of the Congress-led United Democratic Front (UDF) in Kerala, expressed its displeasure on the lack of coordination between the two parties on important issues like Ayodhya, Article 370 abrogation and NRC, they said. Though there were reports that discussions on the Congress' move to align with the Shiv Sena in Maharashtra too came up, IUML's MPs PK Kunhalikuttuy and K Navas Kani denied it.
READ | Mamata Banerjee defiant; contradicts Amit Shah's 'nationwide NRC' statement
"We will discuss about that if at all the Congress decides to go with the Shiv Sena for government formation,'' Mr Kunhalakutty told PTI. In a clear indication of joining hands with the Shiv Sena, leaders of the Congress and the NCP on Wednesday expressed confidence of forming a "stable" government in Maharashtra in the coming days.
After a marathon meeting of senior leaders of the two parties at NCP supremo Sharad Pawar's residence, former chief minister and Congress leader Prithviraj Chavan said the alliance is hopeful of ending the spell of political uncertainty in the state and working to provide a stable government.
READ | MASSIVE: 'NRC process will be carried across country,' says Amit Shah in Rajya Sabha


ROS Documentation
ROS (Robot Operating System) provides libraries and tools to help software developers create robot applications. It provides hardware abstraction, device drivers, libraries, visualizers, message-passing, package management, and more. ROS is licensed under an open source, BSD license. »
Presentation Video
You can see the presentation of our project through this link. And you can see turtlebot's button control and navigation through demo video Click the button on the web and the Turtlebot will act accordingly. Button control - the turtlebot can be controlled freely through the stop button. navigation - if you click roomA, self-driving to the location corresponding to roomA. »
Turtlebot
What is a TurtleBot?
TurtleBot is a low-cost, personal robot kit with open-source software. TurtleBot was created at Willow Garage by Melonee Wise and Tully Foote in November 2010. With TurtleBot, you’ll be able to build a robot that can drive around your house, see in 3D, and have enough horsepower to create exciting applications. »
Robotics e-Manual
e-manual of Turtlebot 3.
Turtlebot's overview, feature, and quick start guide help people who are new to it. It also explains the code and description of SLAM, navigation, simulation, etc. that can be done via the Turtlebot. »


CUT(1) User Commands CUT(1) NAME cut - remove sections from each line of files SYNOPSIS cut OPTION... [FILE]... DESCRIPTION Print selected parts of lines from each FILE to standard output. Mandatory arguments to long options are mandatory for short options too. -b, --bytes=LIST select only these bytes -c, --characters=LIST select only these characters -d, --delimiter=DELIM use DELIM instead of TAB for field delimiter -f, --fields=LIST select only these fields; also print any line that contains no delimiter character, unless the -s option is specified -n (ignored) --complement complement the set of selected bytes, characters or fields -s, --only-delimited do not print lines not containing delimiters --output-delimiter=STRING use STRING as the output delimiter the default is to use the input delimiter --help display this help and exit --version output version information and exit Use one, and only one of -b, -c or -f. Each LIST is made up of one range, or many ranges separated by commas. Selected input is written in the same order that it is read, and is written exactly once. Each range is one of: N N'th byte, character or field, counted from 1 N- from N'th byte, character or field, to end of line N-M from N'th to M'th (included) byte, character or field -M from first to M'th (included) byte, character or field With no FILE, or when FILE is -, read standard input. AUTHOR Written by David M. Ihnat, David MacKenzie, and Jim Meyering. REPORTING BUGS Report cut bugs to<EMAIL_ADDRESS>GNU coreutils home page: <http://www.gnu.org/software/coreutils/> General help using GNU software: <http://www.gnu.org/gethelp/> Report cut translation bugs to <http://translationproject.org/team/> COPYRIGHT Copyright © 2011 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO The full documentation for cut is maintained as a Texinfo manual. If the info and cut programs are properly installed at your site, the command info coreutils 'cut invocation' should give you access to the complete manual. GNU coreutils 8.12.197-032bb September 2011 CUT(1)


