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C
CachedResource
- Class in
org.trellisldp.rosid.file
An object that mediates access to the resource cache files.
CachedResource(File, IRI, ResourceData)
- Constructor for class org.trellisldp.rosid.file.
CachedResource
Create a File-based resource reader
compact(IRI, Instant, Instant)
- Method in class org.trellisldp.rosid.file.
FileResourceService
F
FileResourceService
- Class in
org.trellisldp.rosid.file
FileResourceService(Map<String, String>, Map<String, String>, CuratorFramework, Producer<String, String>, EventService, Supplier<String>, Boolean)
- Constructor for class org.trellisldp.rosid.file.
FileResourceService
Create a File-based repository service
FileUtils
- Class in
org.trellisldp.rosid.file
find(File, String, Instant)
- Static method in class org.trellisldp.rosid.file.
VersionedResource
Find the resource at a particular point in time
find(File, IRI)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Retrieve a cached resource, if it exists
find(File, IRI, Instant)
- Static method in class org.trellisldp.rosid.file.
VersionedResource
Find the resource at a particular point in time
G
get(IRI)
- Method in class org.trellisldp.rosid.file.
FileResourceService
get(IRI, Instant)
- Method in class org.trellisldp.rosid.file.
FileResourceService
I
isMemento()
- Method in class org.trellisldp.rosid.file.
VersionedResource
L
LENGTH
- Static variable in class org.trellisldp.rosid.file.
FileUtils
M
MAX
- Static variable in class org.trellisldp.rosid.file.
FileUtils
O
org.trellisldp.rosid.file
- package org.trellisldp.rosid.file
Trellis Rosid: an implementation of the core Trellis API, using file-based persistence
P
partition(String)
- Static method in class org.trellisldp.rosid.file.
FileUtils
Partition an identifier into a directory structure
partition(IRI)
- Static method in class org.trellisldp.rosid.file.
FileUtils
Partition an identifier into a directory structure
R
read(File)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Read the cached resource from a directory
read(File, String, Instant)
- Static method in class org.trellisldp.rosid.file.
VersionedResource
Read the state of the resource data at a particular point in time
read(File, IRI, Instant)
- Static method in class org.trellisldp.rosid.file.
VersionedResource
Read the state of the resource data at a particular point in time
resourceDirectory(Map<String, String>, String)
- Static method in class org.trellisldp.rosid.file.
FileUtils
Get the resource directory for a given identifier
resourceDirectory(Map<String, String>, IRI)
- Static method in class org.trellisldp.rosid.file.
FileUtils
Get the resource directory for a given identifier
S
scan(String)
- Method in class org.trellisldp.rosid.file.
FileResourceService
stream()
- Method in class org.trellisldp.rosid.file.
CachedResource
stream()
- Method in class org.trellisldp.rosid.file.
VersionedResource
stringToQuad(RDF, String)
- Static method in class org.trellisldp.rosid.file.
FileUtils
Parse a string into a Quad
T
tryPurge(IRI)
- Method in class org.trellisldp.rosid.file.
FileResourceService
V
VersionedResource
- Class in
org.trellisldp.rosid.file
An object that mediates access to the resource version files.
VersionedResource(File, IRI, ResourceData, Instant)
- Constructor for class org.trellisldp.rosid.file.
VersionedResource
Create a File-based versioned resource
W
write(File, String)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Write the resource data into a file as JSON
write(File, String, Instant)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Write the resource data into a file as JSON
write(File, Stream<? extends Quad>, Stream<? extends Quad>, Instant)
- Static method in class org.trellisldp.rosid.file.
VersionedResource
Write a stream of added/deleted quads to a resource
write(File, IRI)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Write the resource data into a file as JSON
write(File, IRI, Instant)
- Static method in class org.trellisldp.rosid.file.
CachedResource
Write the resource data into a file as JSON
write(IRI, Stream<? extends Quad>, Stream<? extends Quad>, Instant, Boolean)
- Method in class org.trellisldp.rosid.file.
FileResourceService
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In the last few months I've seen a couple of astonishing and frightening stories about the US. I'm not sure how much of a problem those stories really are.
Police, Agencies and Justice
Faking Terrorism
On Thursday, roughly 67% of prosecutions involving suspected ISIS supporters include evidence from undercover operations, according to The New York Times.
In many cases, agents will seek out people who have somehow demonstrated radical views, and then coax them into plotting an act of terrorism — often providing weapons and money. Before the suspects can carry out their plans, though, they're arrested.
Busiess Insider: The FBI is 'manufacturing terrorism cases' on a greater scale than ever before
Police legally robbing people
It is called "Civil Forfeiture":
More
- John Oliver: Mandatory Minimums
- John Oliver: Death Penalty - costly, they make faults
- John Oliver: Bail
- John Oliver: Municipal Violations
- No Fly List
- John Oliver: Torture
- Guantanamo Bay detention camp
- John Oliver: Elected Judges
- John Oliver: Public Defenders
- not having enough time to properly prepare
Democracy
In the US there seem to be several measures in place solely to make people not being able to vote. And if they can vote, then they can't get what they want with their vote. Namely:
- John Oliver: Voting - voter registration votes which were designed to make minorities vote less
- An overly complicated, unintuitive voting process (John Oliver: Primaries and Caucuses),
- John Oliver: Washington DC Statehood
- John Oliver: Puerto Rico
- Felony disenfranchisement: Making people not being allowed to vote - this seems to be a problem in Germany, too.
- Voter suppression in the United States
- John Oliver: Gerrymandering
- Excluding larger groups of the population by
- Having the day of vote not on Sunday (e.g. Super Tuesday)
- Voter ID laws
- Having extremely long queues in some areas (having to wait several HOURS! - I'm used to be finished in about 10 minutes)
- Tactical voting: People don't vote for the candidate they like best, but for the one they think has the highest chance to win. This would be fixed by ranked-choice voting.
Consumer Safety
Education
- John Oliver: Sex Education
- John Oliver: Native Advertising - I think we have that problem in Germany, too (Apotheken Umschau, if I recall correctly)
- John Oliver: Student Debt
- John Oliver: Texas Republicans. Mary Lee Bruner on the Texas State Board of Education.
- Creationism (e.g. Creation and evolution in public education in the United States)
- John Oliver: The Lottery - Cuts in education spendings which should be filled by gains from Lottery.


If you have 50 different plug types, appliances wouldn't be available and would be very
expensive. But once an electric outlet becomes standardized, many companies can design
appliances, and competition ensues, creating variety and better prices for consumers.
-- Bill Gates
You are given a non-empty list of integers (X).
For this task, you should return a list consisting of only the non-unique elements in this list.
To do so you will need to remove all unique elements (elements which are contained in a given
list only once).
When solving this task, do not change the order of the list.
Example: [1, 2, 3, 1, 3] 1 and 3 non-unique elements and result will be [1, 3, 1, 3].
