5079f35e40
better method names for read based reference ordered data access.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 16:13:31 +00:00
49117819f5
For the cleaner to clean, it must beat the entropy produced by the aligner (and not just the raw reads).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3068 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 15:21:58 +00:00
60dfba997b
added some sample annotations to VariantEval2 analysis modules, and some changes to the report system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3067 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 05:40:10 +00:00
1f451e17e5
Changing preloaded index to only "preload" reference sequences on demand.
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Results in drastic lowering of startup cost when multiple BAM files are
merged.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 22:02:28 +00:00
884a577013
Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 16:48:11 +00:00
7462a0b2d1
cleaned-up of VariantContextAdapter tests, fixed the double comparisons in equals() in RodGeliText (nice MathUtils.compareDoubles Kiran)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3064 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 15:18:30 +00:00
a69b8555dd
Geli to variant context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3063 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 06:45:29 +00:00
eafdd047f7
GLF to variant context. Added some methods in GLF to aid testing; and added a test that reads GLF, converts to VC, writes GLF and reads back to compare.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3062 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 03:43:25 +00:00
3767adb0bb
Processing intervals as they stream in means much lower memory usage and
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quicker runtime. Making change as minimal as possible to avoid conflicts
with BT's incoming patch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 22:04:45 +00:00
0097106938
VariantFiltration can now filter specific samples.
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This is *NOT* an ideal implementation. One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL. For now, though, this will have to do.
Docs coming tonight.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 20:45:11 +00:00
543aefc3d7
Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 19:20:34 +00:00
ee1dc6092f
Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 17:37:52 +00:00
d2944461ef
We also have to allow the window to be (partially) outside the bounds and trimming to the contig size is not enough (thanks to shards). Now we trim to the current bounds too (i.e. if the interval is not completely within current bounds, we create reference context that contains only bases from the overlap between the interval and the bounds).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3057 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 17:36:29 +00:00
9053406798
LocusReferenceView: If the locus a view is requested for spans beyond the reference contig ends, create the actual window bounded by contig ends (so that the locus will not be fully contained in the window!!).
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ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3056 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 15:59:15 +00:00
439c34ed38
clean-up before annotating VariantEval2 for output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3055 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 07:39:20 +00:00
076d21d394
Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3054 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 02:47:09 +00:00
6cd97b78ab
An additional safety check to ensure that we only walk over coordinate-sorted
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data when doing locus traversals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3053 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-21 23:31:45 +00:00
b4b4e8d672
For Sarah Calvo: initial implementation of read pair traversal, for BAM files
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sorted by read name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3052 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-21 23:22:25 +00:00
c0eb5c27ea
Lower memory support for merged sharding. Merged sharding is still not available.
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WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
distribute picard-private.jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 22:03:47 +00:00
4d4db7fe63
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 18:45:01 +00:00
4c4d048f14
Moving VariantFiltration over to use VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 18:35:23 +00:00
c88a2a3027
Fixing/cleaning up the vcf merge util
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 15:13:32 +00:00
cdec84aa8f
Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3046 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 15:07:32 +00:00
d8ff552311
Support for EXPERIMENT sampling-based genotype likelihoods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3044 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:19:40 +00:00
7b17bcd0af
Refactoring a few useful routines for detecting mendelian violations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3043 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:19:01 +00:00
56092a0fc2
Slight cleanup for mathutils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:18:08 +00:00
b221ce94ce
Still being tested trio-aware genotyper that calculates P(de novo)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3041 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:11:39 +00:00
03480c955c
And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 04:58:37 +00:00
e757f6f078
Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3038 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 03:56:27 +00:00
0311980668
The VariantAnnotator can now officially annotate genotype (FORMAT) fields.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 03:30:14 +00:00
9b61d95d9c
Khalid found an out-of-memory condition with the new sharding system when
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merging lots of BAMs, and the fix is taking longer than I thought. Disable
experimental sharding when merging until the fix is ready.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 02:43:46 +00:00
b8e8852b4f
Better interface for the Annotator in how it interacts with VariantContext.
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Also, added a proof of concept genotype-level annotation (not working yet, almost there).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3035 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 20:41:57 +00:00
96662d8d1b
Moving from GATK dependencies on isolated classes checked into the GATK
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codebase to a dependency on a jar file compiled from my private picard branch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 17:43:42 +00:00
8a5f0b746e
some cleanup for the output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 12:54:39 +00:00
c78fc23ec5
Minor updates to output of variant optimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 12:46:47 +00:00
0247548400
Fixed one test and (temporarily) punted on another
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 06:22:48 +00:00
ee0e833616
Some significant changes to the annotator:
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1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1 . Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 05:38:32 +00:00
58a31bab6a
Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 20:41:42 +00:00
d9398dc347
Remove some of the restrictions on getStart() and getStop(); getStart() and getStop()
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now do the minimum validation rather than the more rigorous only-within-the-contig-bounds
header validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 19:39:30 +00:00
182f1061ff
Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3025 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 17:56:48 +00:00
5e29d0c219
Be smarter about dealing with infinite quals for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 17:35:23 +00:00
1bb4394aa9
Adding a skeleton for the second step of the variant optimization process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3023 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 17:03:40 +00:00
ded4ba8966
Let's make artificial reads that actually adhere to the specs...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 16:51:42 +00:00
5b34bb9ab0
Adding three minor new features:
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+ -L all now walks over all intervals
+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.
+ Error is thrown if the start position on an interval is higher number than the end position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 16:24:10 +00:00
4340601c26
-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically
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-Better integration test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3020 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 16:00:10 +00:00
76d14d17dc
oops, need to update class names too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3019 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 14:01:31 +00:00
85a030069d
renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3018 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 14:00:28 +00:00
af5fd99444
Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 13:53:42 +00:00
2cc040aa1c
New sharding system is live. Disable with -ds.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 03:32:45 +00:00
1fd909cdaf
Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 00:20:15 +00:00
aaron
ebanks
hanna
asivache
depristo
rpoplin
bthomas