e5e6d515c3
Fix misunderstanding of GenomeLoc interval
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2138 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 15:12:49 +00:00
cb6d6f2686
Very minor performance improvements
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2137 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 05:21:07 +00:00
c90bea39a1
read.getReadString().charAt(offset) --> read.getReadBases()[offset]
...
[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 04:25:19 +00:00
ec321abd7b
Added ability to filter on the QUAL field
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2135 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 04:08:22 +00:00
36d493e645
All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2134 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 03:55:12 +00:00
ee5093d2c6
-Added VariantFiltration integration tests
...
-Added integration test for GLFs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:36:27 +00:00
be6a549e7b
Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:34:48 +00:00
903342745d
Basic integration test for the aligner.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2131 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 23:08:05 +00:00
4837fe919c
Convenience changes. If no -BWT option is specified, pull the BWT location from the reference.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2130 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 22:46:05 +00:00
9e4eadc37c
CountCovariates v2.0.2: Added a --process_nth_locus <int> argument to only use every Nth covered locus when creating the recalibration table.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2129 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 22:07:38 +00:00
6a52ca3db6
Update to the UG integration test. Why I had to rm -rf my entire sting directory to get it to correctly fail we may never know.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2128 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 21:23:00 +00:00
ed4cf3de57
Check that we're biallelic before calling isSNP()
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2127 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:20:48 +00:00
5744a1d968
The covariates don't care about SAMRecord's anymore - Cleaning up the import statements.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2126 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:10:12 +00:00
23983b2fd8
New annotation: ResidualQuality
...
Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.
Update to the integration test so bamboo doesn't look as though someone murdered it with a spork
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:04:01 +00:00
70059a0fc9
Refactored joint estimation model to allow subclasses to overload PofD calculation over all frequencies. Pooled model now takes only 20% of time that it used to.
...
Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2123 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:03:38 +00:00
7f947f6b60
Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2122 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 19:51:36 +00:00
c299ca5f49
It would help if I copied the MD5s from the right integration test...
...
I hate Mondays.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2121 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:21:36 +00:00
ff4797acbb
Forgot to check in integration test update
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2120 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:13:51 +00:00
14bf6ce83c
1. Newest version of the joint estimation model. Faster than previous version and now qscores can get to be > 39.8 for hets.
...
2. More sanity checks in annotations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2119 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:05:50 +00:00
ee2abd30c4
Count the best alignments and emit them to a file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2118 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 16:37:59 +00:00
1d46de6d34
The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2117 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 14:58:33 +00:00
dfe7d69471
1. VCF: don't print slod if it's never set
...
2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 02:55:43 +00:00
753cb100a3
Add checks for weird situations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2115 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 02:14:25 +00:00
04d6ac940c
Always print out VCF header - not just when there is genotype data present.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2114 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 01:44:10 +00:00
bf935a6ab1
1. Fixed bug in PrimaryBaseSecondaryBaseSymmetry code (not checking for null before trying to access object's methods) which was causing Integration Tests to fail.
...
2. Retired allele frequency range from UG, which wasn't very useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 01:31:48 +00:00
b24240664f
Reduced the number of calls to new ArrayList() in TableRecalibration. This results in a speed up of perhaps up to 6 percent (timed trials are hard).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2112 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 17:24:31 +00:00
c9c4999354
BWA: odds and ends. Get rid of some spurious debug code that was accidentally
...
checked in. Add a better way to write out unmapped reads (thanks Kiran!) Add
a pre-built version of the shared library to the repository for early adoption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 15:26:07 +00:00
9c206abb97
removing unnecessary printing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2110 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 12:41:48 +00:00
59416ae06a
This is an annotation adapted from one that Mark Daly suggested some time ago. Right now it calculates:
...
- For all reference bases, the proportion of their second best bases that support the SNP
- the proportion of non-reference bases that support the SNP
and reports the difference between the two. Initially I was taking depth into account as well, but that did not appear to work as nicely as I'd like (even at 20,000x depth, if 95% of the non-reference bases are C, and 98% of the reference second-best-bases are C, then we would want to be suspicious of it; but perhaps slightly less so than if the depth were only 20...)
Anyway it's now available. I'm not sure how useful it will be, but I spawned the FHS annotation jobs again, so we'll see.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2109 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 00:47:49 +00:00
98f921fe24
The refactored CountCovariates now hashes the read object into a HashMap which holds all the properties the covariates pull out of the read over and over again such as read group string, bases string and its complement string, quality scores, etc. This results in a big speed up. CountCovariatesRefactored is now just slightly slower than CountCovariates (perhaps 1.07x according to my latest time trial). Thanks to Alec for suggesting IdentityHashMap. CycleCovariate now warns the user that is is defaulting to the Solexa definition of cycle when the platform string pulled out of the read is unrecognized instead of halting with an Exception.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2108 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-21 20:38:17 +00:00
27122f7f97
Performance improvements for pooled caller. Now possible to actually run on real data in a finite amount of time. Minor changes to GL interface (making strandIndex public) to support cached calculations in pooled caller.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2107 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-21 15:07:40 +00:00
797bb83209
New VariantFiltration.
...
Wiki docs are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2105 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 19:50:26 +00:00
a78bc60c0f
Minor tweak to improve ease-of-use of iterator system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 18:24:19 +00:00
4fbb6d05d0
Refactoring. Push the revisions to the common aligner interface down into
...
the aligner base classes. Hack the managed implementation to support the
new interface.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 17:08:09 +00:00
d84444200b
The Unified Genotyper now sorts the sample names in the vcf that it outputs.
...
[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 16:13:18 +00:00
38a030f2ba
Finishing off data transfer conduits for single alignment generator.
...
Misc bug fixes elsewhere.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 15:21:59 +00:00
2a5349d886
VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied and it's not already set for a record
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2100 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 03:26:09 +00:00
b434c1c240
Check for null entries before adding
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2099 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 03:12:20 +00:00
82fd824c4d
Continuing improvements to unified genotyper
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2098 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 01:39:29 +00:00
33dcfc858d
updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing.
...
Also a 250% improvement in the getBases() and getQuals() of BasicPileup, which was nearly all of the runtime for the genotyper (using primitives instead of objects when possible).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2097 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 23:06:49 +00:00
22aaf8c5e0
Added the old recalibrator integration tests to the refactored recalibrator sitting in playground.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2096 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 22:43:28 +00:00
a95302fe98
Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still
...
needs to plumbed through and it may leak memory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 21:20:03 +00:00
a972b2769f
Checkpoint. Add first phase of single alignment interface.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 19:03:43 +00:00
306f4624c6
oops forgot to update the md5s
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2093 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 18:22:29 +00:00
6ba1f3321d
Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.
...
Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 18:17:47 +00:00
b4babb82eb
adding an extra bit of data to come out of CTT (number of chips with actual data)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2091 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:46:10 +00:00
7623b39927
Add rodPicardDbSNP
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2088 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:27:46 +00:00
b2b4ff7eca
Cache SAMReadGroup rather than get it twice
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2087 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:27:18 +00:00
b3872386c9
Test to ensure that ConcordanceTruthTable and those walkers which rely on it for tabulating pooled truth information from truth information of the individuals within the pool is doing that calculation correctly. Tests single het, single hom (with/without reference), together, together without reference, and a mix of everything.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2082 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 15:26:32 +00:00
eeb3a3fffb
comments for Aaron
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2081 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 12:56:04 +00:00
alecw
ebanks
hanna
rpoplin
chartl
depristo
aaron