Input: A list of integers.
Output: An iterable of integers.
Example:
checkio([1, 2, 3, 1, 3]) == [1, 3, 1, 3]
checkio([1, 2, 3, 4, 5]) == []
checkio([5, 5, 5, 5, 5]) == [5, 5, 5, 5, 5]
checkio([10, 9, 10, 10, 9, 8]) == [10, 9, 10, 10, 9]
checkio([2]) == []
How it is used:
This mission will help you to understand how to manipulate arrays,
something that is the basis for solving more complex tasks.
The concept can be easily generalized for real world tasks.
For example: if you need to clarify statistics by removing low frequency elements (noise).
You can find out more about Python arrays in one of our articles featuring lists, tuples, array.array and numpy.array.
Precondition:
0 < len(data) < 1000
View solutions
See the task on CheckiO


Radiative Monte Carlo¶
We assume the supernova is in homologous expansion and we assume that there is photon injection from an inner boundary and we assume an outer boundary where these photons can leave the simulation again.
Montecarlo packets¶
Montecarlo packets have a frequency, angle (\(\mu=\cos{\theta}\) ) and an energy: \(P(\nu, \mu, \epsilon)\). A large number \(n\) are generated at the start of each Montecarlo run in TARDIS by drawing \(\nu\) from a black-body distribution distribution with a \(\mu\) being drawn from a \(\sqrt[2]{z}\) distribution and an energy that is \(1/n\).
These packets are then launched into the simulation and there are two possible outcomes for each packet.
- packet leaves the simulation through the outer bound and count towards the
- spectrum
- packet leaves the simulation through the inner boundary and are lost
- (reabsorbed)
The packets can gain and loose energy throughout the simulation. If these packets scatter (through the various mechanisms), we transform into the comoving frame at that position \(v(r) = r / t_\textrm{explosion}\), where \(t_explosion\) is the time since explosion with the doppler factor \(d_\textrm{rest \rightarrow comoving}\) then change direction from \(\mu_\textrm{in}\) to \(mu_\textrm{out}\) and transform back and change the energy accordingly:
This way the montecarlo packets can gain or loose energy in the simulation:
(Source code, png, hires.png, pdf)
The spectrum is then generated as a weighted histogram. For each bin with edges \(\nu_{n}, \nu_{n+1}\) we get all the packets that left the simulation through the outer boundary and add up their remaining energies.
Montecarlo Geometry¶
- Before any packet action is performed we calculate four different distances
- ( \(d_\textrm{inner}, d_\textrm{outer}, d_\textrm{line}, d_{\textrm{e}^{-}}\) )
The calculations for the distance to the outer boundary:
The calculations for the distance to the inner boundary:
Radiationfield estimators¶
During the monte-carlo run we collect two estimators for the radiation field:
where \(\epsilon, \nu\) are comoving energy and comoving frequency of a packet respectively.
To calculate the temperature and dilution factor we first calculate the mean intensity in each cell ( \(J = \frac{1}{4\pi\, \Delta t\, V} J_\textrm{estimator}\) )., [2003A&A...403..261L].
The weighted mean frequency is used to obtain the radiation temperature. Specifically, the radiation temperature is chosen as the temperature of a black body that has the same weighted mean frequency as has been computed in the simulation. Accordingly,
where the evaluation comes from the mean value of
and so
With the radiation temperature known, we can then obtain our estimate for for the dilution factor. Our radiation field model in the nebular approximation is
i.e. a dilute blackbody. Therefore we use our value of the mean intensity derrived from the estimator (above) to obtain the dilution factor
There endeth the lesson.


Low on Time? Skip the log in for a Non-Persisted Macro
(This Macro will NOT be saved)
MacroMatic is a SPA syntax generator for common macro-supported entertainment applications. Model design has been structured in a way to allow for additional applicaiton-syntaxes to be supported.
The application is still in its early stages of development, and YOU have the opportunity to shape its feature growth.
Contact me about any of new features you would like to see, or current features you want improved.
Macro syntax can wildly vary from applicaiton to applicaiton; here is list of the applications currenlty supoorted:


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Temperature current: , Average: , Target: Heat source is --- Control program is ---
Enabled Settings Auto Refresh History Edit Profiles View Logs


1D1F: Wenchi Municipal Assembly to get biscuit, chocolate factories
The chief and people of the Wenchi Municipal Assembly in the Bono Region will soon have a biscuit and chocolate factories. These projects are under government’s One District One Factory initiative.
Kofi Appiah Frimpong, the designated Chief Executive Officer for the factories who spoke about the factories has given the indication that the first stage of the project when completed will employ about 500 workers.
Mr Frimpong was speaking at a stakeholder meeting held at Wenchi, the Municipal’s capital, between investors and the District Implementation Committee of the 1D1F.
He revealed that an amount of $ 2.1 million dollars was expected to be invested in the construction of the factories.
The factory when constructed will produce chocolate, biscuits, drinks and honey jams for the local and international markets.


Zend Framework
LICENSE
This source file is subject to the new BSD license that is bundled with this package in the file LICENSE.txt. It is also available through the world-wide-web at this URL: http://framework.zend.com/license/new-bsd If you did not receive a copy of the license and are unable to obtain it through the world-wide-web, please send an email to<EMAIL_ADDRESS>so we can send you a copy immediately.
string|null
$_defaultField= ''
Default field for the context.
null means, that term should be searched through all fields Zend_Search_Lucene_Search_Query::rewriteQuery($index) transletes such queries to several
array
$_entries= 'array'
Query entries Each entry is a Zend_Search_Lucene_Search_QueryEntry object or boolean operator (Zend_Search_Lucene_Search_QueryToken class constant)
array
Detailsboolean
$_nextEntrySign= 'null'
True means, that term is required.
