babb9fb825
snp cluster filter should ignore ref calls when determining the clusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 17:57:33 +00:00
3330666780
Add CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3092 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 15:45:53 +00:00
24461a2503
Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:59:01 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
1e8b3ca6ba
Fare thee well, oh LocusWindowTraversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:17:26 +00:00
8ea98faf47
Deleting the pooled calcluation model -- no longer supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 11:44:27 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
a45ac220aa
Removing unnecessary printing routines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 22:34:54 +00:00
b8ab74a6dc
Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 21:45:22 +00:00
e9e53f68ab
Filter lists can now end with .list or .txt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 17:41:24 +00:00
074ec77dcc
First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be
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specified with the reportType command line option in VE2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3083 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 03:59:32 +00:00
85f4f66180
Updated to use VariantContext. Output has been reformatted: variant and genotype concordance are emitted for every coverage level per variant. If the requested sampling level is higher than what's available, the maximum available coverage at that locus is used. This makes it much easier to make plots indicating the percentage of comparison callset recovered at a certain sampling depth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3082 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 21:02:43 +00:00
391e5843e4
If the annotation engine has not been supplied, don't try to annotate anything.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 20:52:21 +00:00
8048b709a0
Selects a single sample on which to operate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3080 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 20:50:58 +00:00
20e3ba15ca
Added an optional argument -rgbl --read_group_black_list to filter read groups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3079 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 19:38:57 +00:00
73a14a985b
Moving VariantsToVCF to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 18:55:12 +00:00
14bf6923a8
HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3077 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 18:34:59 +00:00
78af6d5a40
New sharding system is going live again for on-the-fly merging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3076 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 18:39:04 +00:00
46c14ec63f
New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation
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that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 17:41:22 +00:00
4398a8b370
Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3074 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 04:53:31 +00:00
2373a4618f
bug caused by a misprint: context != contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3073 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 03:08:24 +00:00
3176715c74
1. Alignability mask returns null when not available.
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2. --list now prints out the available classes/groups too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3072 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 20:49:07 +00:00
06a212e612
Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 19:43:10 +00:00
47e30aba92
Rods for reads hooked up into the cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 18:17:56 +00:00
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
169d0c6e8f
Up the svn revision number in an attempt to force an update, again due to an
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artifact of the way we build picard-private-parts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3051 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 22:39:56 +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
bb7e0c27fd
updating the package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3045 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:42:31 +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
ebanks
chartl
depristo
hanna
kshakir
aaron
kiran
rpoplin
asivache