gatk-3.8

Author	SHA1	Message	Date
kshakir	fd5970fdd4	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them. 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	2010-09-02 21:30:48 +00:00
kshakir	0105e8d063	Updated Queue GATK generation to reflect -B and -I changes. 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	2010-08-25 22:17:36 +00:00
kshakir	542d394e09	Cleaning up Queue debugging output. -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	2010-08-13 15:54:08 +00:00

Author

SHA1

Message

Date

kshakir

At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.

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

2010-09-02 21:30:48 +00:00

kshakir

0105e8d063

Updated Queue GATK generation to reflect -B and -I changes.

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

2010-08-25 22:17:36 +00:00

kshakir

542d394e09

Cleaning up Queue debugging output.

-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

2010-08-13 15:54:08 +00:00

3 Commits (eb1fa4bff3daf8a6be9a4c055250d9a1c2af6e77)