False means, that term is prohibited. null means, that term is neither prohibited, nor required
null
Details__construct(
string $encoding, string|null $defaultField
=
null
)
:
void
Context object constructor
| Name | Type | Description |
|---|---|---|
| $encoding | string | |
| $defaultField | string|null |
_booleanExpressionQuery(
)
:
\Zend_Search_Lucene_Search_Query
Generate 'boolean style' query from the context
'term1 and term2 or term3 and (
| Type | Description |
|---|---|
| \Zend_Search_Lucene_Search_Query |
| Exception | Description |
|---|---|
| \Zend_Search_Lucene |
_signStyleExpressionQuery(
)
:
\Zend_Search_Lucene_Search_Query
Generate 'signs style' query from the context
'+term1 term2 -term3 +(
| Type | Description |
|---|---|
| \Zend_Search_Lucene_Search_Query |
addEntry(
\Zend_Search_Lucene_Search_QueryEntry $entry
)
:
void
Add entry to a query
| Name | Type | Description |
|---|---|---|
| $entry | \Zend_Search_Lucene_Search_QueryEntry |
addLogicalOperator(
integer $operator
)
:
void
Process logical operator
| Name | Type | Description |
|---|---|---|
| $operator | integer |
boost(
float $boostFactor
)
:
void
Set boost factor to the entry
| Name | Type | Description |
|---|---|---|
| $boostFactor | float |
getQuery(
)
:
\Zend_Search_Lucene_Search_Query
Generate query from current context
| Type | Description |
|---|---|
| \Zend_Search_Lucene_Search_Query |
processFuzzyProximityModifier(
$parameter
=
null
)
:
void
Process fuzzy search or proximity search modifier
| Name | Type | Description |
|---|---|---|
| $parameter |
| Exception | Description |
|---|---|
| \Zend_Search_Lucene_Search_QueryParserException |
setNextEntryField(
string $field
)
:
void
Set field for next entry
| Name | Type | Description |
|---|---|---|
| $field | string |
setNextEntrySign(
integer $sign
)
:
void
Set sign for next entry
| Name | Type | Description |
|---|---|---|
| $sign | integer |
| Exception | Description |
|---|---|
| \Zend_Search_Lucene_Exception |


Call germline SNPs and indels via local re-assembly of haplotypes
The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. In other words, whenever the program encounters a region showing signs of variation, it discards the existing mapping information and completely reassembles the reads in that region. This allows the HaplotypeCaller to be more accurate when calling regions that are traditionally difficult to call, for example when they contain different types of variants close to each other. It also makes the HaplotypeCaller much better at calling indels than position-based callers like UnifiedGenotyper.
In the so-called GVCF mode used for scalable variant calling in DNA sequence data, HaplotypeCaller runs per-sample to generate an intermediate genomic gVCF (gVCF), which can then be used for joint genotyping of multiple samples in a very efficient way, which enables rapid incremental processing of samples as they roll off the sequencer, as well as scaling to very large cohort sizes (e.g. the 92K exomes of ExAC).
In addition, HaplotypeCaller is able to handle non-diploid organisms as well as pooled experiment data. Note however that the algorithms used to calculate variant likelihoods is not well suited to extreme allele frequencies (relative to ploidy) so its use is not recommended for somatic (cancer) variant discovery. For that purpose, use MuTect2 instead.
Finally, HaplotypeCaller is also able to correctly handle the splice junctions that make RNAseq a challenge for most variant callers.
The program determines which regions of the genome it needs to operate on, based on the presence of significant evidence for variation.
For each ActiveRegion, the program builds a De Bruijn-like graph to reassemble the ActiveRegion, and identifies what are the possible haplotypes present in the data. The program then realigns each haplotype against the reference haplotype using the Smith-Waterman algorithm in order to identify potentially variant sites.
For each ActiveRegion, the program performs a pairwise alignment of each read against each haplotype using the PairHMM algorithm. This produces a matrix of likelihoods of haplotypes given the read data. These likelihoods are then marginalized to obtain the likelihoods of alleles for each potentially variant site given the read data.
For each potentially variant site, the program applies Bayes' rule, using the likelihoods of alleles given the read data to calculate the likelihoods of each genotype per sample given the read data observed for that sample. The most likely genotype is then assigned to the sample.
Input bam file(s) from which to make calls
Either a VCF or gVCF file with raw, unfiltered SNP and indel calls. Regular VCFs must be filtered either by variant recalibration (best) or hard-filtering before use in downstream analyses. If using the reference-confidence model workflow for cohort analysis, the output is a GVCF file that must first be run through GenotypeGVCFs and then filtering before further analysis.
These are example commands that show how to run HaplotypeCaller for typical use cases. Square brackets ("[ ]") indicate optional arguments.
These Read Filters are automatically applied to the data by the Engine before processing by HaplotypeCaller.
This tool can be run in multi-threaded mode using this option.
This tool applies the following downsampling settings by default.
This tool uses ActiveRegions on the reference.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Inputs | |||
| --alleles |
none | The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES | |
| --dbsnp -D |
none | dbSNP file | |
| Optional Outputs | |||
| --activeRegionOut -ARO |
NA | Output the active region to this IGV formatted file | |
| --activityProfileOut -APO |
NA | Output the raw activity profile results in IGV format | |
| --graphOutput -graph |
NA | Write debug assembly graph information to this file | |
| --out -o |
stdout | File to which variants should be written | |
| Optional Parameters | |||
| --contamination_fraction_to_filter -contamination |
0.0 | Fraction of contamination in sequencing data (for all samples) to aggressively remove | |
| --genotyping_mode -gt_mode |
DISCOVERY | Specifies how to determine the alternate alleles to use for genotyping | |
| --group -G |
[StandardAnnotation, StandardHCAnnotation] | One or more classes/groups of annotations to apply to variant calls | |
| --heterozygosity -hets |
0.001 | Heterozygosity value used to compute prior likelihoods for any locus | |
| --indel_heterozygosity -indelHeterozygosity |
1.25E-4 | Heterozygosity for indel calling | |
| --maxReadsInRegionPerSample |
10000 | Maximum reads in an active region | |
| --min_base_quality_score -mbq |
10 | Minimum base quality required to consider a base for calling | |
| --minReadsPerAlignmentStart -minReadsPerAlignStart |
10 | Minimum number of reads sharing the same alignment start for each genomic location in an active region | |
| --output_mode -out_mode |
EMIT_VARIANTS_ONLY | Specifies which type of calls we should output | |
| --sample_name -sn |
NA | Name of single sample to use from a multi-sample bam | |
| --sample_ploidy -ploidy |
2 | Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). | |
| --standard_min_confidence_threshold_for_calling -stand_call_conf |
30.0 | The minimum phred-scaled confidence threshold at which variants should be called | |
| --standard_min_confidence_threshold_for_emitting -stand_emit_conf |
30.0 | The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) | |
| Optional Flags | |||
| --annotateNDA -nda |
false | If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site | |
| Advanced Inputs | |||
| --activeRegionIn -AR |
NA | Use this interval list file as the active regions to process | |
| --comp |
[] | Comparison VCF file | |
| Advanced Outputs | |||
| --bamOutput -bamout |
NA | File to which assembled haplotypes should be written | |
| Advanced Parameters | |||
| --activeProbabilityThreshold -ActProbThresh |
0.002 | Threshold for the probability of a profile state being active. | |
| --activeRegionExtension |
NA | The active region extension; if not provided defaults to Walker annotated default | |
| --activeRegionMaxSize |
NA | The active region maximum size; if not provided defaults to Walker annotated default | |
| --annotation -A |
