 We have already tackled the interaction with the ship wheel for our MVP as well as the anchor last week. This week we continued to work on refining those interactions, as well as implementing the following new ones: raising/lowering sails, bracing sails, and the hoist system to move crates. We chose to implement these interactions through a UI menu rather than physically with ropes (at least for now) because we feel that the menu provides more convenient access. If time permits, we will consider making these interactions more physical, which should not take too much more work since we have the consequences implemented already.
We ran into a couple bugs, however, due to the purchased ship model having origins for individual parts not precisely in the center of each part. This led to issues in rotation for the bracing interaction, as well as bounding boxes being improperly located for the sails when adding a cloth component to them. We were able to fix the rotation issue by going back into the model in Maya and performing the union boolean on all the parts of the mast to make it one object with a central origin. Unfortunately we cannot do the same for the sails as the issue only arises when the cloth component is added. We tried to fix it using the ProBuilder tools, which allows us to center the pivots, however this required a MeshRenderer which conflicted with the SkinnedMeshRenderer which is necessary for the cloth component. We will continue to attempt to fix this bug going forward next week.
We also made progress on the hoist system, modeling our own custom asset for a simple hoist and platform. Our target for next week is modeling the crates to go along with this hoist and make animations for the hoist raising and lowering for the interaction.
Remodeling the World
Having gone back to the drawing board after discovering the limitations in place on the Unity Terrain Engine for optimization during runtime. We found some low poly models to replace the full tiled terrain. WIth the environment assets now consisting of polygon models, we can not only translate, but rotate the environment. While re-prototyping the world, we also discovered that the values used for rotation in the Unity inspector are misleading, they are not he float values stored in a rotation object, called a Quaternion, but a relation of two or more floating point values that create the rotational angle about an axis. This will require up to rethink a few of the core sailing mechanics to properly translate the sail trim, rudder position, and ship speed to values that correctly move the world in response.
Now that we have a world rotation mechanic we will have to deal with the view distance limit of the Oculus Quest to prevent pop-in or dynamic rendering of only part of the landscape as it comes into view. We have an idea or using a fog or a mirage effect. The end goal being that landscapes look as if they are coming over the horizon.
Destination: Interesting
Most of the work has been focused on the ship assets and the backend for multiplayer interactions and sailing mechanics. With these components becoming more robust we can turn our attention to the aesthetics of the environment. Currently we want to have a few destination types, an island resort and a harbor to start. These are going to be caricatures, meaning low modeling detail with focus on features that make them simple to identify, but still add to the overall appeal of the environment.
Sailing in Sound
Now is a great time to add another dimension to our experience: audio. We found sounds for the water, wind, sails, ship, and more that we can add to Hands on Deck. A tutorial showed us how to create an Audio Manager script that we can use to keep all of our sound components under one GameObject, simplifying adding, removing, and replacing sound effects. Some adjustments to the script allow us to make any GameObject a source so that we can implement 3D spatial audio. In addition, we are looking into adding voice chat through Photon Voice 2, the same service we use for multiplayer, so that users of the app won’t have to rely on a third party app for communication. We have run into some difficulties with finding tutorials and thorough documentation, so some discovery is in order. All in all, we’re hoping this new element to Hands on Deck will greatly enhance the experience.
- Work Log -
James: Reworked world modeling component and worked on ship sailing mechanics. Collected assets for low poly environments to replace use of Unity terrain objects.
Patrick: Finished moving progress onto new ship model. Implemented raise/lower sail, brace sail interactions, and modeled a hoist system for the cargo transportation idea.
Abhinav: Found sound effects, created Audio Manager, started adding voice chat with Photon Voice 2.
Julian: Adjusting ship mechanics for the new ship, such as the ship’s wheel. Made tweaks to network scripts for better network performance. Still looking into adjusting player positions across the network.
- Work Plan -
James: Add center of mass calculations to world model for increased boat drift. Build at least 3 points of interest destinations. Layout basic gameplay mechanics and improve VR avatar.
Patrick: Fix cloth bug on new ship sails. Model crates, make animations for hoist interaction.
Abhinav: Finish and test Photon voice chat, help with adding interactions and UI elements to ship.
Julian: Continue optimizing network interactions, look into and hopefully solve slow network updates on world transformation (make it mostly client side, doing rpc call on player join to tell the server to send their world information to new players). Continue bug fixing for incorrect player position across the network. Assist with adding interactions and UI elements.


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S.M. Oliva
Writer
My Recent Work
How I Configured My BunsenLabs Desktop
-- A brief tutorial on customizing
BunsenLabs
, a Debian-based Linux distribution featuring the Openbox window manager.
Contact Me
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Server Roles
– SQL Server administration
Database Roles
– Add/remove users
– Read/Write/Delete data
– Backup the database
Application Roles
– For applications where you want the user to access SQL Server, but only heightened privileges when they use the app


