adam-gfa

Graphical Fragment Assembly (GFA) support for ADAM.

Hacking adam-gfa

Install

• JDK 1.8 or later, http://openjdk.java.net
• Apache Maven 3.3.9 or later, http://maven.apache.org
• Apache Spark 2.4.6 or later, built for Scala 2.11 http://spark.apache.org

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

Graphical Fragment Assembly (GFA) version 1.0 schema in Parquet format

Gfa1Record

Gfa1Record (scaladoc)

message spark_schema {
  optional binary recordType (UTF8);
  optional binary id (UTF8);
  optional binary sequence (UTF8);
  optional int32 length;
  optional int32 readCount;
  optional int32 fragmentCount;
  optional int32 kmerCount;
  optional binary sequenceChecksum (UTF8);
  optional binary sequenceUri (UTF8);
  optional group source {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional group target {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional binary overlap (UTF8);
  optional int32 mappingQuality;
  optional int32 mismatchCount;
  optional binary pathName (UTF8);
  optional group segments (LIST) {
    repeated group list {
      optional group element {
        optional binary id (UTF8);
        optional binary orientation (UTF8);
      }
    }
  }
  optional group overlaps (LIST) {
    repeated group list {
      optional binary element (UTF8);
    }
  }
  optional int32 ordinal;
  optional group tags (MAP) {
    repeated group key_value {
      required binary key (UTF8);
      optional group value {
        optional binary name (UTF8);
        optional binary type (UTF8);
        optional binary value (UTF8);
      }
    }
  }
}

Link

Link (scaladoc)

message spark_schema {
  optional binary id (UTF8);
  optional group source {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional group target {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional binary overlap (UTF8);
  optional int32 mappingQuality;
  optional int32 mismatchCount;
  optional int32 readCount;
  optional int32 fragmentCount;
  optional int32 kmerCount;
  optional group tags (MAP) {
    repeated group key_value {
      required binary key (UTF8);
      optional group value {
        optional binary name (UTF8);
        optional binary type (UTF8);
        optional binary value (UTF8);
      }
    }
  }
}

Path

Path (scaladoc)

message spark_schema {
  optional binary pathName (UTF8);
  optional group segments (LIST) {
    repeated group list {
      optional group element {
        optional binary id (UTF8);
        optional binary orientation (UTF8);
      }
    }
  }
  optional group overlaps (LIST) {
    repeated group list {
      optional binary element (UTF8);
    }
  }
  optional group tags (MAP) {
    repeated group key_value {
      required binary key (UTF8);
      optional group value {
        optional binary name (UTF8);
        optional binary type (UTF8);
        optional binary value (UTF8);
      }
    }
  }
}

Segment

Segment (scaladoc)

message spark_schema {
  optional binary id (UTF8);
  optional binary sequence (UTF8);
  optional int32 length;
  optional int32 readCount;
  optional int32 fragmentCount;
  optional int32 kmerCount;
  optional binary sequenceChecksum (UTF8);
  optional binary sequenceUri (UTF8);
  optional group tags (MAP) {
    repeated group key_value {
      required binary key (UTF8);
      optional group value {
        optional binary name (UTF8);
        optional binary type (UTF8);
        optional binary value (UTF8);
      }
    }
  }
}

Traversal

Traversal (scaladoc)

message spark_schema {
  optional binary pathName (UTF8);
  optional int32 ordinal;
  optional group source {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional group target {
    optional binary id (UTF8);
    optional binary orientation (UTF8);
  }
  optional binary overlap (UTF8);
  optional group tags (MAP) {
    repeated group key_value {
      required binary key (UTF8);
      optional group value {
        optional binary name (UTF8);
        optional binary type (UTF8);
        optional binary value (UTF8);
      }
    }
  }
}