[] | One or more specific annotations to apply to variant calls | |
| --bamWriterType |
CALLED_HAPLOTYPES | Which haplotypes should be written to the BAM | |
| --bandPassSigma |
NA | The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default | |
| --contamination_fraction_per_sample_file -contaminationFile |
NA | Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be " |
|
| --emitRefConfidence -ERC |
false | Mode for emitting reference confidence scores | |
| --excludeAnnotation -XA |
[] | One or more specific annotations to exclude | |
| --gcpHMM |
10 | Flat gap continuation penalty for use in the Pair HMM | |
| --GVCFGQBands -GQB |
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] | GQ thresholds for reference confidence bands | |
| --indelSizeToEliminateInRefModel -ERCIS |
10 | The size of an indel to check for in the reference model | |
| --input_prior -inputPrior |
[] | Input prior for calls | |
| --kmerSize |
[10, 25] | Kmer size to use in the read threading assembler | |
| --max_alternate_alleles -maxAltAlleles |
6 | Maximum number of alternate alleles to genotype | |
| --max_num_PL_values -maxNumPLValues |
100 | Maximum number of PL values to output | |
| --maxNumHaplotypesInPopulation |
128 | Maximum number of haplotypes to consider for your population | |
| --minDanglingBranchLength |
4 | Minimum length of a dangling branch to attempt recovery | |
| --minPruning |
2 | Minimum support to not prune paths in the graph | |
| --numPruningSamples |
1 | Number of samples that must pass the minPruning threshold | |
| --pcr_indel_model -pcrModel |
CONSERVATIVE | The PCR indel model to use | |
| --phredScaledGlobalReadMismappingRate -globalMAPQ |
45 | The global assumed mismapping rate for reads | |
| Advanced Flags | |||
| --allowNonUniqueKmersInRef |
false | Allow graphs that have non-unique kmers in the reference | |
| --allSitePLs |
false | Annotate all sites with PLs | |
| --consensus |
false | 1000G consensus mode | |
| --debug |
false | Print out very verbose debug information about each triggering active region | |
| --disableOptimizations |
false | Don't skip calculations in ActiveRegions with no variants | |
| --doNotRunPhysicalPhasing |
false | Disable physical phasing | |
| --dontIncreaseKmerSizesForCycles |
false | Disable iterating over kmer sizes when graph cycles are detected | |
| --dontTrimActiveRegions |
false | If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping | |
| --dontUseSoftClippedBases |
false | Do not analyze soft clipped bases in the reads | |
| --emitDroppedReads -edr |
false | Emit reads that are dropped for filtering, trimming, realignment failure | |
| --forceActive |
false | If provided, all bases will be tagged as active | |
| --useAllelesTrigger -allelesTrigger |
false | Use additional trigger on variants found in an external alleles file | |
| --useFilteredReadsForAnnotations |
false | Use the contamination-filtered read maps for the purposes of annotating variants |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Threshold for the probability of a profile state being active.
Double 0.002 [ [ 0 1 ] ]
The active region extension; if not provided defaults to Walker annotated default
Integer NA
Use this interval list file as the active regions to process
List[IntervalBinding[Feature]] NA
The active region maximum size; if not provided defaults to Walker annotated default
Integer NA
Output the active region to this IGV formatted file
If provided, this walker will write out its active and inactive regions
to this file in the IGV formatted TAB deliminated output:
http://www.broadinstitute.org/software/igv/IGV
Intended to make debugging the active region calculations easier
PrintStream NA
Output the raw activity profile results in IGV format
If provided, this walker will write out its activity profile (per bp probabilities of being active)
to this file in the IGV formatted TAB deliminated output:
http://www.broadinstitute.org/software/igv/IGV
Intended to make debugging the activity profile calculations easier
PrintStream NA
The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
Allow graphs that have non-unique kmers in the reference
By default, the program does not allow processing of reference sections that contain non-unique kmers. Disabling
this check may cause problems in the assembly graph.
boolean false
Annotate all sites with PLs
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_SITES output mode is set, when we set this argument then we will also emit PLs at all sites.
This will give a measure of reference confidence and a measure of which alt alleles are more plausible (if any).
WARNINGS:
- This feature will inflate VCF file size considerably.
- All SNP ALT alleles will be emitted with corresponding 10 PL values.
- An error will be emitted if EMIT_ALL_SITES is not set, or if anything other than diploid SNP model is used
boolean false
If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.
boolean false
One or more specific annotations to apply to variant calls
Which annotations to add to the output VCF file. The single value 'none' removes the default annotations.
See the VariantAnnotator -list argument to view available annotations.
List[String] []
File to which assembled haplotypes should be written
The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. This is
intended to be used only for troubleshooting purposes, in specific areas where you want to better understand
why the caller is making specific calls. Turning on this mode may result in serious performance cost for the
caller, so we do NOT recommend using this argument systematically as it will significantly increase runtime.
The candidate haplotypes (called or all, depending on mode) are emitted as single reads covering the entire
active region, coming from sample "HC" and a special read group called "ArtificialHaplotype". This will increase
the pileup depth compared to what would be expected from the reads only, especially in complex regions.
The reads are written out containing an "HC" tag (integer) that encodes which haplotype each read best matches
according to the haplotype caller's likelihood calculation. The use of this tag is primarily intended
to allow good coloring of reads in IGV. Simply go to "Color Alignments By > Tag" and enter "HC" to more
easily see which reads go with these haplotype. You can also tell IGV to group reads by sample, which will
separate the potential haplotypes from the reads. These features are illustrated in
this screenshot.
Note that only reads that are actually informative about the haplotypes are emitted with the HC tag.
By informative we mean that there's a meaningful difference in the likelihood of the read coming from one
haplotype compared to the next best haplotype. When coloring reads by HC tag in IGV, uninformative reads will
remain grey.
Note also that not every input read is emitted to the bam in this mode. To include all trimmed, downsampled,
filtered and uninformative reads, add the --emitDroppedReads
argument.
If multiple BAMs are passed as input to the tool (as is common for MuTect2), then they will be combined in the
-bamout
output and tagged with the appropriate sample names.
GATKSAMFileWriter NA
Which haplotypes should be written to the BAM
The type of -bamout
output we want to see. This determines whether HC will write out all of the haplotypes it
considered (top 128 max) or just the ones that were selected as alleles and assigned to samples.
The --bamWriterType argument is an enumerated type (Type), which can have one of the following values:
Type CALLED_HAPLOTYPES
The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default
Double NA
Comparison VCF file
If a call overlaps with a record from the provided comp track, the INFO field will be annotated
as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are
filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
List[RodBinding[VariantContext]] []
1000G consensus mode
This argument is specifically intended for 1000G consensus analysis mode. Setting this flag will inject all
provided alleles to the assembly graph but will not forcibly genotype all of them.
boolean false
Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be "
This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples.
Samples that do not appear in this file will be processed with CONTAMINATION_FRACTION.
