zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
1,192 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

15 Commits (aacec3aeb02dac4df4b17a752030ad0a52708e7e)

Author SHA1 Message Date
hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given 
the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 18:23:35 +00:00
hanna a3e0ec20c4 Kill the TraverseByLocusWindows traversal. TraverseLocusWindows will take its place. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1138 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 13:46:35 +00:00
hanna ad3a3aa350 First pass at passing lists of files / lists of interval arguments work. Note that the interval 
ROD system will throw up its hands and not deal with intervals at all if multiple interval files 
are passed in (see JIRA GSA-95). 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 20:44:23 +00:00
hanna 102b38c055 Sketch of new version of TraverseByLocusWindow, and a flag to conditionally turn it on. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1097 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 18:20:56 +00:00
aaron 94b0e46d12 checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 20:46:16 +00:00
aaron 72a81f8f25 removed the requirement that a bam file list be present in the XML version of the command line arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@975 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 20:01:13 +00:00
hanna dc6a9ca196 Pooling resources to lower memory consumption. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 13:39:32 +00:00
aaron a8a2d0eab9 added support for the -M option in traversals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@935 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-08 15:12:24 +00:00
ebanks 36fb6ca3c5 Allow user to specify the compression to be used when writing out BAM files. 
Updated most of the walkers to reflect this change.
Now it won't take forever to write BAMs!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@909 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-05 08:48:34 +00:00
depristo e0803eabd9 enabled underlying filtering of zero mapping quality reads, vastly improves system performance 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@853 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-29 14:51:08 +00:00
hanna dc748d9c9c Integrate more feedback on command-line argument system. Focus on help 
formatter: separate required from optional but otherwise keep ordering
the same, reorder GATK arguments by usage.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@764 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-20 19:01:25 +00:00
hanna 2c4de7b5c5 Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along 
the pathway from command line to traversal engine.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-15 21:02:12 +00:00
aaron 9f942fdfa0 Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine. 
Also fixed a bug where we'd exception-out if we didn't provide a interval region.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-12 15:33:55 +00:00
hanna 862b8a6787 intervals_file + genome_loc => intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-12 01:04:18 +00:00
aaron 898f65547e Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 02:07:20 +00:00