de969f7cc7
logger != null check
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3774 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 23:07:14 +00:00
2e445262f2
Promotion to . for variable numbers of arguments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3773 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 22:53:53 +00:00
297f15a60c
Protect ProduceBeagleInputWalker against evil users who feed to it VCF's with indels, no variation sites or other interesting markers: Write to Beagle input only in biallelic SNP sites since that's the only thing Beagle can do.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3772 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:54:42 +00:00
80a5ddfa2f
Memory string added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3771 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:43:19 +00:00
52c534a8f2
Updating to VCF 4.0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:18:30 +00:00
5992b79159
a) Simplify normalization code in ProduceBeagleInputWalker, as to always normalize, and use MathUtils.normalizeFromLog10 to do this.
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b) Several improvements to BeagleOutputToVCFWalker:
1. If a Hapmap input track is provided (e.g. -B comp,VCF,file), Hapmap sites will be annotated with Hapmap Allele count and allele frequency (key ACH, AFH).
2. If probability of correct genotype is lower than ncthr (optional argument provided by user, default = 0.0), walker will keep original calls instead of using Beagle calls.
3. Instead of annotating just whether Beagle had modified a site, annotate instead HOW MANY genotypes in a site were actually changed by Beagle.
All three improvements are mostly for debugging and analysis only.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3769 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 19:54:58 +00:00
46c39f2d53
Quick python scripts for going from genotype VCFs to site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at non-variant sites)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3768 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 19:13:32 +00:00
e50627a49e
1. Updated tests and added integration test for liftover code.
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2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 17:58:18 +00:00
2a7112302a
More archiving
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3766 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 17:04:41 +00:00
221e01fb27
deleting/archiving as instructed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 16:59:45 +00:00
8086ab1f75
Pulled sample/header merging routines out of CombineVariants and into util classes. Added more generalized methods for retrieving samples. Updated the Beagle walkers to use these methods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3764 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 16:51:54 +00:00
0c4a32843c
No longer uses VCFRecord
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3763 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 13:57:39 +00:00
f130d29318
No longer uses VCFRecord.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3762 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 13:34:10 +00:00
e75b3e13bd
updating unit test for previous fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3761 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 03:23:53 +00:00
0427f3554b
Bug fix: valid fields were being stripped off the FORMAT for samples because String.match was used instead of String.equals. Also, please use VCFConstants from now on instead of hard-coding e.g. missing values into the code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3760 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 03:06:51 +00:00
fb717fe128
First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 07:19:16 +00:00
6b960bd9c5
Fix for Steve: genotype filters still want to see the values from the VC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3758 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 04:30:15 +00:00
1d399aa2f3
Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3757 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 03:27:32 +00:00
c3c66e853c
Improvements for Jason
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3756 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 20:18:37 +00:00
405be230d0
Various code improvements based on FindBugs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3755 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 15:04:48 +00:00
abaec13e38
Bug fix: if there are samples in the VCF but all of them are no-calls, we still need to emit GT for the FORMAT field to be on spec. Note that this is a holdover from 3.3 writing but can't easily be fixed there. Fortunately, that code is all going away soon...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3754 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 14:08:25 +00:00
ea8fd506bf
Update to PickSequenomProbes: Option to ignore mask sites within X bp of a variant (very useful for indels where dbSNP entries near the indel are almost always false SNP calls). Also fixed an integration test where the variant site itself, being in dbSNP, was represented as [N/C] rather than [A/C]. Added integration test for 1bp no-mask window.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3753 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 04:03:19 +00:00
179067e3f4
Support for . values in qual field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3752 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 01:47:02 +00:00
dd978dd525
misc. changes to python scripts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3751 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 00:13:35 +00:00
6ffcaa0afe
Can run R scripts on the command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 00:13:18 +00:00
45fb614296
Fixes to VE for obscure bug, as well as disabled integration test for CombineVariants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3749 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 00:13:07 +00:00
67f1589652
--fdr_filter_level isn't mandatory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3748 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 22:48:30 +00:00
5d39cd5db8
Added --fdr_filter_level to ApplyVariantCuts so that you can create beautiful tranche plots and also decide which tranche level to filter at. The previous version always filtered at the smallest tranche. The tranche filter names are appropriately added to the VCF header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3747 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 22:44:10 +00:00
760aaeda88
Update to CombineVariants. Now splits merge options into variant and genotype options separately.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3746 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 20:09:48 +00:00
bd2ba3eb37
deal with very large known indels that fall off our ref context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3745 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 20:05:16 +00:00
7ff6106c14
adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3744 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 19:10:19 +00:00
12fecc8d8f
remove the picard DbSNP ROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3743 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 17:46:00 +00:00
c80a257f37
Updated for CentOS changes.
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See: http://iwww.broadinstitute.org/itsystems/wiki/Dotkit#Job_Specific_Wrapper_Script
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3742 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 14:36:24 +00:00
56a0c7ee6f
All headers are now converted to VCF4 by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3741 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 14:14:17 +00:00
6e6ad36523
reallow MNP events through
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 06:26:52 +00:00
ed0d0d78fa
corresponding fix for dealing with insertions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3739 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 05:25:03 +00:00
ada8c9931f
We were never clipping the VCF-provided ref base off the left end of the alleles for insertions, so the reference allele was never null (and downstream walkers would fail). Didn't this get tested with insertions at some point?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3738 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 05:24:27 +00:00
9a81f1d7ef
Fixed this tool for chartl so that it now properly handles deletions. Added deletion case to integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3737 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:45:59 +00:00
47a42b1507
trivial cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3736 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:42:32 +00:00
b7a3d1e61f
Bug fix: if the FORMAT field consisted of just GT, we were exceptioning out. How did we not catch this until now?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3735 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:41:40 +00:00
1c146aebe8
Fix logic bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3734 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:32:46 +00:00
9fc05ac2ae
eagerDecode is now false.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3733 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 22:51:48 +00:00
4bc3ad2194
Shame on me: UG was emitting negative QUALs (-0) in all_bases mode. Thanks, Matt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3732 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 20:30:22 +00:00
30714ec8d9
As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 20:12:59 +00:00
8ff1a4b929
Don't try to clean reads that fail the PF, in preparation for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3730 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 19:49:36 +00:00
6a0483ee95
fixed typos
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3729 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 17:41:44 +00:00
2ac74a862d
updated to deal with new cleaner options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3728 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 17:06:00 +00:00
b934cc7554
Updates to fix some bugs in merger. Now able to merge into project wide indel VCF files. Integration teests coming tomorrow
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3727 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:16:33 +00:00
7be8c35eb2
Workaround for scala trait erasing parameterized types:
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- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:15:10 +00:00
120f90da5b
Interval support for ref walkers while streaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3725 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-07 03:14:59 +00:00
depristo
delangel
chartl
ebanks
kshakir
rpoplin
aaron
hanna