a4d494c38b
Add option to adhere to the PlinkRod naming convention [ProjectName]|c[Chrom]_p[Pos]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2927 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 18:31:27 +00:00
0dd65461a1
Various improvements to plink, variant context, and VCF code.
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We almost completely support indels. Not yet done with plink stuff.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 17:58:01 +00:00
c8077b7a22
Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 16:02:21 +00:00
6759acbdef
Coverage statistics now fully implements DepthOfCoverage functionality, including the ability to print base counts. Minor changes to BaseUtils to support 'N' and 'D' characters. PickSequenomProbes now has the option to not print the whole window as part of the probe name (e.g. you just see PROJECT_NAME|CHR_POS and not PROJECT_NAME|CHR_POS_CHR_PROBESTART-PROBEND). Full integration tests for CoverageStatistics are forthcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2924 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 15:00:02 +00:00
023654696e
First pass at handling SAMFileReaders using a SAMReaderID. This allows us to firewall
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GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2923 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 00:59:32 +00:00
b241e0915b
Incremental update to VariantOptimizer. Refactored parts of the clustering code to make it more clear. More comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2922 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 20:33:35 +00:00
073fdd8ec7
Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2921 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 17:34:30 +00:00
6ca6c98980
Can just give PickSequenomProbes a dbsnp rod to mask
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2920 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 16:50:58 +00:00
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
chartl
ebanks
aaron
hanna
rpoplin
asivache
kcibul
andrewk
depristo