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