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GitHub / bigdatagenomics / adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigdatagenomics%2Fadam

Stars: 967
Forks: 304
Open Issues: 34

License: apache-2.0
Language: Scala
Repo Size: 12.4 MB
Dependencies: 102

Created: over 10 years ago
Updated: 10 days ago
Last pushed: 2 months ago
Last synced: 10 days ago

Commit Stats

Commits: 1643
Authors: 88
Mean commits per author: 18.67
Development Distribution Score: 0.708
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/bigdatagenomics/adam

Topics: avro, big-data, bioinformatics, genomics, java, parquet, python, r, scala, spark

Files

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Readme

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Dependencies

adam-r/bdgenomics.adam/DESCRIPTION cran

R >= 3.0 depends
SparkR >= 2.1.0 imports
methods * imports
testthat * suggests

adam-apis/pom.xml maven

adam-assembly/pom.xml maven

org.bdgenomics.adam:adam-cli-spark3_${scala.version.prefix} compile

adam-cli/pom.xml maven

adam-codegen/pom.xml maven

adam-core/pom.xml maven

com.esotericsoftware.kryo:kryo compile
com.github.samtools:htsjdk compile
com.google.guava:guava compile
commons-io:commons-io compile
it.unimi.dsi:fastutil compile
org.apache.avro:avro compile
org.apache.httpcomponents:httpclient compile
org.apache.parquet:parquet-avro compile
org.bdgenomics.bdg-formats:bdg-formats compile
org.bdgenomics.utils:utils-cli-spark3_${scala.version.prefix} compile
org.bdgenomics.utils:utils-intervalrdd-spark3_${scala.version.prefix} compile
org.bdgenomics.utils:utils-io-spark3_${scala.version.prefix} compile
org.bdgenomics.utils:utils-misc-spark3_${scala.version.prefix} compile
org.clapper:grizzled-slf4j_${scala.version.prefix} compile
org.seqdoop:hadoop-bam compile
org.scala-lang:scala-library provided
org.apache.spark:spark-core_${scala.version.prefix}
org.apache.spark:spark-sql_${scala.version.prefix}
org.bdgenomics.adam:adam-codegen-spark3_${scala.version.prefix}
org.bdgenomics.utils:utils-misc-spark3_${scala.version.prefix} test
org.mockito:mockito-core test
org.scalatest:scalatest_${scala.version.prefix} test
org.slf4j:slf4j-log4j12 test

pom.xml maven

net.razorvine:pyrolite 5.1 provided
org.apache.spark:spark-core_2.12 3.2.1 provided
org.apache.spark:spark-sql_2.12 3.2.1 provided
args4j:args4j 2.33
com.esotericsoftware.kryo:kryo 2.24.0
com.github.samtools:htsjdk 2.19.0
com.google.guava:guava 31.1-jre
com.thoughtworks.paranamer:paranamer 2.8
commons-codec:commons-codec 1.15
commons-io:commons-io 2.11.0
it.unimi.dsi:fastutil 8.5.8
net.codingwell:scala-guice_2.12 5.0.2
org.apache.avro:avro 1.10.2
org.apache.httpcomponents:httpclient 4.5.13
org.apache.parquet:parquet-avro 1.12.1
org.bdgenomics.adam:adam-apis-spark3_2.12 1.1-SNAPSHOT
org.bdgenomics.adam:adam-cli-spark3_2.12 1.1-SNAPSHOT
org.bdgenomics.adam:adam-codegen-spark3_2.12 1.1-SNAPSHOT
org.bdgenomics.adam:adam-core-spark3_2.12 1.1-SNAPSHOT
org.bdgenomics.bdg-formats:bdg-formats 1.0
org.bdgenomics.utils:utils-cli-spark3_2.12 1.0
org.bdgenomics.utils:utils-intervalrdd-spark3_2.12 1.0
org.bdgenomics.utils:utils-io-spark3_2.12 1.0
org.bdgenomics.utils:utils-misc-spark3_2.12 1.0
org.clapper:grizzled-slf4j_2.12 1.3.4
org.scala-lang:scala-library 2.12.15
org.scala-lang:scala-reflect 2.12.15
org.seqdoop:hadoop-bam 7.9.2
org.slf4j:jcl-over-slf4j 1.7.30
org.slf4j:jul-to-slf4j 1.7.30
org.slf4j:slf4j-api 1.7.30
org.slf4j:slf4j-log4j12 1.7.30
org.bdgenomics.adam:adam-apis-spark3_2.12 1.1-SNAPSHOT test
org.bdgenomics.adam:adam-core-spark3_2.12 1.1-SNAPSHOT test
org.bdgenomics.utils:utils-misc-spark3_2.12 1.0 test
org.mockito:mockito-core 4.5.1 test
org.scalatest:scalatest_2.12 3.0.7 test

adam-python/setup.py pypi

pyspark >=1.6.0

docs/requirements.txt pypi

sphinx ==1.7.7

.github/workflows/ci.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-java v2 composite

.github/workflows/deploy.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-java v2 composite