Update flex options for genotype#17

Open

Georgehe4 wants to merge 149 commits intoakmorrow13:masterfrom

Georgehe4:pileup_vis_fix

Commits on Oct 3, 2016

pass all tests

dorisjlee
authored and
Alyssa Morrow
committed
pass all tests

dorisjlee
authored and
Alyssa Morrow
committed
ga4gh data source loaded in, compatible with mango, no error

dorisjlee
authored and
Alyssa Morrow
committed
starting reference
Alyssa Morrow
committed
continued reference implementation
Alyssa Morrow
committed
added test resources for ADAM alignments
Alyssa Morrow
committed
modified alignment json for test
Alyssa Morrow
committed
continue reference
Alyssa Morrow
committed
tests passing for reference
Alyssa Morrow
committed
reference through server now works
Alyssa Morrow
committed
variants now work
Alyssa Morrow
committed
added key to remote request
Alyssa Morrow
committed
starting reference
Alyssa Morrow
committed
continued reference implementation
Alyssa Morrow
committed
added test resources for ADAM alignments
Alyssa Morrow
committed
continue reference
Alyssa Morrow
committed
tests passing for reference
Alyssa Morrow
committed
reference through server now works
Alyssa Morrow
committed
variants now works
Alyssa Morrow
committed
pileup can now display genotypes
Alyssa Morrow
committed
completed the genotype feature and variant class files

justinzh1
authored and
Alyssa Morrow
committed
Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead

justinzh1
authored and
Alyssa Morrow
committed
Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file

justinzh1
authored and
Alyssa Morrow
committed
Finished FeatureDataSouce along with FeatureEndpoint files to work with RemoteRequest file

justinzh1
authored and
Alyssa Morrow
committed
completed the feature test file

justinzh1
authored and
Alyssa Morrow
committed
finished feature.js featuredatasource.js and featuredatasource-test.js

justinzh1
authored and
Alyssa Morrow
committed
removed genotype.js and variant.js since they were incomplete

justinzh1
authored and
Alyssa Morrow
committed
added featuredatasource to pileup.js file

justinzh1
authored and
Alyssa Morrow
committed
completed the genotype feature and variant class files

justinzh1
authored and
Alyssa Morrow
committed
Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead

justinzh1
authored and
Alyssa Morrow
committed
Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file

justinzh1
authored and
Alyssa Morrow
committed
removed genotype.js and variant.js since they were incomplete

justinzh1
authored and
Alyssa Morrow
committed
finished merge conflicts in RemoteRequestjs

justinzh1
authored and
Alyssa Morrow
committed
Started working on creating featuredatasource-test.js

justinzh1
authored and
Alyssa Morrow
committed
completed generic feature visualization
Alyssa Morrow
committed
added check for negative values and restricted alignment fetch size
Alyssa Morrow
committed
completed gene endpoint
Alyssa Morrow
committed
removed prepush hooks
Alyssa Morrow
committed
Passing more tests
Alyssa Morrow
committed
merge in main pileup updates and modified RemoteRequest
Alyssa Morrow
committed
customized ALT REF colors for variants, greyed genotype

dorisjlee
authored and
Alyssa Morrow
committed

Commits on Oct 4, 2016

fixed versions, shorted build time
Alyssa Morrow
committed

Commits on Oct 5, 2016

small formatting nits and removing double 'strict' statement
Alyssa Morrow
committed
fixed genotype samples and added unit tests
Alyssa Morrow
committed
Removed alignment test file and renamed Alignment test suite
Alyssa Morrow
committed
fixed ReferenceDataSource and added new test file for genotypes
Alyssa Morrow
committed

Commits on Oct 12, 2016

Minor fixes for zooming in and out on alignments and coverage
Alyssa Morrow
committed

Commits on Oct 13, 2016

added coverage endpoint
Alyssa Morrow
committed
Modified CoverageDataSource to bin by region size
Alyssa Morrow
committed
continued coverage vis
Alyssa Morrow
committed

