035d4170aa
fix bug in read clipper: output bam can be null, so check for it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 18:49:26 +00:00
411d25c8d1
-Integration tests for walkers that use original quals.
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-framework for pushing -OQ into GATK (not done)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 18:46:31 +00:00
e365d308d4
add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 16:00:55 +00:00
9f519af06d
new method to filter out overlapping PE reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3002 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 15:40:09 +00:00
45f70de6df
Fixed bug that failed to reset an accumulator when crossing contig boundaries,
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meaning that in special cases of shallow coverage, an interval might get dropped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 04:45:55 +00:00
73d6167bd6
Fixing broken integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2998 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-14 23:18:49 +00:00
4dd7c5972c
Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2997 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-14 21:08:14 +00:00
e367a50e9b
Added genotype concordance module. Not at all finished, but needed to give something to Aaron to look at for help in printing the output nicely.
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Also misc cleanup and fixes (e.g. perform evalulation even when no comp tracks are provided).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2996 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-14 19:02:24 +00:00
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
ebanks
aaron
kcibul
hanna
depristo
asivache
chartl
rpoplin