HaplotypeCaller on Spark
This is an implementation of HaplotypeCaller using spark to distribute the computation. It is still in an early stage of development and does not yet support all the options that the non-spark version does. Specifically it does not support the --dbsnp, --comp, and --bam-output options.
gatk HaplotypeCallerSpark \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -O output.vcf.gz
These Read Filters are automatically applied to the data by the Engine before processing by HaplotypeCallerSpark.
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 | |
|---|---|---|---|
| Required Arguments | |||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --output -O |
Single file to which variants should be written | ||
| --reference -R |
Reference sequence file | ||
| Optional Tool Arguments | |||
| --alleles |
The set of alleles to force-call regardless of evidence | ||
| --annotate-with-num-discovered-alleles |
false | If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site | |
| --annotation -A |
One or more specific annotations to add to variant calls | ||
| --annotation-group -G |
One or more groups of annotations to apply to variant calls | ||
| --annotations-to-exclude -AX |
One or more specific annotations to exclude from variant calls | ||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --assembly-region-padding |
100 | Number of additional bases of context to include around each assembly region | |
| --bam-partition-size |
0 | maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block). | |
| --base-quality-score-threshold |
18 | Base qualities below this threshold will be reduced to the minimum (6) | |
| --conf |
Spark properties to set on the Spark context in the format |
||
| --contamination-fraction-to-filter -contamination |
0.0 | Fraction of contamination in sequencing data (for all samples) to aggressively remove | |
| --dbsnp -D |
dbSNP file | ||
| --disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
| --dont-use-dragstr-pair-hmm-scores |
false | disable DRAGstr pair-hmm score even when dragstr-params-path was provided | |
| --dragen-mode |
false | Single argument for enabling the bulk of DRAGEN-GATK features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET). | |
| --dragstr-het-hom-ratio |
2 | het to hom prior ratio use with DRAGstr on | |
| --dragstr-params-path |
location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms | ||
| --enable-dynamic-read-disqualification-for-genotyping |
false | Will enable less strict read disqualification low base quality reads | |
| --founder-id |
Samples representing the population "founders" | ||
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --gcs-project-for-requester-pays |
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed. | ||
| --genotype-assignment-method -gam |
USE_PLS_TO_ASSIGN | How we assign genotypes | |
| --graph-output -graph |
Write debug assembly graph information to this file | ||
| --help -h |
false | display the help message | |
| --heterozygosity |
0.001 | Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept | |
| --heterozygosity-stdev |
0.01 | Standard deviation of heterozygosity for SNP and indel calling. | |
| --indel-heterozygosity |
1.25E-4 | Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --max-assembly-region-size |
300 | Maximum size of an assembly region | |
| --max-reads-per-alignment-start |
50 | Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable. | |
| --min-assembly-region-size |
50 | Minimum size of an assembly region | |
| --min-base-quality-score -mbq |
10 | Minimum base quality required to consider a base for calling | |
| --native-pair-hmm-threads |
4 | How many threads should a native pairHMM implementation use | |
| --native-pair-hmm-use-double-precision |
false | use double precision in the native pairHmm. This is slower but matches the java implementation better | |
| --num-reducers |
0 | For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input. | |
| --num-reference-samples-if-no-call |
0 | Number of hom-ref genotypes to infer at sites not present in a panel | |
| --output-mode |
EMIT_VARIANTS_ONLY | Specifies which type of calls we should output | |
| --output-shard-tmp-dir |
when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used | ||
| --pedigree -ped |
Pedigree file for determining the population "founders" | ||
| --population-callset -population |
Callset to use in calculating genotype priors | ||
| --program-name |
Name of the program running | ||
| --read-shard-padding |
100 | Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions. | |
| --read-shard-size |
5000 | Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size. | |
| --sample-name -ALIAS |
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). | |
| --sharded-output |
false | For tools that write an output, write the output in multiple pieces (shards) | |
| --shuffle |
false | whether to use the shuffle implementation or not | |
| --spark-master |
local[*] | URL of the Spark Master to submit jobs to when using the Spark pipeline runner. | |
| --spark-verbosity |
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE} | ||
| --standard-min-confidence-threshold-for-calling -stand-call-conf |
30.0 | The minimum phred-scaled confidence threshold at which variants should be called | |
| --strict |
false | whether to use the strict implementation or not (defaults to the faster implementation that doesn't strictly match the walker version) | |
| --use-nio |
false | Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.) | |
| --use-posteriors-to-calculate-qual -gp-qual |
false | if available, use the genotype posterior probabilities to calculate the site QUAL | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM index when writing a coordinate-sorted BAM file. | |
| --create-output-bam-splitting-index |
true | If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file. | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --disable-read-filter -DF |
Read filters to be disabled before analysis | ||
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
One or more genomic intervals to exclude from processing | ||
| --gatk-config-file |
A configuration file to use with the GATK. | ||
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
Read filters to be applied before analysis | ||
| --read-index |
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | ||
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --splitting-index-granularity |
4096 | Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points. | |
| --tmp-dir |
Temp directory to use. | ||
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --verbosity |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --active-probability-threshold |
0.002 | Minimum probability for a locus to be considered active. | |
| --adaptive-pruning |
false | Use Mutect2's adaptive graph pruning algorithm | |
| --adaptive-pruning-initial-error-rate |
0.001 | Initial base error rate estimate for adaptive pruning | |
| --all-site-pls |
false | Annotate all sites with PLs | |
| --allele-informative-reads-overlap-margin |
2 | Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs | |
| --allow-non-unique-kmers-in-ref |
false | Allow graphs that have non-unique kmers in the reference | |
| --apply-bqd |
false | If enabled this argument will apply the DRAGEN-GATK BaseQualityDropout model to the genotyping model for filtering sites due to Linked Error mode. | |
| --apply-frd |
false | If enabled this argument will apply the DRAGEN-GATK ForeignReadDetection model to the genotyping model for filtering sites. | |
| --bam-output -bamout |
File to which assembled haplotypes should be written | ||
| --bam-writer-type |
CALLED_HAPLOTYPES | Which haplotypes should be written to the BAM | |
| --comparison -comp |
Comparison VCF file(s) | ||
| --contamination-fraction-per-sample-file -contamination-file |
Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be " |
||
| --debug-assembly -debug |
false | Print out verbose debug information about each assembly region | |
| --disable-cap-base-qualities-to-map-quality |
false | If false this disables capping of base qualities in the HMM to the mapping quality of the read | |
| --disable-optimizations |
false | Don't skip calculations in ActiveRegions with no variants | |
| --disable-spanning-event-genotyping |
false | If enabled this argument will disable inclusion of the '*' spanning event when genotyping events that overlap deletions | |
| --disable-symmetric-hmm-normalizing |
false | Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype | |
| --disable-tool-default-annotations |
false | Disable all tool default annotations | |
| --do-not-correct-overlapping-quality |
false | Disable overlapping base quality correction | |
| --do-not-run-physical-phasing |
false | Disable physical phasing | |
| --dont-increase-kmer-sizes-for-cycles |
false | Disable iterating over kmer sizes when graph cycles are detected | |
| --dont-use-dragstr-priors |
false | Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params) | |
| --dont-use-soft-clipped-bases |
false | Do not analyze soft clipped bases in the reads | |
| --emit-ref-confidence -ERC |
NONE | Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature) | |
| --enable-all-annotations |
false | Use all possible annotations (not for the faint of heart) | |
| --expected-mismatch-rate-for-read-disqualification |
0.02 | Error rate used to set expectation for post HMM read disqualification based on mismatches | |
| --floor-blocks |
false | Output the band lower bound for each GQ block regardless of the data it represents | |
| --force-active |
false | If provided, all regions will be marked as active | |
| --force-call-filtered-alleles -genotype-filtered-alleles |
false | Force-call filtered alleles included in the resource specified by --alleles | |
| --gvcf-gq-bands -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] | Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) | |
| --indel-size-to-eliminate-in-ref-model |
10 | The size of an indel to check for in the reference model | |
| --kmer-size |
[10, 25] | Kmer size to use in the read threading assembler | |
| --linked-de-bruijn-graph |
false | If enabled, the Assembly Engine will construct a Linked De Bruijn graph to recover better haplotypes | |
| --mapping-quality-threshold-for-genotyping |
20 | Control the threshold for discounting reads from the genotyper due to mapping quality after the active region detection and assembly steps but before genotyping. NOTE: this is in contrast to the --minimum-mapping-quality argument which filters reads from all parts of the HaplotypeCaller. If you would like to call genotypes with a different threshold both arguments must be set. | |
| --max-alternate-alleles |
6 | Maximum number of alternate alleles to genotype | |
| --max-effective-depth-adjustment-for-frd |
0 | Set the maximum depth to modify FRD adjustment to in the event of high depth sites (0 to disable) | |
| --max-genotype-count |
1024 | Maximum number of genotypes to consider at any site | |
| --max-mnp-distance -mnp-dist |
0 | Two or more phased substitutions separated by this distance or less are merged into MNPs. | |
| --max-num-haplotypes-in-population |
128 | Maximum number of haplotypes to consider for your population | |
| --max-prob-propagation-distance |
50 | Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions | |
| --max-unpruned-variants |
100 | Maximum number of variants in graph the adaptive pruner will allow | |
| --min-dangling-branch-length |
4 | Minimum length of a dangling branch to attempt recovery | |
| --min-pruning |
2 | Minimum support to not prune paths in the graph | |
| --num-pruning-samples |
1 | Number of samples that must pass the minPruning threshold | |
| --pair-hmm-gap-continuation-penalty |
10 | Flat gap continuation penalty for use in the Pair HMM | |
| --pair-hmm-implementation -pairHMM |
FASTEST_AVAILABLE | The PairHMM implementation to use for genotype likelihood calculations | |
| --pcr-indel-model |
CONSERVATIVE | The PCR indel model to use | |
| --phred-scaled-global-read-mismapping-rate |
45 | The global assumed mismapping rate for reads | |
| --pruning-lod-threshold |
2.302585092994046 | Ln likelihood ratio threshold for adaptive pruning algorithm | |
| --pruning-seeding-lod-threshold |
9.210340371976184 | Ln likelihood ratio threshold for seeding subgraph of good variation in adaptive pruning algorithm | |
| --recover-all-dangling-branches |
false | Recover all dangling branches | |
| --showHidden |
false | display hidden arguments | |
| --smith-waterman |
JAVA | Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice | |
| --soft-clip-low-quality-ends |
false | If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model) | |
| --transform-dragen-mapping-quality |
false | If enabled this argument will map DRAGEN aligner aligned reads with mapping quality <=250 to scale up to MQ 50 | |
| --use-filtered-reads-for-annotations |
false | Use the contamination-filtered read maps for the purposes of annotating variants | |
| Deprecated Arguments | |||
| --recover-dangling-heads |
false | This argument is deprecated since version 3.3 | |
| --use-new-qual-calculator -new-qual |
true | Use the new AF model instead of the so-called exact model |
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.
Minimum probability for a locus to be considered active.
double 0.002 [ [ -∞ ∞ ] ]
Use Mutect2's adaptive graph pruning algorithm
A single edge multiplicity cutoff for pruning doesn't work in samples with variable depths, for example exomes
and RNA. This parameter enables the probabilistic algorithm for pruning the assembly graph that considers the
likelihood that each chain in the graph comes from real variation.
boolean false
Initial base error rate estimate for adaptive pruning
Initial base error rate guess for the probabilistic adaptive pruning model. Results are not very sensitive to this
parameter because it is only a starting point from which the algorithm discovers the true error rate.
double 0.001 [ [ -∞ ∞ ] ]
If true, adds a command line header line to created VCF files.
boolean true
Annotate all sites with PLs
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_ACTIVE_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_ACTIVE_SITES is not set, or if anything other than diploid SNP model is used
boolean false
Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs
int 2 [ [ -∞ ∞ ] ]
The set of alleles to force-call regardless of evidence
FeatureInput[VariantContext] null
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
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 add to variant calls
Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.
List[String] []
One or more groups of annotations to apply to variant calls
Which groups of annotations to add to the output variant calls.
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] []
One or more specific annotations to exclude from variant calls
Which annotations to exclude from output in the variant calls. 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.
List[String] []
If enabled this argument will apply the DRAGEN-GATK BaseQualityDropout model to the genotyping model for filtering sites due to Linked Error mode.
boolean false
If enabled this argument will apply the DRAGEN-GATK ForeignReadDetection model to the genotyping model for filtering sites.
boolean false
read one or more arguments files and add them to the command line
List[File] []
Number of additional bases of context to include around each assembly region
Parameters that control assembly regions
int 100 [ [ -∞ ∞ ] ]
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. Really
for debugging purposes only. Note that the output here does not include uninformative reads so that not every
input read is emitted to the bam.
Turning on this mode may result in serious performance cost for the caller. It's really only appropriate to
use in specific areas where you want to better understand why the caller is making specific calls.
