0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
f75e54e3f7
fixes for new package names in tribble 74
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:47:04 +00:00
354262eabe
New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:54:18 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
f497213933
DbSNP moved over to tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 06:02:35 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
0e10359a5e
Okay, finished up the ability to cap a base's qual by its read's mapping quality.
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This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:58:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
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1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
8bb15ef812
Checking in the reference implementation of the downsampler for back comparison.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:41:13 +00:00
1714c322c2
Reorg of UG args; checking in first before upcoming changes that will break integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:48:46 +00:00
cbed0b1ade
Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 22:50:17 +00:00
82818a417b
Allow header fields to come in any order...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 18:33:10 +00:00
4617abf1ff
Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 20:42:04 +00:00
e2ff4167af
Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:38:33 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
d9bf441391
Have UG emit calls at sites from one or more 'trigger' tracks when provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:04:43 +00:00
8f2bfac7a6
Bug fix for NullPointerException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:02:09 +00:00
f5a3b128c8
Fixing bug that's not caught by integration tests:
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If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics. Instead, just check that any eval's no-call count is 0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 02:40:34 +00:00
29ab59a7b3
Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-24 21:31:03 +00:00
c8d09a29ed
some quick changes to the VE output system - more to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 21:55:08 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
e0b51d0df0
Trigger cleaning of duplicate reads. Also beeter debug output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:12:28 +00:00
3adf7fbf64
bug fix for known-indels used as consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00
536f22f3bd
adding VC adaptor for GELI, along with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:28:39 +00:00
8c94df6f00
Bug fix for Chris: deal with sites that have "semi-deletions"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 18:34:41 +00:00
20379c3f82
Added location-caching optimization, temporary attributes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 11:35:45 +00:00
84ebceb9a6
Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 02:05:10 +00:00
ef6d900eb8
for now, set log error to -1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:21:06 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
1373fee278
Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.
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VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument.
SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:19:03 +00:00
ab34397d2e
Continuing to stamp out the non-ASCII copyright virus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:50:45 +00:00
2fdc1cf490
Bed ROD track support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:42 +00:00
51b3998082
deleting unused code from VariationFiltration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:19 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
114819d980
Allow user to set min confidence score for comp tracks too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:09:09 +00:00
3db73e0791
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 03:00:43 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
80c4f88a72
removing the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:56:45 +00:00
7d952a34ae
Fixing copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3215 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:28:57 +00:00
cdc175f7e3
Synchronizing version to make sure everything compiles; this model is not operational yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:52 +00:00
4437456bb5
Pass array of ref bases to callExtendedLocus()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:41:13 +00:00
5d2fab93f4
Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:40:30 +00:00
01e6492ba9
Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:38:09 +00:00
4723cad1be
New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 17:35:09 +00:00
cac125b35c
Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:37:28 +00:00
124b7a2a58
Moved ApplyVariantClusters over to VariationContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:20:25 +00:00
200d3e2c47
added copyright note
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3205 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:44:26 +00:00
546dfb629e
A draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3204 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:38:16 +00:00
asivache
aaron
chartl
ebanks
hanna
depristo
rpoplin
weisburd