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4016 Commits (ee348ac9d4049a4e142779f9a7ac95f7e4c0b596)

Author SHA1 Message Date
ebanks ee348ac9d4 Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-10 20:27:04 +00:00
fromer 01c2091cd9 A LocusWalker to print the haploid reference genome as a VCF file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-10 16:59:41 +00:00
delangel 9648399630 Boneheaded silly bug in indel caller - posterior probability computation was using priors gotten from SNP heterozygosity, not indel heterozygosity. Added then indel het. argument to command line and hook it up (not a radical change in calls though, just a few dubious calls around the edges fall off) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4967 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-10 14:56:28 +00:00
aaron b24e1134f9 unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 22:32:50 +00:00
kshakir b34e2f733f Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list. 
Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 22:03:36 +00:00
ebanks 60f45a7c49 Stupid me. Forgot to put this check in the last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4959 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 19:16:41 +00:00
aaron 56b87da8f9 a better error message for the situation where a RMD track generates a negitive length interval; the user will now see a message like "Bad input: A feature produced by the reference metadata track named "bed" at position chr1:10434-10433 has a start greater than the stop; this is an invalid position " 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4958 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 19:06:04 +00:00
ebanks 4272b824d6 unused imports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4957 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 18:33:12 +00:00
chartl 3e7802a3e0 Minor changes to a qscript and the GQ constants on PrivatePermutations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4956 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 18:26:21 +00:00
kiran 79fcff13ff Fixed import statement that was erroneously referring to VE3 rather than VE2. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4955 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 03:22:25 +00:00
ebanks f3ca2cc9de Add safety net to BAQ calculation: explicitly cast to byte/int and check for bad values 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4954 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 18:09:12 +00:00
ebanks 2ac5c52281 Better error message as per Mark 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4953 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:44:02 +00:00
ebanks e0d091b3db Die gracefully if the bam is malformed with quals that are too high 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4952 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:39:08 +00:00
kiran 3163970ad5 Updates that slipped from my last commit: fixed some imports and calls to super(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4951 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:34:40 +00:00
kiran d88fd7212f Changes to allow the primary key of a table to be hidden. Formatting changes to account for when that column is hidden. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4948 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:27:19 +00:00
kiran 307c41c128 Changes to allow the primary key of a table to be hidden. Formatting changes to account for when that column is hidden. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4947 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:26:38 +00:00
kiran fdc514ded3 Intermediate commit for VariantEval 3.0. Among the changes: 
* Stratifications (by comp rod, by eval rod, novelty, filter status, etc.) have been generalized.  They are very symmetric with evaluators now.  Each stratification can have multiple states (e.g. known, novel, all).  New stratifications can be added and optionally applied.  Some new stratifications include:
  - by sample
  - by functional class
  - by CpG status

* Output is to a single file in GATKReport format, rather than having the options of CSV, R, table, etc.

* Rather than needing to state up front that the allowable variant type is a SNP or an indel, each eval record is inspected and the appropriate record type is fetched from the comp track.  (This will require a bit more testing...)

* Evaluation context (basically a single row in a VariantEval report) generation and retrieval has been overhauled.  Now, every possible configuration of stratification state is generated recursively and stored in a HashMap.  The key of the HashMap is a key that represents that exact state configuration.  When examining a comp track and eval track, this key is computed based on the data, providing easy lookup for the appropriate evaluation context.  When there are only a handful of stratification configurations, this isn't a big deal.  But when operating on a file with hundreds of samples, multipled by 3 states for novelty, 3 states for filtration, 3 states for CpG status, etc., it becomes a very big deal.

There are still some known issues:
* When the per-sample stratification is turned off, things are getting overcounted (too many variants are showing up when compared to the VariantEval 2.0 code).  It's probably because I break out the VariantContext by sample even when not necessary, and those irrelevant contexts are still being counted.  Or my recursion is overaggressively creating evaluation contexts, and they all get added up in a weird way.  But that's why I'm committing now - so I can track down this issue without losing my work so far.

* The Jexl expressions are sometimes throwing an exception that I don't yet understand (they complain of an incorrect specification on the command-line... *after* the program has made it through a few thousand records.