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.
Note that the 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.
Note also that only reads that are actually informative about the haplotypes are emitted. By informative we mean
that there's a meaningful difference in the likelihood of the read coming from one haplotype compared to
its next best haplotype.
If multiple BAMs are passed as input to the tool (as is common for M2), then they will be combined in the bamout
output and tagged with the appropriate sample names.
The best way to visualize the output of this mode is with IGV. Tell IGV to color the alignments by tag,
and give it the "HC" tag, so you can see which reads support each haplotype. Finally, you can tell IGV
to group by sample, which will separate the potential haplotypes from the reads. All of this can be seen in
this screenshot
String null
maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).
long 0 [ [ -∞ ∞ ] ]
Which haplotypes should be written to the BAM
The type of BAM 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 --bam-writer-type argument is an enumerated type (WriterType), which can have one of the following values:
WriterType CALLED_HAPLOTYPES
Base qualities below this threshold will be reduced to the minimum (6)
Bases with a quality below this threshold will reduced to the minimum usable qualiy score (6).
byte 18 [ [ -∞ ∞ ] ]
Comparison VCF file(s)
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).
List[FeatureInput[VariantContext]] []
Spark properties to set on the Spark context in the format
List[String] []
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 null
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 [ [ -∞ ∞ ] ]
If true, create a BAM index when writing a coordinate-sorted BAM file.
boolean true
If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
boolean true
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
dbSNP file
A dbSNP VCF file.
FeatureInput[VariantContext] null
Print out verbose debug information about each assembly region
boolean false
If false this disables capping of base qualities in the HMM to the mapping quality of the read
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 --force-active flag may also be necessary.
boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
If enabled this argument will disable inclusion of the '*' spanning event when genotyping events that overlap deletions
boolean false
Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype
boolean false
Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
Disable overlapping base quality correction
Base quality is capped at half of PCR error rate for bases where read and mate overlap, to account for full correlation of PCR errors at these bases. This argument disables that correction.
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
disable DRAGstr pair-hmm score even when dragstr-params-path was provided
boolean false
Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params)
boolean false
Do not analyze soft clipped bases in the reads
boolean false
Single argument for enabling the bulk of DRAGEN-GATK features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET).
DRAGEN-GATK mode changes a long list of arguments to support running DRAGEN-GATK with FRD + BQD + STRE (with or without
a provided STRE table provided):
Boolean false
het to hom prior ratio use with DRAGstr on
int 2 [ [ -∞ ∞ ] ]
location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms
GATKPath null
Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature)
The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs.
For Mutect2, this is a BETA feature that functions similarly to the HaplotypeCaller reference confidence/GVCF mode.
The --emit-ref-confidence argument is an enumerated type (ReferenceConfidenceMode), which can have one of the following values:
ReferenceConfidenceMode NONE
Use all possible annotations (not for the faint of heart)
You can use the -AX argument in combination with this one to exclude specific annotations. Note that some
annotations may not be actually applied if they are not applicable to the data provided or if they are
unavailable to the tool (e.g. there are several annotations that are currently not hooked up to
HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be
skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although
this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have
additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation
for individual annotations' requirements).
boolean false
Will enable less strict read disqualification low base quality reads
If enabled, rather than disqualifying all reads over a threshold of minimum hmm scores we will instead choose a less strict
and less aggressive cap for disqualification based on the read length and base qualities.
boolean false
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite).
This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals).
List[String] []
Error rate used to set expectation for post HMM read disqualification based on mismatches
double 0.02 [ [ -∞ ∞ ] ]
Output the band lower bound for each GQ block regardless of the data it represents
Output the band lower bound for each GQ block instead of the min GQ -- for better compression
boolean false
If provided, all regions will be marked as active
boolean false
Force-call filtered alleles included in the resource specified by --alleles
boolean false
Samples representing the population "founders"
List[String] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
String ""
How we assign genotypes
The --genotype-assignment-method argument is an enumerated type (GenotypeAssignmentMethod), which can have one of the following values:
GenotypeAssignmentMethod USE_PLS_TO_ASSIGN
Write debug assembly graph information to this file
This argument is meant for debugging and is not immediately useful for normal analysis use.
String null
Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
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 bands. HC expects a list of strictly increasing GQ values
that will act as exclusive upper bounds for the GQ bands. To pass multiple values,
you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on
(this would set the GQ bands to be `[0, 10), [10, 20), [20, 30)` and so on, for example).
Note that GQ values are capped at 99 in the GATK, so values must be integers in [1, 100].
If the last value is strictly less than 100, the last GQ band will start at that value (inclusive)
and end at 100 (exclusive).
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]
display the help message
boolean false
Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
The default priors are for provided for humans:
het = 1e-3
which means that the probability of N samples being hom-ref at a site is:
1 - sum_i_2N (het / i)
Note that heterozygosity as used here is the population genetics concept:
http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics
That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms
would differ from each other (one being A and the other B) at a rate of 1 in 100 bp.
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 [ [ -∞ ∞ ] ]
Standard deviation of heterozygosity for SNP and indel calling.
The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the
*mean* of this distribution; this parameter gives its spread.
double 0.01 [ [ -∞ ∞ ] ]
Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
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 [ [ -∞ ∞ ] ]
BAM/SAM/CRAM file containing reads
R List[GATKPath] []
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
IntervalMergingRule ALL
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Kmer size to use in the read threading assembler
Multiple kmer sizes can be specified, using e.g. `--kmer-size 10 --kmer-size 25`.
List[Integer] [10, 25]
If enabled, the Assembly Engine will construct a Linked De Bruijn graph to recover better haplotypes
Disables graph simplification into a seq graph, opts to construct a proper De Bruijn graph with potential loops
NOTE: --linked-de-bruijn-graph is currently an experimental feature that does not directly match with
the regular HaplotypeCaller. Specifically the haplotype finding code does not perform correctly at complicated
sites. Use this mode at your own risk.
boolean false
Control the threshold for discounting reads from the genotyper due to mapping quality after the active region detection and assembly steps but before genotyping. NOTE: this is in contrast to the --minimum-mapping-quality argument which filters reads from all parts of the HaplotypeCaller. If you would like to call genotypes with a different threshold both arguments must be set.
int 20 [ [ -∞ ∞ ] ]
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.
See also {@link #MAX_GENOTYPE_COUNT}.
int 6 [ [ -∞ ∞ ] ]
Maximum size of an assembly region
int 300 [ [ -∞ ∞ ] ]
Set the maximum depth to modify FRD adjustment to in the event of high depth sites (0 to disable)
int 0 [ [ -∞ ∞ ] ]
Maximum number of genotypes to consider at any site
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used.
The possible genotypes are simply different ways of partitioning alleles given a specific ploidy asumption.
Therefore, we remove genotypes from consideration by removing alternate alleles that are the least well supported.
The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step.
Note that the reference allele is always kept.
Note that genotyping sites with large genotype counts is both CPU and memory intensive.
Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter.
The maximum number of alternative alleles used in the genotyping step will be the lesser of the two:
1. the largest number of alt alleles, given ploidy, that yields a genotype count no higher than {@link #MAX_GENOTYPE_COUNT}
2. the value of {@link #MAX_ALTERNATE_ALLELES}
See also {@link #MAX_ALTERNATE_ALLELES}.
int 1024 [ [ -∞ ∞ ] ]
Two or more phased substitutions separated by this distance or less are merged into MNPs.
Two or more phased substitutions separated by this distance or less are merged into MNPs.
int 0 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions
int 50 [ [ -∞ ∞ ] ]
Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable.
Other parameters
int 50 [ [ -∞ ∞ ] ]
Maximum number of variants in graph the adaptive pruner will allow
The maximum number of variants in graph the adaptive pruner will allow
int 100 [ [ -∞ ∞ ] ]
Minimum size of an assembly region
Parameters that control active regions
int 50 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
How many threads should a native pairHMM implementation use
int 4 [ [ -∞ ∞ ] ]
use double precision in the native pairHmm. This is slower but matches the java implementation better
boolean false
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 [ [ -∞ ∞ ] ]
For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.
int 0 [ [ -∞ ∞ ] ]
Number of hom-ref genotypes to infer at sites not present in a panel
When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength)
that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0,
AN=2000".
int 0 [ [ -∞ ∞ ] ]
Single file to which variants should be written
R String null
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
when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used
Exclusion: This argument cannot be used at the same time as sharded-output
.
String null
Flat gap continuation penalty for use in the Pair HMM
int 10 [ [ -∞ ∞ ] ]
The PairHMM implementation to use for genotype likelihood calculations
The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
The --pair-hmm-implementation argument is an enumerated type (Implementation), which can have one of the following values:
Implementation FASTEST_AVAILABLE
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 (PCRErrorModel), which can have one of the following values:
PCRErrorModel CONSERVATIVE
Pedigree file for determining the population "founders"
GATKPath null
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 [ [ -∞ ∞ ] ]
Callset to use in calculating genotype priors
Supporting external panel. Allele counts from this panel (taken from AC,AN or MLEAC,AN or raw genotypes) will
be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later.
Note that unlike CalculateGenotypePosteriors, HaplotypeCaller only allows one supporting callset.
FeatureInput[VariantContext] null
Name of the program running
String null
Ln likelihood ratio threshold for adaptive pruning algorithm
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
double 2.302585092994046 [ [ -∞ ∞ ] ]
Ln likelihood ratio threshold for seeding subgraph of good variation in adaptive pruning algorithm
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
double 9.210340371976184 [ [ -∞ ∞ ] ]
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions.
int 100 [ [ -∞ ∞ ] ]
Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size.
int 5000 [ [ -∞ ∞ ] ]
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency SILENT
Recover all dangling branches
By default, the read threading assembler does not recover dangling branches that fork after splitting from the reference. This argument
tells the assembly engine to recover all dangling branches.
boolean false
This argument is deprecated since version 3.3
As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details.
boolean false
Reference sequence file
R GATKPath null
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 null
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 [ [ -∞ ∞ ] ]
For tools that write an output, write the output in multiple pieces (shards)
Exclusion: This argument cannot be used at the same time as output-shard-tmp-dir
.
boolean false
display hidden arguments
boolean false
whether to use the shuffle implementation or not
boolean false
Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice
The --smith-waterman argument is an enumerated type (Implementation), which can have one of the following values:
Implementation JAVA
If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model)
boolean false
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
String local[*]
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
String null
Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points.
long 4096 [ [ 1 ∞ ] ]
The minimum phred-scaled confidence threshold at which variants should be called
The minimum phred-scaled confidence threshold at which variants should be called. Only variant sites with QUAL equal
or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence
from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve
high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after
calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode
(using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding
will then be performed in the subsequent GenotypeGVCFs command.
Note that the default was changed from 10.0 to 30.0 in version <IP_ADDRESS> to accompany the switch to use the the new quality score by default.
double 30.0 [ [ -∞ ∞ ] ]
whether to use the strict implementation or not (defaults to the faster implementation that doesn't strictly match the walker version)
boolean false
Temp directory to use.
GATKPath null
If enabled this argument will map DRAGEN aligner aligned reads with mapping quality <=250 to scale up to MQ 50
boolean false
Use the contamination-filtered read maps for the purposes of annotating variants
boolean false
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
Use the new AF model instead of the so-called exact model
As of version <IP_ADDRESS>, this argument is no longer needed because the new qual score is now on by default. See GATK 3.3 release notes for more details.
boolean true
Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.)
boolean false
if available, use the genotype posterior probabilities to calculate the site QUAL
boolean false
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
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.


