7fac4afab3
Fixed priors (now initialized upon engine startup in a multi-dimensional array) and cell coefficients (properly handles the generalized closed form representation for multiple alleles).
2011-12-05 15:57:25 -05:00
1ba03a5e72
Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction
2011-12-05 14:06:00 -05:00
a7cb941417
The posteriors vector is now 2 dimensional so that it supports multiple alleles (although the UG is still hard-coded to use only array[0] for now); the exact model now collapses probabilities for all conformations over a given AC into the posteriors array (in the appropriate dimension). Fixed a bug where the priors and posteriors were being passed in swapped.
2011-12-04 13:02:53 -05:00
eab2b76c9b
Added loads of comments for future reference
2011-12-03 23:54:42 -05:00
29662be3d7
Fixed bug where k=2N case wasn't properly being computed. Added optimization for BB genotype case not in old model. At this point, integration tests pass except for 1 case where QUALs differ by 0.01 (this is okay because I occasionally need to compute extra cells in the matrix which affects the approximations) and 2 cases where multi-allelic indels are being genotyped (some work still needs to be done to support them).
2011-12-03 23:12:04 -05:00
71f793b71b
First partially working version of the multi-allelic version of the Exact AF calculation
2011-12-02 14:13:14 -05:00
d014c7faf9
Queue now properly escapes all shell arguments in generated shell scripts
...
This has implications for both Qscript authors and CommandLineFunction authors.
Qscript authors:
You no longer need to (and in fact must not) manually escape String values to
avoid interpretation by the shell when setting up Walker parameters. Queue will
safely escape all of your Strings for you so that they'll be interpreted literally. Eg.,
Old way:
filterSNPs.filterExpression = List("\"QD<2.0\"", "\"MQ<40.0\"", "\"HaplotypeScore>13.0\"")
New way:
filterSNPs.filterExpression = List("QD<2.0", "MQ<40.0", "HaplotypeScore>13.0")
CommandLineFunction authors:
If you're writing a one-off CommandLineFunction in a Qscript and don't really
care about quoting issues, just keep doing things the direct, simple way:
def commandLine = "cat %s | grep -v \"#\" > %s".format(files, out)
If you're writing a CommandLineFunction that will become part of Queue and
will be used by other QScripts, however, it's advisable to do things the
newer, safer way, ie.:
When you construct your commandLine, you should do so ONLY using the API methods
required(), optional(), conditional(), and repeat(). These will manage quoting
and whitespace separation for you, so you shouldn't insert quotes/extraneous
whitespace in your Strings. By default you get both (quoting and whitespace
separation), but you can disable either of these via parameters. Eg.,
override def commandLine = super.commandLine +
required("eff") +
conditional(verbose, "-v") +
optional("-c", config) +
required("-i", "vcf") +
required("-o", "vcf") +
required(genomeVersion) +
required(inVcf) +
required(">", escape=false) + // This will be shell-interpreted
required(outVcf)
I've ported the Picard/Samtools/SnpEff CommandLineFunction classes to the new
system, so you'll get free shell escaping when you use those in Qscripts just
like with walkers.
2011-12-01 18:13:44 -05:00
b5b5ffe71d
Parameterize intervals.
2011-12-01 13:18:18 -05:00
ef81224dcf
Parameter to customize # CPU threads.
2011-11-30 23:47:46 -05:00
c9eae32f6e
Revving Tribble to actually close file handles when close() is called.
2011-11-30 22:42:21 -05:00
3060a4a15e
Support for list of known CNVs in VariantEval
...
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
2011-11-30 17:05:16 -05:00
b65db6a854
First draft of a test script for I/O performance with the new asynchronous I/O processing.
...
Also includes convenience parameters for specifying the IO/CPU threading balance outside of a tag. Will be killed when
Queue gets better support for tagged arguments (hopefully soon).
2011-11-30 13:13:16 -05:00
1d5d200790
Cleaned up unused import statements
2011-11-30 15:30:30 +01:00
28b286ad39
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-30 09:11:53 -05:00
20bffe0430
Adapted for the new version of MendelianViolation
2011-11-30 14:46:38 +01:00
1cb5e9e149
Removed outdated (and unused) -familyStr commandline argument
2011-11-30 14:45:04 +01:00
9574be0394
Updated MendelianViolationEvaluator integration test
2011-11-30 14:44:15 +01:00
f49dc5c067
Added functionality to get all children that have both parents (useful when trios are needed)
2011-11-30 14:43:37 +01:00
a4606f9cfe
Merge branch 'MendelianViolation'
...
