5539c2d9f3
--performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4921 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:34:21 +00:00
586d3f05d9
Better cumhist function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4920 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:32:20 +00:00
4c9746f463
Disabled performance log intermediate commit. Will be refactored and committed to the responsiblity along with documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4919 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 22:18:12 +00:00
2448b859e4
no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4918 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 13:27:37 +00:00
3fc9862964
Unit test fixed - Tribble codecs aren't designed to be stateless, but I was
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using one as though it was. Fixed, and debug code reverted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4917 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 17:47:52 +00:00
b9cb57f4b9
A unit test is failing on bamboo in a way I can't reproduce (or even explain).
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Checking in some debugging info.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4916 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 16:35:04 +00:00
cba18116e4
A significant refactoring of the ROD system, done largely to simplify the process of
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streaming/piping VCFs into the GATK. Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build
RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
are the walkers that feel the need to access the ROD system directly. (We need to stamp out
this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs. These'll be
fixed as part of the VCF streaming project.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 04:52:22 +00:00
d70483c50a
Automatically filter out reads with consecutive indel operators in the CIGAR string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4914 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 04:42:54 +00:00
848977678d
No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 22:06:19 +00:00
85f2968104
add convenience methods for RODs-for-reads: the ability to get all the RODs covering the read, regardless of their type or position on the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4912 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 20:46:03 +00:00
d7e74f8be6
Temporary phasing evalution walker that needs to be incorporated into the newest VariantEval, whenever it is available
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4911 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 20:43:15 +00:00
501d44fa04
Minor bug fixee, replace double quotes with single quotes in strings so that R can read the resulting table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4910 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 16:25:59 +00:00
a31f6e4e99
Need to check isBiallelic before calling getSNPSubstitutionType for the allele swap warning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4909 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 20:17:14 +00:00
8a0c07b865
Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4908 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 07:37:46 +00:00
6d809321d3
Updating combien variants memory limit and dcov default for the full calling pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4907 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-24 03:06:50 +00:00
6ebf5b30de
Transposing the table, and fixing some null pointer exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4906 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 16:22:57 +00:00
cebfd01857
Properly output .bed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4905 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 14:49:24 +00:00
464d0e18e3
Bringing us back to passing integrationtests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4904 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 14:36:11 +00:00
8c583ea405
RBP now operates correctly at non-variant sites so we can phase hom-ref genotypes with -sampleToPhase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4903 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 13:11:22 +00:00
376bc563d4
Trivial change to allow GenerateVariantClusters to be run on indels - not that VQSR now works on indels, far from it, but at least it's a first step and it allows us to generate cluster plots to see how well known/novel sites differentiate in their covariates (short answer: no difference/separation :( ).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4902 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 22:39:09 +00:00
a61f0047f0
Better queue status messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4901 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:17:28 +00:00
7ec805bef7
should be uncommented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4900 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:17:04 +00:00
b024b85798
misc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4899 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:16:41 +00:00
5265f943b0
phasing per sample. tmp checkin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4898 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:14:06 +00:00
e313eeede8
Push command-line expansions, such as BAM list unpacking and -B tag parsing, out
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into the CommandLine* classes. This makes it easier for external functionality
(such as the VCF streamer) to use GenomeAnalysisEngine directly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4897 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 19:00:17 +00:00
66cca7de0f
renamed genotypesArePhased to isPhased, as the previous name was incorrect for several reasons. Added setPhase() to MutableGenotype. Other classes changed to reflect renaming to isPhased(). CombineVariants now supports an experimental MASTER mode where it consumes -B:master,vcf and -B:xi,vcf for any number i and updates the master with phasing information in xi.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4896 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 17:42:05 +00:00
e7569cfe6f
Updated dbsnp version usage. Calling with 132, but still using 129 for eval to maintain consistant known/novel eval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4895 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 17:37:27 +00:00
2235245af0
PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 15:16:15 +00:00
a1653f0c83
Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable.
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Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default.
Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call.
Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 02:38:06 +00:00
cd4883f4da
Be certain to include core GATK reference metadata features and codecs in the
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final package.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4892 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:30:07 +00:00
7185fcb47b
Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4891 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:14:20 +00:00
cc909602c7
Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4890 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 17:18:26 +00:00
09c7ea879d
Merging GenomeAnalysisEngine and AbstractGenomeAnalysisEngine back together.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4889 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 02:09:46 +00:00
80770dc032
Expanded target pipeline complete. Stop trying to be clever about scatter-gather; wait until functional SG is built-in to Q. Til then, a lazy version of the fullCallingPipeline. Seems to take a long time to generate the graph though...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4888 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 00:56:16 +00:00
758d14a261
Checking in scripts used for testing the linear index MAX_FEATURES_PER_BIN.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4887 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 21:25:36 +00:00
fc33901810
Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4886 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 21:22:58 +00:00
61d5daa65c
EXTREME interval processing. Still undergoing testing.
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+ GroupIntervals allows user-defined scattering (e.g. take an interval list file, split it into k smaller interval list files by number of lines)
+ ExpandIntervals expands the intervals, either by widening them, or allowing the definition for nearby intervals (e.g. flanks starting 1bp before and after, ending 10bp after that)
+ IntersectIntervals takes n interval lists, writes 1 interval list that is the n-way intersection of all of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4885 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 19:42:50 +00:00
a829284d84
Return analyzed window sizes as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4884 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 17:00:17 +00:00
b3ac47812c
No longer emits records at filtered sites, in sub-sampling mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4883 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:43:50 +00:00
60880b925f
VC utils prune method now will keep genotype attributes as well as info keys. RBP now emits a far reduce (NO INFO, only GT:GQ:PG) records, further reducing size of phasing output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4882 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:33:14 +00:00
8604335566
Minor improvements to further reduce debugging output. When running in -samplesToPhase mode, now only including the samples to phase in the output VCF, making it very much smaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4881 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:19:47 +00:00
ff90c24f28
RBP now supports operating on a subset of samples, outputting a much reduced VCF file appropriate for merging later. Also, general optimization to avoid printing enormous amounts of data to logger.debug by using a glocal static variable DEBUG that conditionally allows writing to the variable. Passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4880 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:03:28 +00:00
4ca1da1d07
Updating the NA12878.HiSeq bam file to be the correct bam file in the methods development qscript.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4879 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 14:53:10 +00:00
8fac346ac1
Misc cleanup in Methods Development Qscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4878 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 04:24:25 +00:00
34ab5b4889
Turning on BAQ in Methods Development pipeline. A new dataset is added: 363 EUR samples from the November 1000G release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4877 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-19 21:13:25 +00:00
8118a439c0
Commit for Khalid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4876 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:24:18 +00:00
15a33545f4
Updating Methods development pipeline qscript with the bam lists for all the data sets. It is ready for people to start running with it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4875 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:19:14 +00:00
6db86ae0c6
PAC sets the refseq file to optional.
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Additional ipf for expanding interval lists. Either there's heavy latency on the toro -- or it's not working properly yet (e.g. the system print in the same scope as the file print outputs a line, but no file shows up on the system)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4874 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 19:04:52 +00:00
f0ab7b849a
Adding a window size variable to avoid indel genotyper error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4873 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 04:19:54 +00:00
a3729bd59c
Now I call BeforeMethod correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4872 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:45:45 +00:00
depristo
hanna
ebanks
aaron
corin
chartl
delangel
rpoplin
fromer
kshakir