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
849bd1f451
Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 22:01:23 +00:00
933823c8bc
Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 19:45:02 +00:00
2525ecaa43
Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 16:34:50 +00:00
59045ccb28
Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3011 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 16:23:37 +00:00
6dd5f192e7
Performance improvements for RODs in conjunction with new sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 14:54:12 +00:00
f20f78d77f
Don't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3009 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 04:00:04 +00:00
10e76abbbc
adding some VE2 report infrastructure; work-in-progress.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3008 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 03:57:42 +00:00
586f87fa35
Quick fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 02:59:26 +00:00
202231141c
-Push the --use_original_qualities argument into the engine.
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-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 02:06:11 +00:00
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
ebanks
hanna
aaron
rpoplin
bthomas
kiran
kcibul
depristo
asivache