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In this example we calculate π
by placing random points in the square below, and counting
the number that fall within the circle. The ratio of the
number that fall within the circle to the total number of
points (number of MC
iterations, niter) is
proportional to π.
The MC iterations are split into batches of n_trial iterations. After each batch, an estimate of π is calculated, πsub. The average of these gives our estimate of π, while the standard deviation can be used to find the statistical error (given here as the 95% confidence interval), shown in the top left plot. The error will decrease as (niter)-0.5, shown in the bottom left plot.
We are essentially sampling from a binomial distribution
which has probability P = π/4
of a success (i.e. the point is within the circle)
for n = n_trial independent
experiments. According to the central-limit theorem, if we
draw a large number of random samples from any type of
distribution, the distribution
of πsub values will
always be a normal distribution (so long as the sample
size is large enough, typically > 30), shown in the bottom
right plot. Try varying n_trial
to see how this changes.
π against number of MC iterations
Zoom: click and drag, Restore: double click
Percentage error (given here as the 95% confidence interval) in π against the number of MC iterations niter. Red circles shows the result, while the solid black line shows the expected value, given as the standard deviation of the underlying distribution function divided by the square-root of the number of iterations, (niter)-0.5.
The error in our result is given by:
where 〈...〉 denotes the mean after niter iterations
Probability density function of πsub values. Red circles are calculated result, solid black line is the expected result based on the central-limit theorem i.e. a normal distribution.


