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commandline argument collections #67

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akiezun opened this issue Dec 16, 2014 · 1 comment
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commandline argument collections #67

akiezun opened this issue Dec 16, 2014 · 1 comment
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@akiezun
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akiezun commented Dec 16, 2014

It;s useful to have groups of arguments shared between tools - for code reuse and name consistency
@akiezun akiezun added the Engine label Dec 16, 2014
@akiezun akiezun added this to the Aye-aye milestone Dec 16, 2014
@droazen droazen closed this as completed Jan 13, 2015
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droazen commented Jan 13, 2015

(dupe)

@droazen droazen removed this from the Aye-aye milestone Jan 13, 2015
This was referenced Jan 21, 2015
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lbergelson added a commit that referenced this issue Jan 23, 2015
@lbergelson
Merge pull request #135 from broadinstitute/lb_unix_style_options
844f9cd 
Major changes to the command line parsing system

Closes #67, #81, #111
lbergelson pushed a commit that referenced this issue May 31, 2017
@mbabadi
Merge pull request #444 from broadinstitute/mb_bayesian_het_pulldown. C…
837e846 
…loses #56 and #67.

* Bayesian Het pulldown tool

* Updated CNV-methods.tex (reverted the accidentally deleted section)
Renamed naturalLogSumExp to logSumExp everywhere
Added three levels of verbosity (BASIC, INTERMEDIATE, FULL) for writing/reading AllelicCountCollection
Automatic detection of verbosity mode in reading AllelicCountCollection from file
Updated AllelicCount R == L comparator ("equals") to ignore extra metadata when it is not available for both R and L
Refactored DataLine parsers to AllelicCount
New tests for AllelicCountCollection and AllelicCount
New tests in GetBayesianHetCoverageIntegrationTest
Removed extra "add" methods in AllelicCountCollection in favor of just one in order to decouple from the future changes in the constructor of AllelicCount
MANY small fixes from the previous round of review

* New AllelicCountReader and AllelicCountWriter classes and unit tests (in AllelicCountCollectionUnitTest).
Abstraction of Heterozygous priors with balanced and hetergeneous implementations and unit tests.
Refactoring of unit tests.

* Changed POS to POSITION in all unit test Het pulldown resource files to conform with the new AllelicCountTableColumns convention

* Incorporated all suggested changes from the last PR review.
Minor cosmetic changes (blank lines) here and there for conformity with the existing code.

* Generalized the signature of HeterozygousPileupPriorModel#getHetLogLikelihood + minor changes from the last PR review.
lucidtronix pushed a commit that referenced this issue Jul 27, 2021
@paolodi
Tensormaps for LVH criteria and ECG resting plots (#67)
8a9ab06 
* Added extraction of R and S amplitudes from XML during tensorization
* Added TMAPS to compute LVH criteria from amplitudes (new notebook for testing)
* Added plotting functionality for 12-lead resting ECGs including median waveforms and R S amplitudes
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@kshakir @droazen @akiezun @lbergelson