9fca79ed62
Read groups are now sorted in the output data, for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:50:44 +00:00
7ecc43e9a7
Fixed subtle null ptr exception discovered by Kiran. Now deals with the rare situation where you have only say Q28 bases at dbSNP sites, so you fail in the Table recalibration step with a null pointer error into the data structure indexed by quality score. If you are Q score above those seen before you aren't modified in any way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1118 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 18:57:42 +00:00
491ed70b44
TraverseByLocusWindow -- asstd bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:51:38 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
347608cfe0
remove hacked traversal in preparation for move to Matt's new one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:32:05 +00:00
0a50f2e160
Updated and near final version of tabular recalibration system. Uses 'yates' correction for low-occupancy quality bins. Faster and more robust handling of input and output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 03:52:12 +00:00
26eb362f52
Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 21:27:40 +00:00
9e26550b0d
Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 16:00:23 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
d748c85dc4
Cleaned code and reorganized -- moving in the right direction for v2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:28:34 +00:00
1bca144119
Moving things around
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:06:46 +00:00
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
cba9025983
More package-level documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1030 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:28:45 +00:00
11aa715630
added capability for filtering by platform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:19:50 +00:00
8f4bc8cb6e
Move filtering functionality into the PrintReadsWalker. More to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 16:38:08 +00:00
0583459839
Another formatting change to make Hapmap sites more clearly visible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:53:21 +00:00
e9be2a9c60
Changed a formatting issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:40:32 +00:00
b0cc763eb5
Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:31:00 +00:00
3adb4239e4
Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:19:31 +00:00
bf6190b471
cleaned up the PrintReadsWalker, and added a lot of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@952 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:28:32 +00:00
fecba2cae5
Disabled option to show secondary quals as the definition has changed to conform to the spec and thus this printout is non-sensical.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@950 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 03:21:14 +00:00
36fb6ca3c5
Allow user to specify the compression to be used when writing out BAM files.
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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
13be846c2a
qualsAsInt argument for Pileup -- fixing stupid bug [again]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:52:12 +00:00
97c8ff75dd
qualsAsInt argument for Pileup -- fixing stupid bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:51:17 +00:00
9de3e58aa8
qualsAsInt argument for Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:37:39 +00:00
54bb643d19
Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 15:58:21 +00:00
008d677bea
Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy.
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Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-23 20:50:28 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
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compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
30c63daf89
More improvements to the duplicate quality combiner, making progress towards a clean system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:26:57 +00:00
65995887fc
Releasable version of the Pileup walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@786 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:37 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
57918de753
add the @Requires for this walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@762 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:03:12 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
ff798fe483
Reintroduce support for interval-based traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 22:54:18 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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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
862b8a6787
intervals_file + genome_loc => intervals.
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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
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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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
052819bed5
Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@656 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:33:00 +00:00
3aabc144c6
Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.
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(Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@641 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 17:28:16 +00:00
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:46:28 +00:00
7f8850a8a2
Argument validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
2204be43eb
System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@624 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:06:02 +00:00
752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +00:00
dc944ec69b
First stage of ROD plumbing for MicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 23:26:21 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
5bdf653919
Cleanup: prepare for better output handling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:40:46 +00:00
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
84dae06d5a
Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:16:21 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 15:12:13 +00:00
depristo
hanna
ebanks
kiran
aaron
andrewk