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Is there a better way to test out pseudo-class?
Game of Thrones
House of cards


labeled
by None at 2023-07-25 18:05:31.labeled
by None at 2023-07-25 18:04:58.a quick way to reproduce this error:
ssh deploy@bibdata-alma-worker-staging1
cd /opt/bibdata/current/
bundle exec rake -T
WARN -- : Failed to find the `lando` containers in the environment (is Lando installed?)
Top level ::CompositeIO is deprecated, require 'multipart/post' and use `Multipart::Post::CompositeReadIO` instead!
Top level ::Parts is deprecated, require 'multipart/post' and use `Multipart::Post::Parts` instead!
W, [2023-07-25T11:46:38.542323 #5587] WARN -- : Failed to find the `lando` containers in the environment (is Lando installed?): No such file or directory - lando
Test in staging not in production.
labeled
by Jane Sandberg at 2023-07-25 19:01:39.labeled
by Jane Sandberg at 2023-07-25 19:09:42.labeled
by Jane Sandberg at 2023-07-25 19:13:57.labeled
by Jane Sandberg at 2023-07-25 19:13:57.Checked the following documents with axe DevTools and Voice Over and included any issues found on report template.
closed
by Cliff Wulfman at 2023-07-25 17:22:25.referenced
by Cliff Wulfman at 2023-07-25 17:24:17.merged
by Cliff Wulfman at 2023-07-25 17:24:17.closed
by Cliff Wulfman at 2023-07-25 17:24:17.closed
by Cliff Wulfman at 2023-07-25 17:24:19.referenced
by Cliff Wulfman at 2023-07-25 17:37:16.merged
by Cliff Wulfman at 2023-07-25 17:37:16.closed
by Cliff Wulfman at 2023-07-25 17:37:16.closed
by Cliff Wulfman at 2023-07-25 17:37:17.closed
by Cliff Wulfman at 2023-07-25 17:41:52.review_requested
by Cliff Wulfman at 2023-07-25 20:41:36.https://www.smashingmagazine.com/2009/03/breadcrumbs-in-web-design-examples-and-best-practices/
Hierarchical structure seems to be attribute-based (subguides having the attributes of a certain 'sortid' from the parent (guidecard).
I'm no longer observing this; will re-open if it happens again
assigned
by None at 2023-07-25 12:36:14.closed
by None at 2023-07-25 13:09:13.the job to download EADs is done
closed
by Christina Chortaria at 2023-07-25 15:11:49.deployed
by None at 2023-07-25 14:58:50.referenced
by Jane Sandberg at 2023-07-25 16:04:20.merged
by Jane Sandberg at 2023-07-25 16:04:20.closed
by Jane Sandberg at 2023-07-25 16:04:21.head_ref_deleted
by Jane Sandberg at 2023-07-25 16:04:22.


| PostgreSQL 9.0.10 Documentation | ||||
|---|---|---|---|---|
| Prev | Up | Appendix F. Additional Supplied Modules | Next |
The intarray module provides a number of useful functions and operators for manipulating one-dimensional arrays of integers. There is also support for indexed searches using some of the operators.
Table F-8. intarray Functions
| Function | Return Type | Description | Example | Result |
|---|---|---|---|---|
icount(int[]) | int | number of elements in array | icount('{1,2,3}'::int[]) | 3 |
sort(int[], text dir) | int[] | sort array — dir must be asc or desc | sort('{1,2,3}'::int[], 'desc') | {3,2,1} |
sort(int[]) | int[] | sort in ascending order | sort(array[11,77,44]) | {11,44,77} |
sort_asc(int[]) | int[] | sort in ascending order | ||
sort_desc(int[]) | int[] | sort in descending order | ||
uniq(int[]) | int[] | remove adjacent duplicates | uniq(sort('{1,2,3,2,1}'::int[])) | {1,2,3} |
idx(int[], int item) | int | index of first element matching item (0 if none) | idx(array[11,22,33,22,11], 22) | 2 |
subarray(int[], int start, int len) | int[] | portion of array starting at position start, len elements | subarray('{1,2,3,2,1}'::int[], 2, 3) | {2,3,2} |
subarray(int[], int start) | int[] | portion of array starting at position start | subarray('{1,2,3,2,1}'::int[], 2) | {2,3,2,1} |
intset(int) | int[] | make single-element array | intset(42) | {42} |
Table F-9. intarray Operators
| Operator | Returns | Description |
|---|---|---|
| int[] && int[] | boolean | overlap — true if arrays have at least one common element |
| int[] @> int[] | boolean | contains — true if left array contains right array |
| int[] <@ int[] | boolean | contained — true if left array is contained in right array |
| # int[] | int | number of elements in array |
| int[] # int | int | index (same as idx function) |
| int[] + int | int[] | push element onto array (add it to end of array) |
| int[] + int[] | int[] | array concatenation (right array added to the end of left one) |
| int[] - int | int[] | remove entries matching right argument from array |
| int[] - int[] | int[] | remove elements of right array from left |
| int[] | int | int[] | union of arguments |
| int[] | int[] | int[] | union of arrays |
| int[] & int[] | int[] | intersection of arrays |
| int[] @@ query_int | boolean | true if array satisfies query (see below) |
| query_int ~~ int[] | boolean | true if array satisfies query (commutator of @@) |
(Before PostgreSQL 8.2, the containment operators @> and <@ were respectively called @ and ~. These names are still available, but are deprecated and will eventually be retired. Notice that the old names are reversed from the convention formerly followed by the core geometric data types!)
The containment operators @> and <@ are approximately equivalent to PostgreSQL's built-in operators of the same names, except that they work only on integer arrays while the built-in operators work for any array type. An important difference is that intarray's operators do not consider an empty array to be contained in anything else. This is consistent with the behavior of GIN-indexed queries, but not with the usual mathematical definition of containment.
The @@ and ~~ operators test whether an array satisfies a query, which is expressed as a value of a specialized data type query_int. A query consists of integer values that are checked against the elements of the array, possibly combined using the operators & (AND), | (OR), and ! (NOT). Parentheses can be used as needed. For example, the query 1&(2|3) matches arrays that contain 1 and also contain either 2 or 3.
intarray provides index support for the &&, @>, <@, and @@ operators, as well as regular array equality.
Two GiST index operator classes are provided: gist__int_ops (used by default) is suitable for small- to medium-size data sets, while gist__intbig_ops uses a larger signature and is more suitable for indexing large data sets (i.e., columns containing a large number of distinct array values). The implementation uses an RD-tree data structure with built-in lossy compression.
There is also a non-default GIN operator class gin__int_ops supporting the same operators.
The choice between GiST and GIN indexing depends on the relative performance characteristics of GiST and GIN, which are discussed elsewhere. As a rule of thumb, a GIN index is faster to search than a GiST index, but slower to build or update; so GIN is better suited for static data and GiST for often-updated data.
-- a message can be in one or more "sections"
CREATE TABLE message (mid INT PRIMARY KEY, sections INT[], ...);
-- create specialized index
CREATE INDEX message_rdtree_idx ON message USING GIST (sections gist__int_ops);
-- select messages in section 1 OR 2 - OVERLAP operator
SELECT message.mid FROM message WHERE message.sections && '{1,2}';
-- select messages in sections 1 AND 2 - CONTAINS operator
SELECT message.mid FROM message WHERE message.sections @> '{1,2}';
-- the same, using QUERY operator
SELECT message.mid FROM message WHERE message.sections @@ '1&2'::query_int;
The source directory contrib/intarray/bench contains a benchmark test suite. To run:
cd .../bench createdb TEST psql TEST < ../_int.sql ./create_test.pl | psql TEST ./bench.pl
The bench.pl script has numerous options, which are displayed when it is run without any arguments.
All work was done by Teodor Sigaev<EMAIL_ADDRESS>) and
Oleg Bartunov<EMAIL_ADDRESS>). See
http://www.sai.msu.su/~megera/postgres/gist/ for
additional information. Andrey Oktyabrski did a great work on adding new
functions and operations.


