ecb59f5d0d
removed old tests and old code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2995 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 22:57:01 +00:00
e7eae9b61d
High performance, correct implementation of -XL exclusion lists. Enjoy.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2994 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 22:39:20 +00:00
88a48821ea
removed the dependence on removeRegion() in GenomeLocSortedSet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 22:35:49 +00:00
b39b5edca8
Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 19:23:12 +00:00
1eb5f97255
fixed dropping single base intervals from deleteRegion, moving onto performance fixes.
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(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 19:14:21 +00:00
7aa7a5f9b8
Bug fixes for edge cases and filtration in the earlier performance fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 04:46:08 +00:00
5e8654fcdc
Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 23:19:42 +00:00
d804bdf210
New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 21:15:03 +00:00
661a043cef
adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 21:13:39 +00:00
18ba9929f9
notes for eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2983 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 20:34:54 +00:00
cbd529d544
Better chopping up of data for ref walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2982 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 20:13:26 +00:00
a7ba88e649
Rework the way the MicroScheduler handles locus shards to handle intervals that span shards
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with less memory consumption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 18:40:31 +00:00
4a05757a2a
Fixed strand bias calculation because of -Infinity issues.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2980 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 16:05:51 +00:00
dde9fd8a15
some rods-for-reads cleaning and performance improvements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 22:54:58 +00:00
4f4555c80f
PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 22:28:31 +00:00
40d305bc7e
Added test of Nway cleaning for Matt; thanks to Aaron for the help.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 21:00:41 +00:00
486bef9318
Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 16:25:16 +00:00
c85ed1ce90
Plumbing is now in place to emit indel calls from the UnifiedGenotyper.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2975 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 04:30:12 +00:00
5c35be39ef
Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 03:14:06 +00:00
7ddd45d059
Hmm. I thought I removed this already.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2973 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 03:09:13 +00:00
1a576525e9
misc improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 03:00:28 +00:00
6e855809e1
Renaming and moving relevant tools into a sequenom directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 02:31:10 +00:00
c638c29eea
In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 22:18:44 +00:00
bc3761dc16
allow clipper to use original quals if requested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2969 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 21:50:31 +00:00
f096a958d6
Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2967 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 19:13:01 +00:00
0a49dffa8f
Row/Column names are now R-friendly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 19:01:03 +00:00
0e360ea8af
Alleles now hash correctly.
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Special thanks to Matt & Aaron.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2965 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 18:09:44 +00:00
e5475a7ba9
re-enabling PlinkToVCF integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 17:35:49 +00:00
5a20bf0e64
3 changes to UG which break integration tests:
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1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 17:16:47 +00:00
cdce639bae
Partially reclaim performance lost during integration test fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2961 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 12:36:11 +00:00
9f3b99c11b
Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.
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Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 03:41:07 +00:00
02f48b6457
Fix bug that's been in the GATK for a very long time: update nReads (as well
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as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'. While
I'm in there, update TraversalStatistics to store longs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 22:44:54 +00:00
bca9bdcc68
Add integration test for quartiles overflowing on interval reduce
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 16:18:45 +00:00
21bf8b4b93
Odd, what I saw on IntelliJ hadn't saved to sting before committing. Here's the actual change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2956 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 15:54:41 +00:00
fe8a8b9199
Hooked up both optimization models via command line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2955 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 14:49:59 +00:00
cc6a714c09
Handle excess coverage in interval output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2954 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 14:40:05 +00:00
ca2a0266dc
Converting annotation values that are set to Double.Infinity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2953 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 14:04:33 +00:00
b42e0a398e
Bug fix in variant optimizer for when there are more novel variants than known variants in the callset. Changing the magic numbers related to the starting sigma values for the gaussian clusters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2952 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 13:02:08 +00:00
e4360bac6a
More comprehensive support when sharding for ref walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 11:25:20 +00:00
eb165ca844
Celebrate the fact that the new sharding system works with integration tests
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by removing the scary debug line.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2950 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 23:40:56 +00:00
9e107513d0
In the new sharding system, if no read group is present, hallucinate one. Added
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for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 23:01:34 +00:00
a7fe07c404
A few stopgap fixes to get the GATK to the point where the old sharding
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infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 21:01:25 +00:00
dd6122f682
Fixed another bug in the original sharding system. Updated integration tests
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as appropriate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 15:32:18 +00:00
ee2ec7ced9
Fix off-by-one error in original implementation of read sharding. Tested by
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awking output of BamToFastq vs. samtools until the outputs matched exactly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-06 18:52:53 +00:00
1ef1091f7c
Cleanup and simplification of read interval sharding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2944 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 23:34:38 +00:00
ee913eca07
Forgot to check in fix this morning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2943 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 21:07:19 +00:00
7fa0f77721
add output for number of variants that validated as true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2942 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 18:57:44 +00:00
037ac9c9af
Actually calculate base counts by read group when "both" is specified. Modified integration test to cement the now-correct "both" behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2941 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 18:31:48 +00:00
8738c544f1
Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 17:06:52 +00:00
95d560aa2f
More incremental updates to the variant optimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2939 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 16:42:42 +00:00
7a7e85188c
Better eagerDecode default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2938 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 16:42:23 +00:00
33cefddf55
Better INFO field annotation for Mendel violations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2937 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 15:22:04 +00:00
9f7ebe1e1c
- add name to vcf od field
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- don't do HW calculation if everything is a no-call
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2936 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 01:43:01 +00:00
7104a3a96c
Fix for accumulator exception when running reduce by interval walkers without
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intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 01:04:08 +00:00
366771d5a6
another test-with-multiple outputs fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 22:46:15 +00:00
9eb122924f
misc cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2933 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 21:34:13 +00:00
706d49d84c
Commit for Aaron
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 21:29:07 +00:00
c20d3e567e
Now outputs fully spec-compliant VCF with proper annotations. Emits statistics as to number of good/bad records.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2931 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 21:28:17 +00:00
54f04dc541
forgot to uncomment the auto-deletion of temp files...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2930 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 20:29:42 +00:00
80cc6bbeb4
add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2929 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 20:20:58 +00:00
adea38fd5e
Sharding system fixes for corner cases generally related to lack of coverage
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in the BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2928 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 18:59:21 +00:00
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
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
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
aaron
depristo
hanna
asivache
ebanks
chartl
rpoplin
kcibul