Commits on Oct 15, 2016

Finished coverage with Resolution cache. Thresholded view to length of chromosome.
Alyssa Morrow
committed

Commits on Nov 1, 2016

Variant end tracking
Georgehe4
committed

Commits on Nov 3, 2016

completed coverage tracks and binning
Alyssa Morrow
committed

Commits on Dec 11, 2016

Merge pull request #4 from Georgehe4/variant_end
akmorrow13
authored
fixed reference offset visualization
Alyssa Morrow
committed
Merge pull request #5 from akmorrow13/reference
akmorrow13
authored

Commits on Dec 19, 2016

added checks for null data return types
Alyssa Morrow
committed

Commits on Dec 20, 2016

Merge pull request #6 from akmorrow13/remove-null
akmorrow13
authored

Commits on Jan 2, 2017

added score visualization for features
Alyssa Morrow
committed

Commits on Jan 3, 2017

added click and loading functionality for features
Alyssa Morrow
committed

Commits on Jan 10, 2017

updated features to view correctly and show info on click
Alyssa Morrow
committed
Merge pull request #7 from akmorrow13/standardizeFeatures
akmorrow13
authored
added limit for visualizing large Feature areas
Alyssa Morrow
committed

Commits on Jan 12, 2017

Interval.isCoveredBy() fix for regions not overlapping first interval
Alyssa Morrow
committed
bump version up top 0.6.7

armish
authored and
Alyssa Morrow
committed
rename poorly-named parameter

ryan-williams
authored and
Alyssa Morrow
committed
handle non-compressed BigBed files

ryan-williams
authored and
Alyssa Morrow
committed
relax BigBed version number constraint

ryan-williams
authored and
Alyssa Morrow
committed
spacing nit

ryan-williams
authored and
Alyssa Morrow
committed
CR: add types, clean up test

ryan-williams
authored and
Alyssa Morrow
committed
Resolve load alignment jump issues

Georgehe4
authored and
Alyssa Morrow
committed
bump version up to 0.6.8

armish
authored and
Alyssa Morrow
committed
pass all tests

dorisjlee
authored and
Alyssa Morrow
committed
pass all tests

dorisjlee
authored and
Alyssa Morrow
committed
ga4gh data source loaded in, compatible with mango, no error

dorisjlee
authored and
Alyssa Morrow
committed
starting reference
Alyssa Morrow
committed
continued reference implementation
Alyssa Morrow
committed
added test resources for ADAM alignments
Alyssa Morrow
committed
modified alignment json for test
Alyssa Morrow
committed
continue reference
Alyssa Morrow
committed
tests passing for reference
Alyssa Morrow
committed
reference through server now works
Alyssa Morrow
committed
variants now work
Alyssa Morrow
committed
added key to remote request
Alyssa Morrow
committed
starting reference
Alyssa Morrow
committed
continued reference implementation
Alyssa Morrow
committed
added test resources for ADAM alignments
Alyssa Morrow
committed
continue reference
Alyssa Morrow
committed
tests passing for reference
Alyssa Morrow
committed
reference through server now works
Alyssa Morrow
committed
variants now works
Alyssa Morrow
committed
pileup can now display genotypes
Alyssa Morrow
committed
completed the genotype feature and variant class files

justinzh1
authored and
Alyssa Morrow
committed
Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead

justinzh1
authored and
Alyssa Morrow
committed
Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file

justinzh1
authored and
Alyssa Morrow
committed
Finished FeatureDataSouce along with FeatureEndpoint files to work with RemoteRequest file

justinzh1
authored and
Alyssa Morrow
committed
completed the feature test file

justinzh1
authored and
Alyssa Morrow
committed
finished feature.js featuredatasource.js and featuredatasource-test.js

justinzh1
authored and
Alyssa Morrow
committed
removed genotype.js and variant.js since they were incomplete

justinzh1
authored and
Alyssa Morrow
committed
added featuredatasource to pileup.js file

justinzh1
authored and
Alyssa Morrow
committed
completed the genotype feature and variant class files