File NA
Fraction of contamination in sequencing data (for all samples) to aggressively remove
If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we
will try to remove (N * contamination fraction) bases for each alternate allele.
double 0.0 [ [ -∞ ∞ ] ]
dbSNP file
rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
dbSNP is not used in any way for the calculations themselves.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
Print out very verbose debug information about each triggering active region
boolean false
Don't skip calculations in ActiveRegions with no variants
If set, certain "early exit" optimizations in HaplotypeCaller, which aim to save compute and time by skipping
calculations if an ActiveRegion is determined to contain no variants, will be disabled. This is most likely to be
useful if you're using the -bamout
argument to examine the placement of reads following reassembly
and are interested in seeing the mapping of reads in regions with no variations. Setting the -forceActive
and -dontTrimActiveRegions
flags may also be helpful.
boolean false
Disable physical phasing
As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.
boolean false
Disable iterating over kmer sizes when graph cycles are detected
When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are
resolved. Disabling this behavior may cause the program to give up on assembling the ActiveRegion.
boolean false
If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping
boolean false
Do not analyze soft clipped bases in the reads
boolean false
Emit reads that are dropped for filtering, trimming, realignment failure
Determines whether dropped reads will be tracked and emitted when -bamout
is specified. Use this in combination
with a specific interval of interest to avoid accumulating a large number of reads in the -bamout
file.
boolean false
Mode for emitting reference confidence scores
Records whether the trimming intervals are going to be used to emit reference confidence, {@code true},
or regular HC output {@code false}.
The --emitRefConfidence argument is an enumerated type (ReferenceConfidenceMode), which can have one of the following values:
ReferenceConfidenceMode false
One or more specific annotations to exclude
Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the
-A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
options. When HaplotypeCaller is run with -ERC GVCF or -ERC BP_RESOLUTION, some annotations are excluded from the
output by default because they will only be meaningful once they have been recalculated by GenotypeGVCFs. As
of version 3.3 this concerns ChromosomeCounts, FisherStrand, StrandOddsRatio and QualByDepth.
List[String] []
If provided, all bases will be tagged as active
For the active region walker to treat all bases as active. Useful for debugging when you want to force something like
the HaplotypeCaller to process a specific interval you provide the GATK
boolean false
Flat gap continuation penalty for use in the Pair HMM
int 10 [ [ -∞ ∞ ] ]
Specifies how to determine the alternate alleles to use for genotyping
The --genotyping_mode argument is an enumerated type (GenotypingOutputMode), which can have one of the following values:
GenotypingOutputMode DISCOVERY
Write debug assembly graph information to this file
This argument is meant for debugging and is not immediately useful for normal analysis use.
PrintStream NA
One or more classes/groups of annotations to apply to variant calls
Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because
it obscures the specific requirements of individual annotations. Any requirements that are not met (e.g. failing
to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
List[String] [StandardAnnotation, StandardHCAnnotation]
GQ thresholds for reference confidence bands
When HC is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference
sites are compressed into bands of similar genotype quality (GQ) that are emitted as a single VCF record. See
the FAQ documentation for more details about the GVCF format.
This argument allows you to set the GQ boundaries. HC expects a list of multiple GQ threshold values. To pass
multiple values, you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on. Note
that GQ values are capped at 99 in the GATK.
List[Integer] [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99]
Heterozygosity value used to compute prior likelihoods for any locus
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
From the heterozygosity we calculate the probability of N samples being hom-ref at a site as 1 - sum_i_2N (hets / i)
where hets is this case is analogous to the parameter theta from population genetics. See https://en.wikipedia.org/wiki/Coalescent_theory for more details.
Note that heterozygosity as used here is the population genetics concept. (See http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics.
We also suggest the book "Population Genetics: A Concise Guide" by John H. Gillespie for further details on the theory.) That is, a hets value of 0.001
implies that two randomly chosen chromosomes from the population of organisms would differ from each other at a rate of 1 in 1000 bp.
The default priors provided for humans (hets = 1e-3)
Also note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype,
which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there
may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK
only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the
het parameters only increases the chance that a site will be called non-reference across all samples, but
doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all.
The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy,
which determines how many chromosomes each individual in the species carries.
Double 0.001 [ [ -∞ ∞ ] ]
Heterozygosity for indel calling
This argument informs the prior probability of having an indel at a site.
double 1.25E-4 [ [ -∞ ∞ ] ]
The size of an indel to check for in the reference model
This parameter determines the maximum size of an indel considered as potentially segregating in the
reference model. It is used to eliminate reads from being indel informative at a site, and determines
by that mechanism the certainty in the reference base. Conceptually, setting this parameter to
X means that each informative read is consistent with any indel of size < X being present at a specific
position in the genome, given its alignment to the reference.
int 10 [ [ -∞ ∞ ] ]
Input prior for calls
By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model,
see e.g. Waterson (1975) or Tajima (1996).
This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N
There are instances where using this prior might not be desirable, e.g. for population studies where prior might not be appropriate,
as for example when the ancestral status of the reference allele is not known.
By using this argument, the user can manually specify a list of probabilities for each AC>1 to be used as priors for genotyping,
with the following restrictions:
a) User must specify 2N values, where N is the number of samples.
b) Only diploid calls supported.
c) Probability values are specified in Double format, in linear space (not log10 space or Phred-scale).
d) No negative values allowed.
e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one.
f) If user-defined values add to more than one, an error will be produced.
If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g.
-inputPrior 0.33 -inputPrior 0.33
for the single-sample diploid case.
List[Double] []
Kmer size to use in the read threading assembler
Multiple kmer sizes can be specified, using e.g. `-kmerSize 10 -kmerSize 25`.
List[Integer] [10, 25]
Maximum number of alternate alleles to genotype
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN_ALLELES),
then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend
that you not play around with this parameter.
As of GATK 2.2 the genotyper can handle a very large number of events, so the default maximum has been increased to 6.
int 6 [ [ -∞ ∞ ] ]
Maximum number of PL values to output
Determines the maximum number of PL values that will be logged in the output. If the number of genotypes
(which is determined by the ploidy and the number of alleles) exceeds the value provided by this argument,
then output of all of the PL values will be suppressed.
int 100 [ [ -∞ ∞ ] ]
Maximum number of haplotypes to consider for your population
The assembly graph can be quite complex, and could imply a very large number of possible haplotypes. Each haplotype
considered requires N PairHMM evaluations if there are N reads across all samples. In order to control the
run of the haplotype caller we only take maxNumHaplotypesInPopulation paths from the graph, in order of their
weights, no matter how many paths are possible to generate from the graph. Putting this number too low
will result in dropping true variation because paths that include the real variant are not even considered.
