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58 Commits (758f8aa89bb3b5ce22e0d3cb3740c2a8e872284b)

Author SHA1 Message Date
hanna ee9077fc69 LocusIterator iterated through LocusContexts, which was fine until now when we need something 
that iterates through loci (GenomeLocs).  Rename LocusIterator to LocusContextIterator.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-12 13:54:57 +00:00
hanna 23e9e29964 Changed reads traversals from providing a LocusContext from which the reference sequence 
could be extracted to a char[] containing the reference bases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 22:45:11 +00:00
aaron c735e1f627 small javadoc cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@653 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 03:44:21 +00:00
aaron e8b8ab5985 Added code to extend Matt's getReferenceBases out to the read walkers, so they can see the corresponding reference for each read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@652 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 03:42:38 +00:00
aaron 8d43ec3d7e a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 01:39:25 +00:00
hanna 55c1b688bd Fix mediocre javadoc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@646 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 22:31:16 +00:00
hanna 522f8b58be Added second method for getting large sequences of the reference for use in reads traversals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@645 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 22:18:04 +00:00
hanna 6e394490cb Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 21:27:54 +00:00
hanna 483a58627b More cleanup -- pushing shared functions down into the traversal engine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 14:12:45 +00:00
hanna 4c269b8496 Cleanup LinearMicroScheduler in preparation for TraverseByLoci inclusion. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@634 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 00:58:37 +00:00
aaron 5136724884 Added code to the schedulers, one step closer to turning on the new reads traversals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@613 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 22:36:25 +00:00
aaron 0aba688e6f Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 21:40:41 +00:00
aaron f5880109a7 Added TraverseReads test, some bug fixes discovered in the traversal test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@594 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 20:36:00 +00:00
aaron daa2163ee8 Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@593 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 19:15:07 +00:00
aaron 09b0b6b57d Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 18:17:07 +00:00
aaron 63403d32cd Changes to the interface to the simple data source rippled out to a bunch of files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-30 20:35:56 +00:00
aaron d4de68e260 added changes for the readsTraversal to accomidate design changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@553 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-28 19:49:58 +00:00
hanna e50ae97fe1 Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 19:40:21 +00:00
jmaguire dd408a2a9a First draft of actual pooled EM caller. 
Produces sane looking output on region of 1kG pilot1:

    CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
    CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
    CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
    CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
    CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084

Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 13:42:15 +00:00
aaron bd4cacb832 Added code to make a read group and sample name for BAM files that don't annotate them on reads. The defaults for both are now the filename, but this may be shortened in the future. 
The sample name for a read can be retrieved with the command:

read.getAttribute(SAMTag.RG.toString());




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@518 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 00:31:00 +00:00
aaron 0208d201c7 Forgot this in the last commit... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@515 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-23 20:47:22 +00:00
aaron 8c13940c5a A lot of changes to support by-read sharding and some from debugging of the by loci traversals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@511 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-23 19:03:14 +00:00
hanna eafb4633ba Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-17 23:14:41 +00:00
hanna d639ec3776 Remove some copied code to make sure the traversal engine stays in sync with the locus context provider. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-17 16:41:56 +00:00
hanna 01be8f09e3 Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-16 22:17:25 +00:00
aaron 12e1f192c4 Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-16 18:42:00 +00:00
aaron e70aecf518 bug fix, but important 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 21:07:20 +00:00
aaron 67ea66c866 Bug fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 19:12:18 +00:00
aaron 180ff13290 Added a bunch of changes to support the new MicroManager code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 18:29:38 +00:00
aaron 12407b5b1a Deleted the old file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 13:55:01 +00:00
aaron 6db9127f90 Added changes to shattering, refactored SAMBAM into SAM 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 13:52:56 +00:00
hanna 0629f79049 Moved fasta support files into their own package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 18:13:23 +00:00
aaron eb4b4a053b A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 14:19:20 +00:00
aaron 887adcfc7f Some minor fixes to the last check-in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 18:24:51 +00:00
aaron f2d0d73309 removed old shard strategy code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 18:13:45 +00:00
aaron dd604799dc Added some new code for shard support over reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@385 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 18:11:43 +00:00
hanna 95753e1b34 Should've been calling queryOverlapping in locus mode. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@360 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-10 20:22:04 +00:00
aaron 9afa101465 Add interval support to the 
.__            __    __                
  _____|  |__ _____ _/  |__/  |_  ___________ 
 /  ___/  |  \\__  \\   __\   __\/ __ \_  __ \
 \___ \|   Y  \/ __ \|  |  |  | \  ___/|  | \/
/____  >___|  (____  /__|  |__|  \___  >__|   
     \/     \/     \/                \/       

classes!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 21:23:43 +00:00
hanna 8a1207e4db Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code. 
Reverts to original TraverseByLociByReference behavior unless a special combination of command-line flags are used.

Lightly tested at best, and major flaws include:
- MicroManager is not doing MicroScheduling right now; it's driving the traversals.
- New database-ish data providers imply by their interface that they're stateless, but they're highly stateful.
- Using static objects to circumvent encapsulation.
- Code duplication is rampant.
- Plus more!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@346 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 20:28:17 +00:00
aaron 8e2f5471a1 Some cleanup to the data source, and another JUnit test case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 14:58:05 +00:00
aaron d56193b6df Cleanup of a couple of output statements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@343 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 14:09:07 +00:00
aaron 12752cf893 Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@341 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 00:20:15 +00:00
aaron d4ab95c098 Added a constructor, took out a copy constructor, and changed some SAMBAM code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@335 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-08 19:53:20 +00:00
aaron 295c269a64 Remove the main() I put in for debugging 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@333 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-08 16:43:44 +00:00
aaron d517245beb Fixes for shattering, added JUnit test case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-08 16:37:34 +00:00
aaron 2663ac3e4a documentation fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@316 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-07 21:39:50 +00:00
aaron 8a357a88a2 right...exponential should be exponential, so I might want to increment the exponent 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@315 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-07 20:12:05 +00:00
aaron 6ce9e0f941 delete the old strategy 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@314 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-07 19:40:03 +00:00
aaron 08fddd43af -Replaced adaptive and linear strategies with an adaptive linear strategy 
-Added the exponential growth strategy
-Added factory code that allows you to transitition between strategies, so if you want to move from linear to exp at a point, and then back when you've hit a runtime threshold, it will take care of it for you.
-Changed the code to return a Shard instead of a GenomeLoc

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@313 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-07 19:37:38 +00:00
aaron 6369d23b43 renamed; these files are more strategy than actual shards 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@312 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-07 16:50:56 +00:00