* The request to have evaluations be smart enough to reject certain stratification states is not implemented yet.

There's still some work to do before I can replace VariantEval 2.0 with VariantEval 3.0, but feel free to take a look.  I'd love comments on the new code.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4946 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 15:20:24 +00:00
kiran e9201b81d1 A more general method for specifying samples to act on from the command-line. Supports samples specified individually on the console, a file of samples, or regular expressions to select multiple samples. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4945 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-06 14:54:56 +00:00
carneiro 5e9a8f9cb3 Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base. 
Adding the first version of the techdev pipeline (tdPipeline)




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 22:25:08 +00:00
aaron cba436fa2f small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 21:20:26 +00:00
fromer 4b37710bcd Added validator for phasing using read information, e.g., PacBio: ReadBasedPhasingValidationWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4940 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 20:05:56 +00:00
delangel d203f5e39a Experimental change in how we classify indels - up to now, an indel of say AA was counted as a 2-mer repeat expansion. But in reality, if the event is sounded by A's it's really a multiple monomer expansion. So, we first reduce the indel bases in case they are made of repeated elements before classifying them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4939 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 17:13:18 +00:00
rpoplin 4ac0590744 Fix for NaNs in the rank sum tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4938 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 15:21:30 +00:00
chartl 445ae06a7a Re-add PrivatePermutations since ACTransitionTable is a little too memory-intensive to generate all the cuts that I need 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4937 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 06:11:18 +00:00
hanna 7cdaffbe5c Create tmpdir if it doesn't exist. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4936 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 03:07:11 +00:00
hanna 0982d35f5b Bug fixes in streaming in Tribble data via /dev/stdin. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4935 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 02:43:04 +00:00
rpoplin 23dbc5ccf3 HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4934 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-05 00:28:05 +00:00
ebanks 85714621be Better interface to Genotypelikelihoods class. Now you need to specify the format (GL vs PL) of the output string when calling getAsString(). All likelihoods are represented as GLs internally. QualByDepth no longer does its own conversion. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4933 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-04 21:48:14 +00:00
ebanks 96729acd0d Optional argument to put the original position into the INFO field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4930 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-04 19:22:44 +00:00
delangel caedfed860 Fix bug where indels being incorrectly classified in VariantEval module 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4929 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-04 18:01:48 +00:00
hanna 8d2c14b29c Update Picard / sam-jdk at Tim's request. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-03 02:17:25 +00:00
depristo d31c658c2e Organized performance monitoring passes unit tests and is more efficient 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4924 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-03 02:09:08 +00:00
depristo c51e745bae The engine can be null in a unit test, so check for it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4923 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-03 01:00:52 +00:00
depristo 75a7d8a76e Trivial formatting error 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4922 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-02 23:44:36 +00:00
depristo 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 
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
depristo 4c9746f463 Disabled performance log intermediate commit. Will be refactored and committed to the responsiblity along with documentation 
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
hanna 3fc9862964 Unit test fixed - Tribble codecs aren't designed to be stateless, but I was 
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
hanna b9cb57f4b9 A unit test is failing on bamboo in a way I can't reproduce (or even explain). 
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
hanna cba18116e4 A significant refactoring of the ROD system, done largely to simplify the process of 
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
ebanks d70483c50a Automatically filter out reads with consecutive indel operators in the CIGAR string 
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
ebanks 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... 
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
aaron 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. 
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
depristo d7e74f8be6 Temporary phasing evalution walker that needs to be incorporated into the newest VariantEval, whenever it is available 
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
ebanks a31f6e4e99 Need to check isBiallelic before calling getSNPSubstitutionType for the allele swap warning 
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
ebanks 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. 
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
chartl 6ebf5b30de Transposing the table, and fixing some null pointer exceptions 
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
ebanks cebfd01857 Properly output .bed 
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
depristo 464d0e18e3 Bringing us back to passing integrationtests 
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
depristo 8c583ea405 RBP now operates correctly at non-variant sites so we can phase hom-ref genotypes with -sampleToPhase 
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
delangel 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 :( ). 
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