{"id":17955463,"url":"https://github.com/heuermh/adam-explorer","last_synced_at":"2025-04-03T16:49:20.579Z","repository":{"id":44544692,"uuid":"168213600","full_name":"heuermh/adam-explorer","owner":"heuermh","description":"Interactive explorer for ADAM genomics data models.  Apache 2 licensed.","archived":false,"fork":false,"pushed_at":"2023-04-21T20:46:26.000Z","size":938,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-09T05:37:51.437Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/heuermh.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2019-01-29T19:20:57.000Z","updated_at":"2022-02-07T17:09:47.000Z","dependencies_parsed_at":"2024-01-15T20:47:26.543Z","dependency_job_id":"83ca295e-d9ea-4334-bdf0-ef6423c66d33","html_url":"https://github.com/heuermh/adam-explorer","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fadam-explorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fadam-explorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fadam-explorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/heuermh%2Fadam-explorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/heuermh","download_url":"https://codeload.github.com/heuermh/adam-explorer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247043325,"owners_count":20874085,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-29T10:28:43.246Z","updated_at":"2025-04-03T16:49:20.552Z","avatar_url":"https://github.com/heuermh.png","language":"Java","funding_links":[],"categories":["Extending ADAM"],"sub_categories":["Libraries"],"readme":"# adam-explorer\nInteractive explorer for ADAM genomics data models.  Apache 2 licensed.\n\n[![Build Status](https://travis-ci.org/heuermh/adam-explorer.svg?branch=master)](https://travis-ci.org/heuermh/adam-explorer)\n[![Maven Central](https://img.shields.io/maven-central/v/com.github.heuermh.adamexplorer/adam-explorer_2.12.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Ccom.github.heuermh.adamexplorer)\n[![API Documentation](http://javadoc.io/badge/com.github.heuermh.adamexplorer/adam-explorer_2.12.svg?color=brightgreen\u0026label=scaladoc)](http://javadoc.io/doc/com.github.heuermh.adamexplorer/adam-explorer)\n\n\n### Hacking adam-explorer\n\nInstall\n\n * JDK 1.8 or later, http://openjdk.java.net\n * Apache Maven 3.3.9 or later, http://maven.apache.org\n * Apache Spark 3.2.0 or later, http://spark.apache.org\n * ADAM: Genomic Data System 0.37.0 or later, https://github.com/bigdatagenomics/adam\n\n\nTo build\n\n    $ mvn install\n\n\n### Running adam-explorer using ```spark-shell```\n\n```\n$ spark-shell \\\n    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \\\n    --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \\\n    --jars target/adam-explorer_2.12-\u003cversion\u003e-SNAPSHOT.jar,$PATH_TO_ADAM_ASSEMBLY_JAR\n\n...\nWelcome to\n      ____              __\n     / __/__  ___ _____/ /__\n    _\\ \\/ _ \\/ _ `/ __/  '_/\n   /___/ .__/\\_,_/_/ /_/\\_\\   version 3.2.0\n      /_/\n\nUsing Scala version 2.12.15 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191)\nType in expressions to have them evaluated.\nType :help for more information.\n\nscala\u003e import org.bdgenomics.adam.ds.ADAMContext._\nimport org.bdgenomics.adam.ds.ADAMContext._\n\nscala\u003e import com.github.heuermh.adam.explorer.ADAMExplorer._\nimport com.github.heuermh.adam.explorer.ADAMExplorer._\n\nscala\u003e val alignments = sc.loadAlignments(\"sample.bam\")\nalignments: org.bdgenomics.adam.ds.read.AlignmentRecordRDD = RDDBoundAlignmentRecordRDD\nwith 85 reference sequences, 3 read groups, and 0 processing steps\n\nscala\u003e explore(alignments)\nres0: Int = 0\n\nscala\u003e\n```\n\n![adam-explorer screenshot](https://github.com/heuermh/adam-explorer/raw/master/images/screen-shot.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fadam-explorer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fheuermh%2Fadam-explorer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fadam-explorer/lists"}