ca2cd9d4f5
a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 16:31:45 +00:00
790d2a7776
adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 15:56:44 +00:00
0e9a6826b0
Update to VCF code to get it up to spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 06:12:42 +00:00
317fac8dff
Better error message for --assume_single_sample_reads screw up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2916 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 01:03:10 +00:00
104f4f7383
Mediocre implementation of reader pooling within the SAM data source. Will fix this week.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2915 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 22:35:02 +00:00
74a5223b11
oops - didn't mean to check this in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2914 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 20:28:22 +00:00
5f3c80d9aa
1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext.
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2. Significant refactoring of Plink code to work in the rods and use VariantContext. More coming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 20:26:40 +00:00
6ceae22793
utility methods for genotype counts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2912 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 20:23:41 +00:00
7578678f99
refactored to provide a sum of mismatch quality scores capability as well (used by Cancer)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2911 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 16:40:03 +00:00
91b3f9745e
removing the package description for the VCF validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2910 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 15:45:51 +00:00
232fcf829a
removing the unsupported VCF validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2909 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 15:45:33 +00:00
1b572b192a
Stopgap fix for temporary problems sharding when indexless. A more compelling solution will come later this week.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2908 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 02:59:14 +00:00
75a541b479
Fix nasty issue where shard boundaries aren't properly clipped during locus traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2907 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 23:31:58 +00:00
9298e13201
Make annotated VCF not be broken
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2906 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 23:22:41 +00:00
af6e476df5
Copyright compliant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2905 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 15:29:34 +00:00
3a863d3e8c
Initial check in of VariantOptimizer in playground. There is a Gaussian Mixture Model version and a k-Nearest Neighbors version. There is still lots of work to do. Nobody should be using it yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2904 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 15:26:18 +00:00
6133d73bf0
Locus (non-intervalled) traversal with new sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2903 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 01:58:44 +00:00
80f5d2829d
Support for read interval sharding with proper filtering.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2902 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-27 20:26:34 +00:00
d8fedd59be
docs, cleanup, and some improvements to the iterators.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 22:36:04 +00:00
b69c2d0f70
Cleanup. Remove some unnecessary methods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2900 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 21:50:48 +00:00
30eb28886b
Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so
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the mode of operation is currently queryOverlapping rather than queryContained.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 21:41:55 +00:00
cfff486338
This commit is for Kiran
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2898 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 18:18:38 +00:00
87f8fb7282
Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2897 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 16:39:47 +00:00
622554d7bd
disable a part of the ROD for Reads code until the rest of the system goes live
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2896 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 16:15:42 +00:00
496ecc8186
Change in how overall coverage and means are stored in the DOCS object; change from keeping track of sample mean coverage to keeping track of sample total coverage (calculate means at the end)
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This is a mid-way commit for Aaron
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2895 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 15:51:12 +00:00
1017a38f38
Initial refactoring of read traversal to make it easier to drop in intervalled reads traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2894 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 15:09:09 +00:00
9a6b384adb
Support for no qual fields in VCF; better support for Mendelian violation calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 00:29:17 +00:00
246fa28386
RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 22:48:55 +00:00
591102a841
Don't close the output stream if we're printing to stdout
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2891 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 21:50:58 +00:00
10cc71ceb0
Another midway commit for teh engineerz
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2890 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 21:24:02 +00:00
3289826892
Fix chartl's issue -- reduceInit() is sometimes called unnecessarily at the
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end of a traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2889 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 21:02:18 +00:00
3d92e5a737
Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt]
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Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output).
Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 20:25:07 +00:00
553d39bb00
Clean up the code a bit following the introduction of reduceByInterval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 01:20:22 +00:00
199b43fcf2
Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a
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simplification of some of the locus traversal code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 00:16:50 +00:00
2572c24935
We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2885 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 23:13:23 +00:00
fef1154fc8
starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 22:11:53 +00:00
9306041cf4
Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2883 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 16:42:56 +00:00
5df37968de
Simplification of code segments; slight alteration to per-locus tabulation; added to-do items for cosmetic changes (mostly binning options and settigns)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2882 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 05:20:18 +00:00
27d3ef9458
Got rid of annoying commented printouts; no functional changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2881 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 05:12:30 +00:00
d73bc490c2
Do not build alt consensuses from insertions that have an N in the inserted sequence. Seems to cause problems rather than solve any
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2880 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 03:00:26 +00:00
94d74d4f78
Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored.
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in class Consensus:
1) use Arrays.equals() to compare java arrays!!
2) if object overrides equals() it also MUST provide appropriate hashCode() (thanks, Matt)
As a side effect, a number of commented out debug prints are committed, still need them...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2879 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 02:09:50 +00:00
1f673e9fab
Float the bins with the given lower bound
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2878 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 20:48:53 +00:00
119d449b46
Formatting changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2877 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 20:43:15 +00:00
173956927b
Summaries generated for firehose from DoC output have been migrated to its own walker to calculate aggregate coverage statistics in a parallelizable and fast way. This is an initial commit, bug-fixing and testing is upcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2876 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 18:41:02 +00:00
491b30e8de
Eliminate a few stray loci that weren't being filtered out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2875 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 18:00:52 +00:00
fff15944fe
Bug fix. Stopping condition of recurrence stopped too soon in some cases where an interval *contained* zero reads but *overlapped* with some reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2874 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 15:58:54 +00:00
36129e01e4
Using bitmap() instead of png() since the former doesn't rely on X11.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2873 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 05:31:51 +00:00
a0e8de40cf
Bug fix: at one locus in the dataset, two reads were dropped.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2872 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 23:54:52 +00:00
5546aa4416
adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2871 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 22:27:39 +00:00
88d0677379
Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2870 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 22:19:06 +00:00
aaron
ebanks
hanna
kcibul
andrewk
rpoplin
chartl
depristo
asivache
kshakir