You can consider increasing this number when calling organisms with high heterozygosity.
int 128 [ [ -∞ ∞ ] ]
Maximum reads in an active region
When downsampling, level the coverage of the reads in each sample to no more than maxReadsInRegionPerSample reads,
not reducing coverage at any read start to less than minReadsPerAlignmentStart
int 10000 [ [ -∞ ∞ ] ]
Minimum base quality required to consider a base for calling
Bases with a quality below this threshold will not be used for calling.
byte 10 [ [ -∞ ∞ ] ]
Minimum length of a dangling branch to attempt recovery
When constructing the assembly graph we are often left with "dangling" branches. The assembly engine attempts to rescue these branches
by merging them back into the main graph. This argument describes the minimum length of a dangling branch needed for the engine to
try to rescue it. A smaller number here will lead to higher sensitivity to real variation but also to a higher number of false positives.
int 4 [ [ -∞ ∞ ] ]
Minimum support to not prune paths in the graph
Paths with fewer supporting kmers than the specified threshold will be pruned from the graph.
Be aware that this argument can dramatically affect the results of variant calling and should only be used with great caution.
Using a prune factor of 1 (or below) will prevent any pruning from the graph, which is generally not ideal; it can make the
calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph). Higher values
tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher
depth to produce calls).
int 2 [ [ -∞ ∞ ] ]
Minimum number of reads sharing the same alignment start for each genomic location in an active region
int 10 [ [ -∞ ∞ ] ]
Number of samples that must pass the minPruning threshold
If fewer samples than the specified number pass the minPruning threshold for a given path, that path will be eliminated from the graph.
int 1 [ [ -∞ ∞ ] ]
File to which variants should be written
A raw, unfiltered, highly sensitive callset in VCF format.
VariantContextWriter stdout
Specifies which type of calls we should output
The --output_mode argument is an enumerated type (OutputMode), which can have one of the following values:
OutputMode EMIT_VARIANTS_ONLY
The PCR indel model to use
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts.
The correction is based on the reference context, and acts specifically around repetitive sequences that tend
to cause PCR errors). The variant likelihoods are penalized in increasing scale as the context around a
putative indel is more repetitive (e.g. long homopolymer). The correction can be disabling by specifying
'-pcrModel NONE'; in that case the default base insertion/deletion qualities will be used (or taken from the
read if generated through the BaseRecalibrator). VERY IMPORTANT: when using PCR-free sequencing data we
definitely recommend setting this argument to NONE.
The --pcr_indel_model argument is an enumerated type (PCR_ERROR_MODEL), which can have one of the following values:
PCR_ERROR_MODEL CONSERVATIVE
The global assumed mismapping rate for reads
The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their
mapping quality. This term effects the probability that a read originated from the reference haplotype, regardless of
its edit distance from the reference, in that the read could have originated from the reference haplotype but
from another location in the genome. Suppose a read has many mismatches from the reference, say like 5, but
has a very high mapping quality of 60. Without this parameter, the read would contribute 5 * Q30 evidence
in favor of its 5 mismatch haplotype compared to reference, potentially enough to make a call off that single
read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype
that this (and any) read could contribute is Q30.
Set this term to any negative number to turn off the global mapping rate.
int 45 [ [ -∞ ∞ ] ]
Name of single sample to use from a multi-sample bam
You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
is especially useful if your samples are all in the same file but you need to run them individually through HC
in -ERC GVC mode (which is the recommended usage). Note that the name is case-sensitive.
String NA
Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy
int 2 [ [ -∞ ∞ ] ]
The minimum phred-scaled confidence threshold at which variants should be called
The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
is the default).
double 30.0 [ [ -∞ ∞ ] ]
The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)
This argument allows you to emit low quality calls as filtered records.
double 30.0 [ [ -∞ ∞ ] ]
Use additional trigger on variants found in an external alleles file
boolean false
Use the contamination-filtered read maps for the purposes of annotating variants
boolean false
See also GATK Documentation Index | Tool Docs Index | Support Forum
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.


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Abu Faraj al-Libyaka Dr. TaufeekHelp wanted: Top terrorist network seeks operational planner. Must have eye for detail, strong work ethic and a thirst for blood. Five to ten years experience, Afghan war a plus. Resemblance to Michael Jackson a plus. Requires masters degree. Salary commensurate with experience. Not an equal opportunity employer.When the government of Pakistan arrested al Qaeda's top military mind, Khalid Shaikh Mohammed, it created a void. After all, the media needs someone to describe as the "mastermind" of any given terrorist attack, whatever that's supposed to mean. Like Richard M. Nixon, Khalid Shaikh was a hard act to follow. Abu Faraj al-Liby could be therefore be considered the Gerald Ford of international terrorism -- although his reign was short and undistinguished, there is a certain historical cachet that comes with simply having the job. Born in Libya, Faraj was KSM's protege. He helped Khalid organize the September 11 attack, in some unknown capacity, perhaps fetching coffee and making Xeroxes. Before his arrest, Faraj's most famous characteristic was a bad case of vitiglio, the skin disease that allegedly transformed Michael Jackson from a black man into an almost-white man. It's not every al Qaeda kingpin who can claim solidarity with the Wacko Jacko, the King of Pop. As far as the West was concerned, Faraj barely existed until 2003, when a series of suspects were arrested around the world, and all of them appeared to be taking orders from the same guy. Most of the Libyan's known exploits were based in Southeast Asia and Northern Africa, where he served as al Qaeda's regional commander. North Africa isn't a bad job to have on your terrorist resume. During his tour of duty, Faraj saw years of extensive infrastructure-building and the execution of a few high-profile attacks on U.S. interests in Somalia and in Tanzania and Kenya. He once served as an assistant to Osama bin Laden, probably while al Qaeda was based in the Sudan during the early 1990s. At some point, Faraj became a deputy to KSM. His contacts stretched around the world, including sleeper cells in Great Britain and the United States. He is also known as "Dr. Taufeek" (Taufiq, Taufeeq, an Arabic name meaning "prosperity"). Presumably Faraj is not the same Dr. Taufiq who routinely offers to send illicit Nigerian oil millions to e-mail recipients who provide a bank account number. After assuming military command of al Qaeda, Faraj hung his hat in Pakistan. His extended visit to the country was a violent one, but he worked to make the country into a more hospitable environment with such political initiatives as his repeated attempts to assassinate Pakistan's president Pervez Musharraf. Musharraf, a virtual dictator who seized power through a military coup, is not an ideal leader by American standards, but he's better than some of the alternatives (and worse than many others). A successful assassination could plunge Pakistan into a civil war, or even worse, allow the sizable contingent of radical Islamists (and al Qaeda sympathizers) in the Pakistani army to seize control of the military -- and Pakistan's nuclear arsenal. Faraj hid out along the border between Pakistan and Afghanistan, where tribal chiefs are the only effective legal authority and the Pakistani military has trouble operating. Al Qaeda's most prominent leaders, bin Laden