MUTATION PHASE Addons
LINK >> https://fancli.com/2t7GSv
The admission control process proceeds in two phases. In the first phase,mutating admission controllers are run. In the second phase, validatingadmission controllers are run. Note again that some of the controllers areboth.
This admission controller calls any validating webhooks which match the request. Matchingwebhooks are called in parallel; if any of them rejects the request, the requestfails. This admission controller only runs in the validation phase; the webhooks it calls may notmutate the object, as opposed to the webhooks called by the MutatingAdmissionWebhook admission controller.
The scm mutation coverage goal analyses only classes that match the filters and the source file has a given status within the project source control system (by default ADDED or MODIFIED). This provides a quick way to check the coverage of changes prior to checking code in / pushing code to a repository.
Will disable the filtering of junk mutations in code the compiler generates to support Java records, and enable the automatic setting of the number of threads based on the number of cores reported by the current machine.
The distance filter is particularly useful when performing a targeted mutation test of a subset of classes withina large project as it avoids the overheads of calculating the times and coverage of tests that cannot exercise the mutees.
Indicates if PIT should attempt to detect the inlined code generated by the java compiler in order to implementfinally blocks. Each copy of the inlined code would normally be mutated separately, resulting in multipleidentical looking mutations. When inlined code detection is enabled PIT will attempt to spot inlined code and createonly a single mutation that mutates all affected instructions simultaneously.
Starting with version 1.1.6, the pit maven plugin has a maven report goal. This goal should only be invoked as part of the maven site lifecycle. To execute this goal, the mutationCoverage goal must have already been executed to produce an HTML report (i.e. the outputFormat parameter must have HTML in it if the parameter is specified. The report goal then copies the latest HTML report to the site directory. If multiple reports exist (as in the case where timestampedReports is set to true), then only the report with the latest create time is used.
Meanwhile, PitMP runs PIT on a complete project: the test suites are executed against the mutants generated in all classes of the project. In return, it produces a global mutation score for the project.The key rationale for the plugin is that some projects include test cases that are meant to assess the correctness of code regions that are in other modules.
Dynamic admission should be used cautiously because it impacts cluster control plane operations. When calling webhook servers through webhook admission plugins in OpenShift Container Platform 4.10, ensure that you have read the documentation fully and tested for side effects of mutations. Include steps to restore resources back to their original state prior to mutation, in the event that a request does not pass through the entire admission chain.
It can be used along with fulvestrant to treat postmenopausal women with advanced hormone receptor-positive, HER2-negative breast cancer with a PIK3CA gene mutation that has grown during or after treatment with an aromatase inhibitor. About 30% to 40% of breast cancers have a mutated PIK3CA gene. Your doctor will test your blood or tumor for this mutation before starting treatment with this drug.
Olaparib (Lynparza) and talazoparib (Talzenna) are drugs known as PARP inhibitors. PARP proteins normally help repair damaged DNA inside cells. The BRCA genes (BRCA1 and BRCA2) also help repair DNA (in a slightly different way), but mutations in one of those genes can stop this from happening. PARP inhibitors work by blocking the PARP proteins. Because tumor cells with a mutated BRCA gene already have trouble repairing damaged DNA, blocking the PARP proteins often leads to the death of these cells. These drugs are pills and are taken once or twice a day. They can be used in different ways to treat breast cancer.
Olaparib can be given to women with a BRCA mutation with early-stage HER2-negative breast cancer after surgery who have been treated with chemotherapy (before or after surgery) and are at high risk of the cancer recurring. It is typically given for one year. When given in this way, it can help some women live longer.
Olaparib and talazoparib can be used to treat advanced or metastatic, HER2-negative breast cancer in women with a BRCA mutation who have already had chemotherapy. If the cancer is hormone receptor-positive, olaparib can also be used in women who have already received hormone therapy.
Only a small portion of women with breast cancer are born with a mutated BRCA gene, which is in all the cells of the body. This is different from the gene change happening after you are born which is found only in the cancer cells. If you are not known to have a BRCA mutation, your doctor will test your blood to be sure you have one before starting treatment with these drugs.