Staic layout is useful for those platform having less menu options and content sections where user required to scroll less.
Default this template has a static layout elements, so there is no any specific classes need to add to create this layout.
To create this layout just need to confirm .fixed-top
, .menu-fixed
and .footer-fixed
not applied to their respective element, in short do not use fixed layout classes.
This section contains HTML Markup to create static layout. No need to add any specific classes just do not use fixed layout classes. This layout has a navigation, content and left sidebar sections with common header & footer.
Modern has a ready to use starter kit, you can use this layout directly by using the starter kit pages from the modern-admin/starter-kit
folder.
<!DOCTYPE html>

...

...

...

...

...

Modern Admin use PUG as template engine to generate pages and whole template quickly using node js, for getting start with PUG usage & template generating process please refer template documentation.
This table contains required PUG variables to generate static layout.
| Block | Variable | Datatype | Value | Description |
|---|---|---|---|---|
pageConfig |
navbarFixed |
boolean |
false |
pageConfig block has a navbarFixed variable, it contains navbar position specific setting in that you need to set false for fixed navbar. |
navbarConfig |
navbarPosition |
string |
'navbar-static-top' |
navbarConfig block has a navbarPosition variable, it contains navbar position type specific classes in that you need to set 'navbar-static-top' for static navbar. |
verticalMenuConfig |
menuType |
string |
'menu-static' |
verticalMenuConfig block has a menuType variable, it contains navigation type specific classes in that you need to set 'menu-static' for static vertical navigation. |
horizontalMenuConfig |
menuType |
string |
'navbar-static' |
verticalMenuConfig block has a menuType variable, it contains navigation type specific classes in that you need to set 'navbar-static' for static horizontal navigation. |
footerConfig |
footerType |
string |
'footer-static' |
footerConfig block has a footerType variable, it contains footer type specific classes in that you need to set 'footer-static' for static footer. |
To generate boxed layout page or template, you need to use following PUG code.
navbarFixed
variable value as false
in pageConfig
block, as our layout is not fixed.navbarPosition
variable value as 'navbar-static-top'
in navbarConfig
block for static navbar.menuType
variable value as 'menu-static'
in verticalMenuConfig
block for static navigation in vertical layout.menuType
variable value as 'navbar-static'
in horizontalMenuConfig
block for static navigation in vertical layout.footerType
variable value as 'footer-static'
in footerConfig
block for static footer.content
block has content section html file included include ../contents/layout-static.html
, which can be customizable on page level.If you want to use this layout on page level you need to define it on page it self. This template has one example pug file for static layout-static.pug
, however you can use it on template level but it will generate whole template as a static.
block pageVars
- var pageTitle = "Static Layout"
- var pageSubTitle = "Static layout with navigation"
- var description = "The static layout page structure have fixed navbar, navigation and footer."
- var activeMenu = "layout-static"
extends template
append pageConfig
- var navbarFixed = false
append navbarConfig
- var navbarPosition = "navbar-static-top"
append verticalMenuConfig
- var menuType = 'menu-static'
append horizontalMenuConfig
- var horizontalMenuType = 'navbar-static'
append footerConfig
- var footerType = "footer-static"
append breadcrumbs
+breadcrumbs([{url:"index.html",name:"Home"},{url:"#",name:"Page Layouts"}, {name:"Static Layout"}])
//- Include page content in page block
append content
include ../contents/layout-static.html
//- Vendor CSS
//------------------------------
//- Add Vendor specific CSS
append vendorcss
//- Page CSS
//------------------------------
//- Add custom page specific CSS
append pagecss
//- Vendor JS
//------------------------------
//- Add vendor specific JS
append vendorjs
//- Page JS
//------------------------------
//- Add custom page specific JS
append pagejs


You must take personal responsibility. You cannot change the circumstances, the seasons, or the wind, but you can change yourself. That is something you have charge of.
When all the world appears to be in a tumult, and nature itself is feeling the assault of climate change, the seasons retain their essential rhythm. Yes, fall gives us a premonition of winter, but then, winter, will be forced to relent, once again, to the new beginnings of soft greens, longer light, and the sweet air of spring.
Every corny thing that's said about living with nature - being in harmony with the earth, feeling the cycle of the seasons - happens to be true.
The coming and going of the seasons give us more than the springtimes, summers, autumns, and winters of our lives. It reflects the coming and going of the circumstances of our lives like the glassy surface of a pond that shows our faces radiant with joy or contorted with pain.
To be interested in the changing seasons is a happier state of mind than to be hopelessly in love with spring.
There are seasons in life. Don't ever let anyone try to deny you the joy of one season because they believe you should stay in another season... Listen to yourself. Trust your instincts. Keep your perspective.
I need the seasons to live to the rhythm of rain and sun.


OVERVIEW
Stranger Things is set in the fictional rural town of Hawkins, Indiana, during the early 1980s. The nearby Hawkins National Laboratory ostensibly performs scientific research for the United States Department of Energy, but secretly does experiments into the paranormal and supernatural, including those that involve human test subjects. Inadvertently, they have created a portal to an alternate dimension, "the Upside Down". The influence of the Upside Down starts to affect the unknowing residents of Hawkins in calamitous ways.
First Season
The first season begins in November 1983, when Will Byers is abducted by a creature from the Upside Down. His mother, Joyce, and the town's police chief, Jim Hopper, search for Will. At the same time, a young psychokinetic girl called Eleven escapes from the laboratory and assists Will's friends, Mike, Dustin, and Lucas, in their own efforts to find Will.
Second Season
The second season is set a year later, starting in October 1984. Will has been rescued, but few know of the details of the events. When it is discovered that Will is still being influenced by entities from the Upside Down, his friends and family learn there is a larger threat to their universe from the Upside Down.
Third Season
The third season is set several months later, in the days leading up to the Fourth of July celebration in 1985. The new Starcourt Mall has become the center of attention for Hawkins' residents, putting most other stores out of business. Hopper becomes increasingly concerned about Eleven and Mike's relationship while still trying to care for Joyce. Unbeknownst to the town, a secret Soviet laboratory under Starcourt seeks to open the gateway to the Upside Down, allowing the entities from the Upside Down to possess people in Hawkins and creating a new horror to deal with.


--- creation_epoch:<PHONE_NUMBER> lastmod_epoch:<PHONE_NUMBER> categories: ['Tech Tricks'] title: Web site tool for testing cron schedules --- I found some useful web sites for testing cron schedules to get a preview of the run times based on your cron string.


