Use org.bdgenomics for package names and groupId #7
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adgirish
referenced
this issue
in adgirish/gnocchi
Sep 20, 2017
* adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml
p-yang
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to p-yang/gnocchi
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Sep 25, 2017
* building and saving models working * Incremental update working * changes model save * creates GnocchiSession * preliminary loadPhenotype changes * stuff * loadPhenotypes working * loadGenotypes working * loadGenotypes working * load from raw VCF optimized * adds in documentation package and documents genotypic dataset info * fixes formatting * filterSamples working * filterVariants working * phenotypes to map * Adds tests for sc.loadGenotypes and sc.filterSamples (bigdatagenomics#7) * adds GnocchiSessionSuite.scala * adds tests for sc.loadGenotypes and sc.filterSamples * fixes tests with a uniqueID * testing broken * tests working with intellij * starts siteRegression refactor * additive linear end to end in gnocchi shell working * linear and logistic working * fixes variantModels * variant models working * refactor stuff * test files * track * checkpoint * gnocchi Model factory working * merge GnocchiModel on additive linear models * merging all gnocchi models, adds logo * regressPhenotypes first pass * working regressPhenotypes
kunalgosar
referenced
this issue
in adgirish/gnocchi
Oct 2, 2017
* adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml
p-yang
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to p-yang/gnocchi
that referenced
this issue
Nov 29, 2017
…omics#32) * Added python binding boilerplate * more boilerplate for bindings * adding todo file for java wrapper * laying out more skeleton code * Implemented gnocchiSession python object * Working on Java Wrapper for Bindings adgirish: * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * Bindings (bigdatagenomics#7) * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml * Fix Project Modules and pom files * adding todo file for java wrapper * laying out more skeleton code * added empty interfaces * todo add method comments * added empty interfaces * todo add method comments * added pom.xml * changing reference in pom.xml * changing reference in pom.xml v2 * added python pointer wrappers * Created and Modified pom files * Updated JavaGnocchiSession and Refactor * make file for gnocchi-python * Added assembly and packaging * Bindingsv3 (bigdatagenomics#12) * v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype * Bindingsv3 (bigdatagenomics#13) * v1 * resolved import issues, fixed JavaGnocchiSession, corrected BetterPhenotype * added test to verify java wrappers * added test to verify java wrappers * resolve conflicts - 2 * remove redundant makefile * updated packing and dependencies * fixes maven build * fixed issues with assembly build * updated load genotypes method * SparkSession Creation fix for compatibility with pySpark (bigdatagenomics#21) * rebasing onto nate's branch and moving remaining packages to org.bdgenomics * resolve dependency issues caused by refactor * Documentation for JVM and Python Gnocchi Session * cleaning unused dependencies * adding JavaGnocchiSession tests (bigdatagenomics#22) * remove unused dependencies * resolved nates comments
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