Conflicts:
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
2011-11-30 11:13:15 +01:00
b279ae4ead
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-30 10:10:21 +01:00
7d58db626e
Added MendelianViolationEvaluator integration test
2011-11-30 10:09:20 +01:00
91413cf0d9
Merged bug fix from Stable into Unstable
2011-11-29 14:01:23 -05:00
cb284eebde
Further updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 14:00:57 -05:00
dcb889665d
Merged bug fix from Stable into Unstable
2011-11-29 09:58:49 -05:00
447e9bff9e
Updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 09:57:45 -05:00
110298322c
Adding Transmission Disequilibrium Test annotation to VariantAnnotator and integration test to test it.
2011-11-29 09:29:18 -05:00
ab67011791
Corrected bug introduced in the last update and causing no families to be returned by getFamilies in case the samples were not specified
2011-11-29 11:18:15 +01:00
d7d8b8e380
Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
2011-11-28 14:18:28 -05:00
a09c01fcec
Removed walker argument FamilyStructure as this is now supported by the engine (ped file)
2011-11-28 17:18:11 +01:00
795c99d693
Adapted MendelianViolation to the new ped family representation. Adapted all classes using MendelianViolation too.
...
MendelianViolationEvaluator was added a number of useful metrics on allele transmission and MVs
2011-11-28 17:13:14 +01:00
e877db8f42
Changed visibility of getSampleDB from protected to public as the sampleDB needs to be accessible from Annotators and Evaluators too.
2011-11-28 17:11:30 +01:00
5c2595701c
Added a function to get families only for a given list of samples.
2011-11-28 17:10:33 +01:00
3c36428a20
Bug fix for TiTv calculation -- shouldn't be rounding
2011-11-28 10:20:34 -05:00
436b4dc855
Updated docs
2011-11-28 08:59:48 -05:00
b1dd632d5d
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
...
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
2011-11-25 16:16:44 +01:00
e60272975a
Fix for changed MD5 in streaming VCF test
2011-11-23 19:01:33 -05:00
12f09d88f9
Removing references to SimpleMetricsByAC
2011-11-23 16:08:18 -05:00
fdd90825a1
Queue now outputs a GATK-like header with version number, build timestamp, etc.
2011-11-23 14:28:35 -05:00
e319079c32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-23 13:02:11 -05:00
4107636144
VariantEval updates
...
-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
2011-11-23 13:02:07 -05:00
e5b85f0a78
A toString() method for IntervalBindings
...
Necessary since we're currently writing things like this to our VCF headers:
intervals=[org.broadinstitute.sting.commandline.IntervalBinding@4ce66f56]
2011-11-23 11:56:12 -05:00
5a4856b82e
GATKReports now support a format field per column
...
-- You can tell the table to format your object with "%.2f" for example.
2011-11-23 11:31:04 -05:00
c8bf7d2099
Check for null comment
2011-11-23 10:47:21 -05:00
c1ea53d088
Solve merge conflicts
2011-11-23 09:17:32 -05:00
d2499bcc33
Cleaning up and institutionalizing several local hacks to ValidationSiteSelector: add argument to ignore polymorphic status in VC (useful when we want to intentionally select monomorphic sites), add dummy NullSampleSelector class that should be used if we really don't want to do any sample selection, and enabled sampleMode=NONE for this purpose.
2011-11-23 09:14:10 -05:00
6c2555885c
Caching getSimpleName() in VariantEval is a big performance improvement
...
-- Removed the SimpleMetricsByAC table, as one should just use the AlleleCount Stratefication and the upcoming VariantSummary table
2011-11-23 08:34:05 -05:00
32adbd614f
Solve merge conflict
2011-11-22 22:48:46 -05:00
941f3784dc
Solve merge conflict
2011-11-22 22:48:03 -05:00
75d93e6335
Another corner condition fix: skip likelihood computation in case we cut so many bases there's no haplotype or read left
2011-11-22 22:46:12 -05:00
a3aef8fa53
Final performance optimization for GenotypesContext
2011-11-22 17:19:30 -05:00
Eric Banks
David Roazen
Matt Hanna
Mark DePristo
Laurent Francioli
Ryan Poplin
Guillermo del Angel