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19 Commits (decf45664aebe5ea37f5fdca782f14c7d8d4f987)

Author SHA1 Message Date
jmaguire b7a67da775 Expose the underlying SAM reader to the walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@270 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-02 21:38:00 +00:00
asivache 5d9b068b8b generic declarations added here and there to eliminate a few annoying warnings; no consequential changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@268 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-02 20:53:01 +00:00
kcibul c192a95998 changes in three files to make the HapMap RODs work: 
- HapMapAlleleFrequenciesROD.java - the referenceOrderedDatum implementation
 - PrepareROD.java - has a static block that loads the known ROD classes, had to add the above
 - GenomeAnalysisTK.java - when supplied a hapmap argument... loads the ROD

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@265 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-02 19:55:19 +00:00
jmaguire 25ace306b9 GenomeAnalysisTK: better documentation of validation option. 
AlleleFrequencyWalker: output the last reference interval if it's left hanging open.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@258 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-02 16:11:20 +00:00
depristo d952790258 GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-01 22:54:38 +00:00
ebanks 6cc2fa24d5 Added ability to downsample to a particular coverage 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@250 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-01 20:27:06 +00:00
ebanks 3af4290a49 Added iterator to randomly downsample to a given fraction of the reads. 
Also, updated sort iterator to allow user to input max sorts.
Put in placeholder for downsampling to given coverage.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@243 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-01 02:11:13 +00:00
depristo d7c0bcc223 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. 
All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array.  System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-28 20:37:27 +00:00
depristo cfee59e0e6 New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 15:40:45 +00:00
hanna 4a6be896b9 Provide out and err PrintStreams to the walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@213 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 15:03:32 +00:00
aaron d115209e86 moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 13:27:04 +00:00
depristo 3abaaa3cc3 Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@206 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 00:12:35 +00:00
hanna 53fe9acf65 Make command-line arguments available in walker constructor, provide back door from 
walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-26 20:45:27 +00:00
depristo d457778283 Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@191 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-25 16:01:58 +00:00
hanna 9e2a373184 Prototype, buggy implementation of walker command-line arguments. Doesn't 
(yet) deal elegantly with even simple cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-25 00:12:00 +00:00
depristo 919a86e876 Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 22:32:45 +00:00
depristo 6df19ab793 Support for byInterval traversals for Jared. Do not use them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 20:55:34 +00:00
andrewk 9dee9ab51c Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 03:58:03 +00:00
hanna 63cd1fe201 Push core / playground lower into the tree. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 23:19:54 +00:00