Chan A, Delaloge S, Holmes FA, Moy B, Iwata H, Harvey VJ et al. Neratinib after trastuzumab-based adjuvant therapy in patients with HER2-positive breast cancer (ExteNET): a multicentre, randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 2016 Mar;17(3):367-77.
This is a plugin for the Ensembl Variant Effect Predictor (VEP) thatlooks up the BLOSUM 62 substitution matrix score for the referenceand alternative amino acids predicted for a missense mutation. It addsone new entry to the VEP's Extra column, BLOSUM62 which is the associated score.
This is a plugin for the Ensembl Variant Effect Predictor (VEP) that calculatesthe Combined Annotation scoRing toOL (CAROL) score (1) for a missense mutation based on the pre-calculated SIFT (2) and PolyPhen-2 (3) scores from the Ensembl API (4). It adds one new entry class to the VEP's Extra column, CAROL which isthe calculated CAROL score. Note that this module is a perl reimplementation of the original R script, available at: ... more
(3) Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutationsNature Methods 7(4):248-249 (2010)doi:10.1038/nmeth0410-248
This is a plugin for the Ensembl Variant Effect Predictor (VEP) that calculatesthe Consensus Deleteriousness (Condel) score (1) for a missense mutation based on the pre-calculated SIFT (2) and PolyPhen-2 (3) scores from the Ensembl API (4). It adds one new entry class to the VEP's Extra column, Condel which isthe calculated Condel score. This version of Condel was developed by the Biomedical Genomics Group of the Universitat Pompeu Fabra, at the Barcelona Biomedical Research Park and available at( ) until April 2014. The code in this plugin is based on a script provided by this group and slightly reformatted to fit into the Ensembl API. ... more
LoFtool provides a rank of genic intolerance and consequentsusceptibility to disease based on the ratio of Loss-of-function (LoF)to synonymous mutations for each gene in 60,706 individuals from ExAC,adjusting for the gene de novo mutation rate and evolutionary proteinconservation. The lower the LoFtool gene score percentile the mostintolerant is the gene to functional variation. For more details please see(Fadista J et al. 2017), PMID:27563026.The authors would like to thank the Exome Aggregation Consortium andthe groups that provided exome variant data for comparison. A fulllist of contributing groups can be found at
Running options:The plugin has multiple parameters, the first one is expected to be the file name path which can be followed by 3 optional flags.Default: the plugin matches the citation data with the specific mutation.Using first flag '1': returns the citations for all mutations/transcripts. Using the second flag '1': only returns the Mastermind variant identifier(s).Using the third flag '1': also returns the Mastermind URL.
The plugin can then be run as default: ./vep -i variations.vcf --plugin Mastermind,/path/to/mastermind_cited_variants_reference-XXXX.XX.XX.GRChXX-vcf.gzor with an option to not filter by mutations (first flag): ./vep -i variations.vcf --plugin Mastermind,/path/to/mastermind_cited_variants_reference-XXXX.XX.XX.GRChXX-vcf.gz,1 or with an option to only return 'MMID3' e.g. the Mastermind variant identifier as gene:key (second flag): ./vep -i variations.vcf --plugin Mastermind,/path/to/mastermind_cited_variants_reference-XXXX.XX.XX.GRChXX-vcf.gz,0,1or with an option to also return the Mastermind URL (third flag): ./vep -i variations.vcf --plugin Mastermind,/path/to/mastermind_cited_variants_reference-XXXX.XX.XX.GRChXX-vcf.gz,0,0,1Note: when running VEP in offline mode Mastermind requires a fasta file (--fasta)
The PrimateAI VEP plugin is designed to retrieve clinical impact scores of variants, as described in -018-0167-z. Please consider citing the paper if using this plugin.In brief, common missense mutations in non-human primate species are usually benign in humans. Thousands of common variants from six non-human primate species were used to train a deep neural network to identify pathogenic mutations in humans with a rare disease. ... more 2b1af7f3a8