UFC Moscow post-fight bonuses: Zabit-Kattar put on exciting FOTN
by Stephie HaynesCSKA Arena in Moscow, Russia was home to a mediocre afternoon of fights. The card saw two (T)KOs, two submissions and nine decisions, including two split-decisions.
Today’s card was a long, drawn-out affair with a multitude of decisions, some of which scored a less-than-exciting rating from fans. The main card saw more voltage than the prelims in the form of a slobberknocker between Ed “Short Fuse” Herman and Khadis Ibragimov, a massive knockout of Zelim Imadaev courtesy of Danny “Hot Chocolate” Roberts, and a sensational three-round battle between Zabit Magomedsharipov and Calvin Kattar.
Performances of the Night: David Zawada, Magomed Ankalaev
There were only four finishes with David Zawada, Karl Roberson, Magomed Ankalaev, and Danny Roberts ending up in the win column. David Zawada’s outstanding round-one triangle choke of Abubakar Nurmagomedov won the first of two performance bonuses and Magomed Ankalaev’s third-round, front kick knockout of Dalcha Lungiambula won the other.
Fight of the Night: Zabit Magomedsharipov vs. Calvin Kattar
The main event was a competitive fight with Calvin Kattar falling short on the scorecards (28-29 x3).  That said, by the beginning of the final stanza, Magomedsharipov’s questionable cardio made an appearance, and Kattar easily took round three, even with a late takedown from Zabit. Had the contest been five rounds, we might have seen a different arm raised.
Nine fights went to decision with Davey Grant, Pannie Kianzad, Roosevelt Roberts, Rustam Khabilov, Shamil Gamzatov, Anthony Rocco Martin, Ed Herman, Alexander Volkov and Zabit Magomedsharipov all charting victories.
Gate: N/A
Announced Attendance: 11,305


Change Log - Crittercism iOS Module for Titanium
08.17.2015 - v1.1.5
- Android: [TIMOB-19293] Updated crittercism library to 5.3.3
- iOS: Bumped version to match Android
06.19.2015 - v1.1.4
- iOS: [MOD-2081] Updated crittercism library to 5.2.0
- Android: Bumped version to match iOS
03.23.2015 - v1.1.3
- iOS: [TIMOB-17695] Fixed enabledRemoteNotificationTypes is not supported shown in log
- Android: Bumped version to match iOS
03.13.2015 - v1.1.2
- Android: [MOD-2101] Fixed init requiring an argument
- iOS: Bumped version to match Android
12.12.2014 - v1.1.1
- iOS: [TIMOB-18197] Fixed init requiring an argument
- Android: Bumped version to match iOS
11.08.2014 - v1.1.0
- Update: [TIMOB-17928] Updated to build for 64-bit
- Adding architectures to manifest
11.17.2014 - v1.0.11
- Bumped version to match Android
- Bumped minsdk to 3.4.0
13.05.2014 - v1.0.10
- Update: Crittercism library to the latest version 4.3.7
- This new version of the library must be initialized on the main thread.
13.05.2014 - v1.0.9
- Update: Crittercism library to the latest version 4.3.3 and code clean up.
12.17.2013 - v1.0.8
- Fix: Crittercism failed to initialize with Appcelerator 3.2.0 SDK
06.13.2013 - v1.0.5
05.10.2013 - v1.0.3
- Updated the property for Crittercism App ID to "com-appcelerator-apm-id"
04.05.2013 - v1.0.2
- Updated to 3.5.1 of Crittercism library
- Update the name of the module to "com.appcelerator.apm"
- Updated docs to reflect above change
- Updated sample app to reflect above change
- Removed support for init boolean "didCrashOnLastLoad", now use API
- Updated docs to reflect above change
- Updated sample app to reflect above change
- Removed support for Objects in setMetadata as this can cause unexpected behavior, will revisit
- Note: This now accepts String objects in the value parameter
- Updated docs and sample app to reflect above change
03.06.2013 - v1.0.1
- Added change log to both native modules
- Added support for "com-crittercism-ti" property in Tiapp.xml
- Demo app currently injects the property manually
- Documentation to reflect the changes of init parameters being optional
- Reduced the init explanation to a single item in docs


{% extends 'base.html' %} {% block content %}
Given n non-negative integers representing an elevation map where the width of each bar is 1, compute how much water it is able to trap after raining.
2 7 1,5,2,3,1,7,2 7 3,0,0,2,0,4
9 10


# Crichton, Admirable Source Configuration Management # Copyright 2012 British Broadcasting Corporation # # 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. # # {% extends "admin/change_form.html" %} {% block extendedextrahead %} {% load release_tags %} {% get_custom_date_fields custom_dates %} {% if custom_dates %} {% endif %} {% endblock %} {% block form_top %} {% get_jira_settings settings %} {% if change %} {% if not original.ops_issue %}
PLEASE NOTE: Submitting this form with a blank Ops Issue field will create a new change ticket in Jira.
{% else %}Go to OPS jira issue: {{original.ops_issue.name}}
{% endif %} {% else %}PLEASE NOTE: Submitting this form with a blank Ops Issue field will create a new change ticket in Jira.
PLEASE ALSO NOTE: once you have created a deployment request for a release, you can no longer modify that release.
{% endif %} {% endblock %}


<floverdevel> - 🙋🏻♂ Clean coder - 🙋🏻♂ Automate all the things </floverdevel>
👉🏻 I’m currently working on the Tab Finder Google Chrome extension 🤭 Fun fact: I spend more time in front of my computer than in my bed
<floverdevel> - 🙋🏻♂ Clean coder - 🙋🏻♂ Automate all the things </floverdevel>
👉🏻 I’m currently working on the Tab Finder Google Chrome extension 🤭 Fun fact: I spend more time in front of my computer than in my bed


--- layout: post title: Named exceptions date: 2012-05-27 10:37:53.000000000 +01:00 type: post parent_id: '0' published: true password: '' status: publish categories: - python tags: [] meta: _edit_last: '1' author: Noel permalink: "/named-exceptions/" ---
Need more on the error being thrown? You need to name the exception like so:
try: raise Exception('MONSTER!') except Exception as ex: print 'The error is a %s' % ex >>> The error is a MONSTER!


Saudi football team arrives in Doha for 24th Gulf Cup
Doha: Saudi national football team arrived in the Qatari capital of Doha to participate in the 24th edition of the Arabian Gulf Cup, which will be held from November 26 to December 8.
The Saudi team received an official reception upon arrival at Hamad International Airport before heading to their residence.
The final list of the team will include Mohammed Al-Yami, Fawaz Al-Qarni and Amin Bukhari. The defense line will include Ziad Al-Sahafi, Mohammed Khabrani, Hassan Timbukti, Sultan Al-Ghannam, Mohammed Al-Buraik, Saud Abdul-Hamid and Yasser Al-Shahrani. Abdullah Atif, Mohammed Kanno, Abdulelah Al-Malki, Salman Al-Faraj, Turki Al-Ammar, Yahya Al-Shehri, Abdulaziz Al-Bishi, Nawaf Al-Abed, Salem Al-Dosari and Abdul-Fattah Asiri will line up in the middle, while Hattan Bahabri, Firas Al-Burikan and , Abdullah Al-Hamdan will line up in the offensive.
Al-Hilal players, who won the Asian Champions League, will also arrive on Tuesday in Doha.
Saudi Arabia will play in Group B alongside Oman, Kuwait and Bahrain.
Read also
Read More
Flamengo, Al Hilal complete FIFA Club World Cup line-up
A weekend of crowning continental champions has seen the line-up of the FIFA Club World Cup Qatar 2019 finally completed ahead of its kick-off on December 11.
Read More
Handball: Qatar's Al Arabi down Saudi's Al Wehda to win Asian Men’s Club League Championship


Build a Simon Game
Gates.
A Microsoft-styled version of Simon made with HTML, CSS, and Javascript
level:
Play/Reset
Strict Mode:
On


We have every solution for your training needs.
From updating the skills of individuals and teams, to large-scale process implementation for organizations.
Software Development
Party girls don't get hurt Can't feel anything, when will I learn I push it down, push it down. I'm the one for a good time call, Phone's blowing up, they're ringing my doorbell I feel the love, feel the love 1, 2 ,3, 1,2 3, drink. 1, 2, 3, drink
Read MoreBusiness Management
What about the children? Look at all the children we can change What about a vision? be a visionary for a change. We're the generation who's gonna be the one to fight for it? We're the inspiration Do you believe enougn to die for it?
Read MoreData Security
Hello, its me I was wondering if after all these years you'd like to meet to go over everything They say that time's supposed to heal ya But i ain't done much healing. Hello, can you hear me? I'm in California dreaming abou who we used to be
Read More