--- layout: default title: Uncertainty propagation ---
Note to the user: all MatLab code is written in MatLab R2014, and some require additional toolboxes (e.g. the statistics toolbox, which is mentioned in the scripts). In case you don’t have access to MatLab, there is a free alternative called Octave available. Both the ipython notebook and the python scripts are written in Python 3.
Uncertainty propagation can be used to propagate uncertainties of input parameters through models to determine e.g. the output uncertainty. To propagate the input uncertainties, simulation techniques can be used such as Monte Carlo sampling, but more exotic sampling techniques, such as Latin hypercube sampling (Figure 1) can also be used. In additon, a Taylor approximation of the original model can be used to propogate the uncertainties analytically.
Code for performing Monte Carlo sampling (MCS) in matrix-based life cycle assessment (LCA) can be found here:
Matlab/Octave: MatLab code MCS LCA
IPython notebook: IPython code MCS LCA
Python: Python code MCS LCA
Code for performing Analytical uncertainty propagation (AUP) in matrix-based life cycle assessment (LCA) can be found here:
Matlab/Octave: MatLab code AUP LCA
IPython notebook: IPython code AUP LCA
Python: Python code AUP LCA
Figure 1: Density plot of Monte Carlo sampling (MCS), Latin hypercube sampling (LHS) and quasi-Monte Carlo sampling (QMCS) on a 16x16 grid; sample size N=1024. QMCS results in an uniform distributed grid, with 4 realizations in each cell.
The MatLab/Octave code for performing Latin hypercube sampling (LHS) in matrix-based life cycle assessment can be found here: MATLAB code LHS LCA
The MatLab/Octave code for performing Quasi Monte Carlo sampling (QMCS) in matrix-based life cycle assessment can be found here: MATLAB code QMCS LCA
The MatLab/Octave code for performing Fuzzy interval arithmetic (FIA) in matrix-based life cycle assessment can be found here: MATLAB code FIA LCA
Uncertainty propagation can be used to propagate uncertainties of input parameters, even if they are correlated. To propagate the input uncertainties of parameters that are correlated, two techniques are used: normal random and a Taylor approximation of the original model can be used to propogate the uncertainties analytically.
Code for performing Latin hypercube sampling (LHS) in matrix-based life cycle assessment (LCA) with correlated input parametes can be found here:
Matlab/Octave: MatLab code LHS LCA (correlated)
Code for performing Analytical uncertainty propagation (AUP) in matrix-based life cycle assessment (LCA) with correlated input parameters can be found here:
Matlab/Octave: MatLab code AUP LCA (correlated)
Source: PhD thesis Evelyne Groen, An uncertain climate: the value of uncertainty and sensitivity analysis in environmental impact assessment of food, 2016
ISBN: 978-94-6257-755-8; DOI: 10.18174/375497
The MatLab code for performing MCS, LHS, QMCS, FIA and AUP in LCA was used in Methods for uncertainty propagation in life cycle assessment, Environmental Modelling & Software, December 2014 (Volume 62, Pages 316 - 325).
The MatLab code for performing MCS and AUP was used in Methods for global sensitivity analysis in life cycle assessment, accepted for publicaiton, 2016.
The MatLab code for performing uncertainty propagation with correlated input parameters (both the analytic and the sampling approach) was used in Ignoring correlation in uncertainty and sensitivity analysis in life cycle assessment: what is the risk?, Environmental Impact Assessment Review, January 201x (Volume 62, Pages 98 - 109).
The MatLab code for performing MCS was used in Benchmarking nutrient losses of dairy farms: the effect of epistemic uncertainty?, xxx, xxx.
The MatLab code for performing uncertainty propagation in LCA with correlated input parameters was used in Assessing greenhouse gas emissions of milk prodution: which parameters are essential?, The international Journal of Life Cycle Assessment, First online: 31 July, 2016.