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https://github.com/heuermh/adam-gfa
Graphical Fragment Assembly (GFA) support for ADAM. Licensed LGPL version 3 or later.
https://github.com/heuermh/adam-gfa
Last synced: 9 days ago
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Graphical Fragment Assembly (GFA) support for ADAM. Licensed LGPL version 3 or later.
- Host: GitHub
- URL: https://github.com/heuermh/adam-gfa
- Owner: heuermh
- License: lgpl-3.0
- Created: 2017-11-14T15:27:24.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2023-04-21T20:46:30.000Z (over 1 year ago)
- Last Synced: 2024-07-30T13:13:30.767Z (3 months ago)
- Language: Scala
- Homepage:
- Size: 98.6 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: COPYING
Awesome Lists containing this project
README
# adam-gfa
Graphical Fragment Assembly (GFA) support for ADAM.
[](https://travis-ci.org/heuermh/adam-gfa)
[](http://search.maven.org/#search%7Cga%7C1%7Ccom.github.heuermh.adamgfa)
[](http://javadoc.io/doc/com.github.heuermh.adamgfa/adam-gfa_2.12)
### 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 3.1.2 or later, built for Scala 2.12 http://spark.apache.org
To build
$ mvn install
### Running adam-gfa
Transform GFA 1.0 to generic [`Gfa1Record`](#gfa1record) records in Parquet format
```
$ spark-submit \
--class com.github.heuermh.adam.gfa.Gfa1ToDataframe \
target/adam-gfa_2.12-${version}.jar \
in.gfa \
out.parquet
```
Transform GFA 1.0 to specific [`Containment`](#containment), [`Link`](#link), [`Path`](#path), [`Segment`](#segment), and [`Traversal`](#traversal) records in Parquet format
```
$ spark-submit \
--class com.github.heuermh.adam.gfa.Gfa1ToDataframes \
target/adam-gfa_2.12-${version}.jar \
in.gfa \
out
```
(creates separate `out.containments.parquet`, `out.links.parquet`, `out.paths.parquet`, `out.segments.parquet`, and `out.traversals.parquet` directories)
### Graphical Fragment Assembly (GFA) version 1.0 schema in Parquet format
#### Gfa1Record
[Gfa1Record (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Gfa1Record.html)
```
message spark_schema {
optional binary recordType (STRING);
optional binary name (STRING);
optional binary sequence (STRING);
optional int32 length;
optional int32 readCount;
optional int32 fragmentCount;
optional int32 kmerCount;
optional binary sequenceChecksum (STRING);
optional binary sequenceUri (STRING);
optional binary stableName (STRING);
optional int32 stableOffset;
optional int32 stableRank;
optional binary id (STRING);
optional group source {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional group target {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional binary overlap (STRING);
optional int32 mappingQuality;
optional int32 mismatchCount;
optional binary pathName (STRING);
optional group segments (LIST) {
repeated group list {
optional group element {
optional binary id (STRING);
optional binary orientation (STRING);
}
}
}
optional group overlaps (LIST) {
repeated group list {
optional binary element (STRING);
}
}
optional int32 ordinal;
optional group container {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional group contained {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional int32 position;
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```
#### Containment
[Link (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Containment.html)
```
message spark_schema {
optional binary id (STRING);
optional group container {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional group contained {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional int32 position;
optional binary overlap (STRING);
optional int32 mismatchCount;
optional int32 readCount;
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```
#### Link
[Link (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Link.html)
```
message spark_schema {
optional binary id (STRING);
optional group source {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional group target {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional binary overlap (STRING);
optional int32 mappingQuality;
optional int32 mismatchCount;
optional int32 readCount;
optional int32 fragmentCount;
optional int32 kmerCount;
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```
#### Path
[Path (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Path.html)
```
message spark_schema {
optional binary pathName (STRING);
optional group segments (LIST) {
repeated group list {
optional group element {
optional binary id (STRING);
optional binary orientation (STRING);
}
}
}
optional group overlaps (LIST) {
repeated group list {
optional binary element (STRING);
}
}
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```
#### Segment
[Segment (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Segment.html)
```
message spark_schema {
optional binary name (STRING);
optional binary sequence (STRING);
optional int32 length;
optional int32 readCount;
optional int32 fragmentCount;
optional int32 kmerCount;
optional binary sequenceChecksum (STRING);
optional binary sequenceUri (STRING);
optional binary stableName (STRING);
optional int32 stableOffset;
optional int32 stableRank;
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```
#### Traversal
[Traversal (scaladoc)](https://www.javadoc.io/static/com.github.heuermh.adamgfa/adam-gfa_2.12/0.8.0/com/github/heuermh/adam/gfa/sql/gfa1/Traversal.html)
```
message spark_schema {
optional binary id (STRING);
optional binary pathName (STRING);
optional int32 ordinal;
optional group source {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional group target {
optional binary id (STRING);
optional binary orientation (STRING);
}
optional binary overlap (STRING);
optional group annotations (MAP) {
repeated group key_value {
required binary key (STRING);
optional group value {
optional binary name (STRING);
optional binary type (STRING);
optional binary value (STRING);
}
}
}
}
```