justinzh1
authored and
Alyssa Morrow
committed
Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead

justinzh1
authored and
Alyssa Morrow
committed
Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file

justinzh1
authored and
Alyssa Morrow
committed
removed genotype.js and variant.js since they were incomplete

justinzh1
authored and
Alyssa Morrow
committed
finished merge conflicts in RemoteRequestjs

justinzh1
authored and
Alyssa Morrow
committed
Started working on creating featuredatasource-test.js

justinzh1
authored and
Alyssa Morrow
committed
completed generic feature visualization
Alyssa Morrow
committed
added check for negative values and restricted alignment fetch size
Alyssa Morrow
committed
completed gene endpoint
Alyssa Morrow
committed
removed prepush hooks
Alyssa Morrow
committed
Passing more tests
Alyssa Morrow
committed
merge in main pileup updates and modified RemoteRequest
Alyssa Morrow
committed
customized ALT REF colors for variants, greyed genotype

dorisjlee
authored and
Alyssa Morrow
committed
fixed versions, shorted build time
Alyssa Morrow
committed
small formatting nits and removing double 'strict' statement
Alyssa Morrow
committed
fixed genotype samples and added unit tests
Alyssa Morrow
committed
Removed alignment test file and renamed Alignment test suite
Alyssa Morrow
committed
fixed ReferenceDataSource and added new test file for genotypes
Alyssa Morrow
committed
Minor fixes for zooming in and out on alignments and coverage
Alyssa Morrow
committed
added coverage endpoint
Alyssa Morrow
committed
Modified CoverageDataSource to bin by region size
Alyssa Morrow
committed
continued coverage vis
Alyssa Morrow
committed
Finished coverage with Resolution cache. Thresholded view to length of chromosome.
Alyssa Morrow
committed
completed coverage tracks and binning
Alyssa Morrow
committed
Variant end tracking

Georgehe4
authored and
Alyssa Morrow
committed
fixed reference offset visualization
Alyssa Morrow
committed
added checks for null data return types
Alyssa Morrow
committed
added score visualization for features
Alyssa Morrow
committed
added click and loading functionality for features
Alyssa Morrow
committed
updated features to view correctly and show info on click
Alyssa Morrow
committed
added limit for visualizing large Feature areas
Alyssa Morrow
committed

Commits on Jan 14, 2017

fixed no data error for alignments and max rows for PileupTrack
Alyssa Morrow
committed
Merge branch 'master' of https://github.com/akmorrow13/pileup.js
Alyssa Morrow
committed
Merge pull request #8 from akmorrow13/alignments
akmorrow13
authored

Commits on Jan 20, 2017

Added loading sign for variants and fixed click functionality
Alyssa Morrow
committed

Commits on Jan 23, 2017

Added resolution cache to variants. Fixed resolution cache to not request areas already in cache.
Alyssa Morrow
committed

Commits on Jan 27, 2017

finished genotypes
Alyssa Morrow
committed
Merge pull request #9 from akmorrow13/variant-fixes
akmorrow13
authored
binning for features
Alyssa Morrow
committed

Commits on Jan 31, 2017

Fixed error in coverage
Alyssa Morrow
committed

Commits on Feb 21, 2017

Merge branch 'master' of https://github.com/hammerlab/pileup.js
Alyssa Morrow
committed

Commits on Feb 22, 2017

Removed unused imports, tests for FeatureDataSource and VariantDataSource now passing
Alyssa Morrow
committed

Commits on Mar 6, 2017

Commits on Apr 22, 2017

added info timers for server requests
Alyssa Morrow
committed

Commits on Jun 12, 2017

Fixed overlap issue for Variants and Coverage display
Alyssa Morrow
committed
Fixed off by 1 error for Variant display
Alyssa Morrow
committed
Merge pull request #16 from akmorrow13/variantFixes
akmorrow13
authored

Commits on Jun 15, 2017

Update flex options for genotype
Georgehe4
committed