Default base class for handlers
| Default handlers for the DocumentHandler interface | |||||||||
Default implementation of DocumentHandler interface
| |||||||||
| Default implementation of DTDHandler interface. | |||||||||
Default implementation of the EntityResolver interface.
| |||||||||
Default implementation of the ErrorHandler interface
|
Constructors and Destructor
The EntityResolver interface
The DTD handler interface
This method helps in reseting the DTD object implementational defaults each time the DTD is begun
The virtual document handler interface
This method helps in reseting the document implementational defaults each time the document is begun
The error handler interface
This method helps in reseting the Error handler object implementational defaults each time the Error handler is begun
Default base class for handlers.This class implements the default behaviour for four SAX interfaces: EntityResolver, DTDHandler, DocumentHandler, and ErrorHandler.
Application writers can extend this class when they need to implement only part of an interface; parser writers can instantiate this class to provide default handlers when the application has not supplied its own.
Note that the use of this class is optional.
By default, do nothing. Application writers may override this method to take specific actions for each chunk of character data (such as adding the data to a node or buffer, or printing it to a file).
By default, do nothing. Application writers may override this
method in a subclass to take specific actions at the beginning
of a document (such as finalising a tree or closing an output
file).
By default, do nothing. Application writers may override this
method in a subclass to take specific actions at the end of
each element (such as finalising a tree node or writing
output to a file).
By default, do nothing. Application writers may override this
method to take specific actions for each chunk of ignorable
whitespace (such as adding data to a node or buffer, or printing
it to a file).
By default, do nothing. Application writers may override this
method in a subclass to take specific actions for each
processing instruction, such as setting status variables or
invoking other methods.
length - The number of characters to use from the
character array.
data - The processing instruction data, or null if
none is supplied.
By default, do nothing. Application writers may override this method in a subclass if they wish to store the locator for use with other document events.
By default, do nothing. Application writers may override this
method in a subclass to take specific actions at the beginning
of a document (such as allocating the root node of a tree or
creating an output file).
By default, do nothing. Application writers may override this
method in a subclass to take specific actions at the start of
each element (such as allocating a new tree node or writing
output to a file).
attributes - The specified or defaulted attributes.
Always return null, so that the parser will use the system identifier provided in the XML document. This method implements the SAX default behaviour: application writers can override it in a subclass to do special translations such as catalog lookups or URI redirection.
The default implementation does nothing. Application writers may override this method in a subclass to take specific actions for each error, such as inserting the message in a log file or printing it to the console.
The default implementation throws a SAXParseException.
Application writers may override this method in a subclass if
they need to take specific actions for each fatal error (such as
collecting all of the errors into a single report): in any case,
the application must stop all regular processing when this
method is invoked, since the document is no longer reliable, and
the parser may no longer report parsing events.
The default implementation does nothing. Application writers
may override this method in a subclass to take specific actions
for each warning, such as inserting the message in a log file or
printing it to the console.
SAXParseException
SAXParseException
By default, do nothing. Application writers may override this method in a subclass if they wish to keep track of the notations declared in a document.
By default, do nothing. Application writers may override this
method in a subclass to keep track of the unparsed entities
declared in a document.
publicId - The entity public identifier, or null if not
available.
systemId - The entity system identifier.
notationName - The name of the associated notation.
alphabetic index hierarchy of classes
|
Xerces-C XML Parser for C++ Version 1.1 |
|
|
generated by doc++


{% load static %}
You have 2 news message
Have sent a photo
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Meeting about new dashboard...
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|
JTS Topology Suite version 1.13 | ||||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object com.vividsolutions.jts.geomgraph.TopologyLocation
public class TopologyLocation
A TopologyLocation is the labelling of a GraphComponent's topological relationship to a single Geometry.
If the parent component is an area edge, each side and the edge itself have a topological location. These locations are named
The possible values of a topological location are {Location.NONE, Location.EXTERIOR, Location.BOUNDARY, Location.INTERIOR}
The labelling is stored in an array location[j] where where j has the values ON, LEFT, RIGHT
| Constructor Summary | |
|---|---|
TopologyLocation(int on)
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TopologyLocation(int[] location)
|
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TopologyLocation(int on,
int left,
int right)
Constructs a TopologyLocation specifying how points on, to the left of, and to the right of some GraphComponent relate to some Geometry. |
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TopologyLocation(TopologyLocation gl)
|
| Method Summary | |
|---|---|
boolean |
allPositionsEqual(int loc)
|
void |
flip()
|
int |
get(int posIndex)
|
int[] |
getLocations()
|
boolean |
isAnyNull()
|
boolean |
isArea()
|
boolean |
isEqualOnSide(TopologyLocation le,
int locIndex)
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boolean |
isLine()
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boolean |
isNull()
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void |
merge(TopologyLocation gl)
merge updates only the NULL attributes of this object with the attributes of another. |
void |
setAllLocations(int locValue)
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void |
setAllLocationsIfNull(int locValue)
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void |
setLocation(int locValue)
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void |
setLocation(int locIndex,
int locValue)
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void |
setLocations(int on,
int left,
int right)
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java.lang.String |
toString()
|
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
| Constructor Detail |
|---|
public TopologyLocation(int[] location)
public TopologyLocation(int on, int left, int right)
Location
public TopologyLocation(int on)
public TopologyLocation(TopologyLocation gl)
| Method Detail |
|---|
public int get(int posIndex)
public boolean isNull()
public boolean isAnyNull()
public boolean isEqualOnSide(TopologyLocation le, int locIndex)
public boolean isArea()
public boolean isLine()
public void flip()
public void setAllLocations(int locValue)
public void setAllLocationsIfNull(int locValue)
public void setLocation(int locIndex, int locValue)
public void setLocation(int locValue)
public int[] getLocations()
public void setLocations(int on, int left, int right)
public boolean allPositionsEqual(int loc)
public void merge(TopologyLocation gl)
public java.lang.String toString()
toString
in class java.lang.Object
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JTS Topology Suite version 1.13 | ||||||||
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Getting Started¶
Install the library:
pip install google-alerts
or python setup.py install
Save your configuration:
google-alerts setup --email<EMAIL_ADDRESS>--password 'password'
Seed your session (driver download, http://chromedriver.chromium.org/downloads, do NOT use the pip package as the version is old):
google-alerts seed --driver /tmp/chromedriver --timeout 60
Create a monitor:
google-alerts create --term "hello world" --delivery 'rss' --frequency 'realtime'
List monitors:
google-alerts list
Delete a monitor:
google-alerts delete --id '89e517961a3148c7:c395b7d271b4eccc:com:en:US'
Sample Code¶
This sample code shows some of the range of functionality within the module:
from google_alerts import GoogleAlerts
# Create an instance
ga =<EMAIL_ADDRESS>'**password**')
# Authenticate your user
ga.authenticate()
# List configured monitors
ga.list()
# Add a new monitor
ga.create("Hello World", {'delivery': 'RSS'})
# Modify an existing monitor
ga.modify("89e517961a3148c7:c395b7d271b4eccc:com:en:US", {'delivery': 'RSS', 'monitor_match': 'ALL'})
# Delete a monitor
ga.delete("89e517961a3148c7:c395b7d271b4eccc:com:en:US")
Example Output¶
Below is an example monitor:
[{
"term": "hello world",
"user_id": "09738342945634096720",
"language": "en",
"monitor_id": "89e517961a3148c7:c395b7d271b4eccc:com:en:US",
"region": "US",
"rss_link": "https://google.com/alerts/feeds/09738342945634096720/9663349274289663466",
"delivery": "RSS",
"match_type": "BEST"
}]