Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a
- More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
Added an example of using a walker with Queue and a custom -classpath.
Removed an unused import statement in NamedFileWrapper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4143 348d0f76-0448-11de-a6fe-93d51630548a
To add support for "-I:tumor tumor.bam", the GATK argument
import_file (-I) is now generated as a List of NamedFile objects.
Could not get sugar working 100%. To activate sugar import the
gatk package. This effectively adds a new method to java.io.File
called toNamedFile. When adding a file to the list call
countReads.import_file :+= myJavaFile.toNamedFile
See scala/qscript/examples for actual examples.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a
-l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run.
More documentation in the examples with a new even simpler CountReads example.
Took out unused option to build Queue GATK extensions separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4025 348d0f76-0448-11de-a6fe-93d51630548a
kshakir