heuermh / adam-gfa

Graphical Fragment Assembly (GFA) support for ADAM. Licensed LGPL version 3 or later.

GitHub

adam-gfa

Graphical Fragment Assembly (GFA) support for ADAM.

Build Status Maven Central

Hacking adam-gfa

Install

To build

$ mvn install

Running adam-gfa

Read and write Graphical Fragment Assembly (GFA) version 1.0

$ spark-submit \
    --class com.github.heuermh.adam.gfa.Gfa1 \
    target/adam-gfa_2.11-${version}.jar \
    in.gfa \
    out.gfa

Transform GFA 1.0 to generic Gfa1Record records in Parquet format

$ spark-submit \
    --class com.github.heuermh.adam.gfa.Gfa1ToDataframe \
    target/adam-gfa_2.11-${version}.jar \
    in.gfa \
    out.parquet

Transform GFA 1.0 to specific Link, Path, Segment, and Traversal records in Parquet format

$ spark-submit \
    --class com.github.heuermh.adam.gfa.Gfa1ToDataframes \
    target/adam-gfa_2.11-${version}.jar \
    in.gfa \
    out

(creates separate out.links.parquet, out.paths.parquet, out.segments.parquet, and out.traversals.parquet directories)

Read and write Graphical Fragment Assembly (GFA) version 2.0

$ spark-submit \
    --class com.github.heuermh.adam.gfa.Gfa2 \
    target/adam-gfa_2.11-${version}.jar \
    in.gfa2 \
    out.gfa2

Documentation

libraryDependencies += "com.github.heuermh.adamgfa" %% "adam-gfa" % "0.3.0"
Ammonite REPL 
import $ivy.`com.github.heuermh.adamgfa::adam-gfa:0.3.0`
<dependency>
  <groupId>com.github.heuermh.adamgfa</groupId>
  <artifactId>adam-gfa_2.11</artifactId>
  <version>0.3.0</version>
</dependency>
compile group: 'com.github.heuermh.adamgfa', name: 'adam-gfa_2.11', version: '0.3.0'
Mill build tool 
ivy"com.github.heuermh.adamgfa::adam-gfa:0.3.0"
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9 Dependencies

Java Dependencies