and Ayman Al-Zawahiri, are also suspected of operating in the region, although the direct evidence for this contention is remarkably slim. The U.S. botched a golden opportunity to collect intelligence on Faraj during the summer of 2004, when a leak exposed a double agent who had been in contact with the Libyan while working for the CIA. Muhammad Naeem Noor Khan was an al Qaeda computer systems expert, who coordinated operations via e-mail from his home base in Karachi, Pakistan. Khan took messages verbally and in writing from top al Qaeda leaders along the Pakistan-Afghanistan border, then encrypted and e-mailed them. Khan processed message traffic for the elite of al Qaeda, including bin Laden, Zawahiri and Faraj, until a story in the New York Times trumpeted his arrest and blew Khan's cover, ending the fruitful operation. Despite this mishap, the Pakistanis finally caught up with Faraj in the spring of 2005 -- or so the story goes. The Pakistanis announced the arrest rather gleefully, prompting an effusive bout of praise from the Bush Administration -- yet another X through the picture of a "senior al Qaeda leader" racked up on the scorecard GW keeps in his desk drawer. Except that the arrest may not have been what it seemed. About a week after the trimphant announcement, rumors began to spread (starting with a report in the Times of London) that the captured al Qaeda operative had been Anas al-Liby, one of the planners of the 1998 African embassy bombings, and not Faraj al-Liby. Both men were, after all, from Libya, and all Libyans look alike. Like Faraj, Anas al-Liby also has a disfigured face, but there's a big difference between having a scar and having vitiglio. After a year of silence on this topic, it appears likely Faraj was actually the guy the Pakistanis apprehended, but then the recriminations about his importance began. Was he al Qaeda's No. 3 commander, as officials claimed? (Probably not. It's not even clear al Qaeda [[mind control and murder cults|works that way].) The Times quoted a bin Laden associate as saying Faraj used to "he used to make the coffee and do the photocopying." It wasn't clear whether Faraj or Anas was the No. 3 guy, if there was a No. 3 guy, or whether one of the half-dozen other guys labeled "al Qaeda's No. 3" might be the actual No. 3, if there ever was such a thing. Regardless of whether Faraj was enriching uranium or straining grounds out of the coffee pot, he appears to be out of the loop now. Fortunately, there is an apparently unending supply of "senior al Qaeda leaders" to fill the gap when one drops out. Pakistan wanted to keep al-Liby for trial, what with the assassination attempts and everything, but they caved and turned him over to the U.S. in June 2005, which promptly deposited him in secret CIA prison in an undisclosed location. Needless to say, Faraj al-Liby will never be seen again if the Bush Administration has its way. But "never" is just another word for 2009, when a new president will step in and presumably try to pick up whatever shattered pieces of the Constitution haven't been already been ground into dust.
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The implications of this would seem to me to be quite colossal. [If a man could influence inanimate objects by the power of thought,] then surely it becomes more than possible that we all either have within our minds or can be in direct touch with powers so massive as to dwarf our mightiest machines and maybe ultimately to make our whole materialist technology obsolete? In medieval times, the Establishment, faced by such a threat to its orthodox beliefs, would quickly have burnt Uri Geller at the stake. In our more sophisticated modern world The Times simply maintains a dignified silence.
Hamish Scott of London SW10, reading perhaps just a teensy bit too much into the conjuring tricks of Uri Geller, in a letter to The Times in 1973, quoted in Francis Wheen's Strange Days Indeed : The Golden Age Of Paranoia (2009). A more sensible response to Mr Geller was uttered by Tara Palmer-Tomkinson, no less, who secured herself a wee corner in history when, on television early in this century, she uttered the immortal words “These are Uri's underpants. Burn them.” A contemporaneous report can be found here.


Troupe for Windows 0.9.9
- created new msi installer using WIX, so that visual studio is not required for msi build (for continuous integration)
- signed MSI using newly created Troupe Test certificate
- menu doesnt display headings when there are no items in the category
- msi software updates package now installs using passive mode
Troupe for Windows 0.9.8
- menu update and adding and removing invites dynamically
- updated menu layout
- fixed bug where new troupes were not appearing in context menu
- added updates and patches to troupe conversations
- Adding and removing troupes dynamically when user accepts invite or exits an existing troupe
- Signed msi installer package
Troupe for Windows 0.9.7
- cleaned up logging;
- #15: Give the login window a frame
- #21: State is not consistent between the client and the server
- #22: On a fresh install of Win7, with only IE9 installed and no chrome/firefox clicking links crashes the app
- #13: Make the toolbar menu appear for left and right menu clicks
- #16: Sign the application with a strong name, so that people don't get a scary message about an unidentified publisher
- #20: Notifications do not open the browser when clicked;
- Removed unnecessary intermediate software update dialog.
Troupe for Windows version 0.9.6
- still need to fix loggout properly
- installer autostart fixed
- multi instance fixed
- extra logging


Greece to shut overcrowded migrant camps and replace with restricted facilities
by GCTGreece’s government has announced plans to overhaul the country’s migration management system. They are set to replace overcrowded camps on the islands with more restricted facilities and will move 20,000 migrants from the islands to the mainland over the next few weeks.
Greece announced plans on Wednesday to overhaul its migration management system, replacing overcrowded camps on the islands with smaller and more restricted facilities.
Greece’s Prime Minister Kyriakos Mitsotakis and his new government said on Wednesday it would tighten controls at Greece’s borders and speed up the application process.
Deputy Defense Minister Alkiviadis Stefanis announced the changes following a huge rise in the number of arrivals from Turkey, with the number of migrants now exceeding the islands’ populations in some cases.
Government spokesman Stelios Petsas said authorities would create “closed pre-departure centres”, which would make it easier to control the movements of asylum seekers and prevent them from moving to the mainland undetected.
“A clear message should be sent to those planning, or thinking of coming to the country illegally when they aren’t entitled to asylum,” he said.
“They should realise, if they give money to a trafficker to bring them to Greece they will lose it.”
“In the short term, we will return security and control to the areas affected by the crisis,” he added. “Normal life will return to these areas and measures will be taken to safeguard them from future threats, with an emphasis placed on deterrence.”
The planned changes are the most significant since a landmark deal in 2016 between Turkey and the European Union to limit migration to Europe.
Stefanis said the facilities would be ready by July 2020 and referring to pending asylum requests, Stefanis said, “The numbers are huge which is why we introduced a law which from Jan. 1 will speed up the process.”


These select one of 13 modulation sources for the attack time of the {_envelope} generators.
The "self" choice modulates the time by its own instantanous value, which distorts the normal linear shape. Setting this to a positive value makes it slow down as it rises. However, the amount it slows down by is greater for larger envelopes.
These are contained in the {Envelope_attack_cluster Envelope attack clusters} within the {Envelope_sections}.
These are contained in the ENVELOPE 1 and ENVELOPE 2 sections of the right panel, under the following parameter numbers:
| Env 1 | Env 2 | |
| {sw-15.png height=48} | {sw-22.png height=48} |
These appear in the display as Env1/2 Att Mod Select.
These are accessed via the following {_NRPN NRPNs}:
| Env 1 | Env 2 | ||
| A | 1,15 | 1,28 | |
| B | 2,15 | 2,28 |
| MIDI | display | ||
| 0 | +lever 1 | ||
| 1 | +lever 2 | ||
| 2 | \-lever 1 | ||
| 3 | \-lever 2 | ||
| 4 | pedal 1 | ||
| 5 | pedal 2 | ||
| 6 | \-pedal 1 | (bipolar pedal only) | |
| 7 | \-pedal 2 | (bipolar pedal only) | |
| 8 | ribbon | ||
| 9 | pitch | (default) | |
| 10 | velocity | ||
| 11 | pressure | ||
| 12 | self |


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As of
03/16/2017 11:05AM
, the Laws database is current
through 2017
Chapters 1-23
|
General Business
§ 899-aa. Notification; person without valid authorization has
acquired private information. 1. As used in this section, the following
terms shall have the following meanings:
(a) "Personal information" shall mean any information concerning a
natural person which, because of name, number, personal mark, or other
identifier, can be used to identify such natural person;
(b) "Private information" shall mean personal information consisting
of any information in combination with any one or more of the following
data elements, when either the personal information or the data element
is not encrypted, or encrypted with an encryption key that has also been
acquired:
(1) social security number;
(2) driver's license number or non-driver identification card number;
or
(3) account number, credit or debit card number, in combination with
any required security code, access code, or password that would permit
access to an individual's financial account;
"Private information" does not include publicly available information
which is lawfully made available to the general public from federal,
state, or local government records.
(c) "Breach of the security of the system" shall mean unauthorized
acquisition or acquisition without valid authorization of computerized
data that compromises the security, confidentiality, or integrity of
personal information maintained by a business. Good faith acquisition of
personal information by an employee or agent of the business for the
purposes of the business is not a breach of the security of the system,
provided that the private information is not used or subject to
unauthorized disclosure.
In determining whether information has been acquired, or is reasonably
believed to have been acquired, by an unauthorized person or a person
without valid authorization, such business may consider the following
factors, among others:
(1) indications that the information is in the physical possession and
control of an unauthorized person, such as a lost or stolen computer or
other device containing information; or
(2) indications that the information has been downloaded or copied; or
(3) indications that the information was used by an unauthorized
person, such as fraudulent accounts opened or instances of identity
theft reported.
(d) "Consumer reporting agency" shall mean any person which, for
monetary fees, dues, or on a cooperative nonprofit basis, regularly
engages in whole or in part in the practice of assembling or evaluating
consumer credit information or other information on consumers for the
purpose of furnishing consumer reports to third parties, and which uses
any means or facility of interstate commerce for the purpose of
preparing or furnishing consumer reports. A list of consumer reporting
agencies shall be compiled by the state attorney general and furnished
upon request to any person or business required to make a notification
under subdivision two of this section.
2. Any person or business which conducts business in New York state,
and which owns or licenses computerized data which includes private
information shall disclose any breach of the security of the system
following discovery or notification of the breach in the security of the
system to any resident of New York state whose private information was,
or is reasonably believed to have been, acquired by a person without
valid authorization. The disclosure shall be made in the most expedient
time possible and without unreasonable delay, consistent with the
legitimate needs of law enforcement, as provided in subdivision four of
this section, or any measures necessary to determine the scope of the
breach and restore the reasonable integrity of the system.
3. Any person or business which maintains computerized data which
includes private information which such person or business does not own
shall notify the owner or licensee of the information of any breach of
the security of the system immediately following discovery, if the
private information was, or is reasonably believed to have been,
acquired by a person without valid authorization.
4. The notification required by this section may be delayed if a law
enforcement agency determines that such notification impedes a criminal
investigation. The notification required by this section shall be made
after such law enforcement agency determines that such notification does
not compromise such investigation.
5. The notice required by this section shall be directly provided to
the affected persons by one of the following methods:
(a) written notice;
(b) electronic notice, provided that the person to whom notice is
required has expressly consented to receiving said notice in electronic
form and a log of each such notification is kept by the person or
business who notifies affected persons in such form; provided further,
however, that in no case shall any person or business require a person
to consent to accepting said notice in said form as a condition of
establishing any business relationship or engaging in any transaction.
(c) telephone notification provided that a log of each such
notification is kept by the person or business who notifies affected
persons; or
(d) Substitute notice, if a business demonstrates to the state
attorney general that the cost of providing notice would exceed two
hundred fifty thousand dollars, or that the affected class of subject
persons to be notified exceeds five hundred thousand, or such business
does not have sufficient contact information. Substitute notice shall
consist of all of the following:
(1) e-mail notice when such business has an e-mail address for the
subject persons;
(2) conspicuous posting of the notice on such business's web site
page, if such business maintains one; and
(3) notification to major statewide media.
6. (a) whenever the attorney general shall believe from evidence
satisfactory to him that there is a violation of this article he may
bring an action in the name and on behalf of the people of the state of
New York, in a court of justice having jurisdiction to issue an
injunction, to enjoin and restrain the continuation of such violation.
In such action, preliminary relief may be granted under article
sixty-three of the civil practice law and rules. In such action the
court may award damages for actual costs or losses incurred by a person
entitled to notice pursuant to this article, if notification was not
provided to such person pursuant to this article, including
consequential financial losses. Whenever the court shall determine in
such action that a person or business violated this article knowingly or
recklessly, the court may impose a civil penalty of the greater of five
thousand dollars or up to ten dollars per instance of failed
notification, provided that the latter amount shall not exceed one
hundred fifty thousand dollars.
(b) the remedies provided by this section shall be in addition to any
other lawful remedy available.
(c) no action may be brought under the provisions of this section
unless such action is commenced within two years immediately after the
date of the act complained of or the date of discovery of such act.
7. Regardless of the method by which notice is provided, such notice
shall include contact information for the person or business making the
notification and a description of the categories of information that
were, or are reasonably believed to have been, acquired by a person
without valid authorization, including specification of which of the
elements of personal information and private information were, or are
reasonably believed to have been, so acquired.
8. (a) In the event that any New York residents are to be notified,
the person or business shall notify the state attorney general, the
department of state and the division of state police as to the timing,
content and distribution of the notices and approximate number of
affected persons. Such notice shall be made without delaying notice to
affected New York residents.
(b) In the event that more than five thousand New York residents are
to be notified at one time, the person or business shall also notify
consumer reporting agencies as to the timing, content and distribution
of the notices and approximate number of affected persons. Such notice
shall be made without delaying notice to affected New York residents.
9. The provisions of this section shall be exclusive and shall preempt
any provisions of local law, ordinance or code, and no locality shall
impose requirements that are inconsistent with or more restrictive than
those set forth in this section.