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1208 Commits (248cc308b23aa12d331c2442b70631ee99fa3d08)

Author SHA1 Message Date
fromer 248cc308b2 ReadBackedPhasing silently ignores sites with ploidy != 2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4272 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 21:14:17 +00:00
fromer 528f6344af Moved ReadBackedPhasingWalker to phasing sub-directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4271 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 19:36:41 +00:00
depristo 7880863eb7 Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 15:07:38 +00:00
depristo 7ad8fbdd5a Moved GATKException to exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:47:19 +00:00
depristo 595907e98e Moving StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:34:15 +00:00
depristo 40e6179911 Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:02:43 +00:00
depristo 8f1a32acae All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 15:25:30 +00:00
depristo ca9c7389ee Not useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4238 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:33:03 +00:00
depristo 8708753a6a checkin for removal 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4237 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:32:46 +00:00
fromer 1b1ec7e52d Changed default phasing window size to 10 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4235 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 21:28:36 +00:00
depristo 7eeabe534a QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4211 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 18:21:43 +00:00
fromer 529eecd4dc Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4208 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:38:46 +00:00
fromer c0ce9ca8cc Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4207 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:32:30 +00:00
fromer c119f64514 Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4205 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:24:18 +00:00
fromer a1cf3398a5 Added basic version of phasing evaluation: GenotypePhasingEvaluator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4196 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 22:09:50 +00:00
fromer 50f7f18cbd Changed ReadBackedPhasing default PQ threshold to 10 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4166 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-30 21:26:15 +00:00
kiran 16b75e3b9a A new version of the ErrorRateByReadPosition walker, using the GATKReport functionality to store and emit its output. This version of the walker is roughly half the number of lines as the previous version, owing simply to the removal of all of the output formatting that's now handled by GATKReport. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4160 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 05:41:13 +00:00
kiran fd19c63aaf A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module). 
This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R.  In the end, you get a table that looks like this:

##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle  errorrate.61PA8.7         qualavg.61PA8.7
0      0.007451835696110506      25.474613284804366
1      0.002362777171937477      29.844949954504095
2      9.087604507451836E-4      32.87590975254731
3      5.452562704471102E-4      34.498999090081895
4      9.087604507451836E-4      35.14831665150137
5      5.452562704471102E-4      36.07223435225619
6      5.452562704471102E-4      36.1217248908297
7      5.452562704471102E-4      36.1910480349345
8      5.452562704471102E-4      36.00345705967977
...

A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession.  Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone.  This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.

The display property of individual columns can be turned off.  This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.

Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations.  For instance, two whole columns can be divided, the results of the operation being stored in a third column.  This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 05:39:24 +00:00
hanna de5ccfb0b1 Moved hasPileupBeenDownsampled() based on Eric's request. Also eliminated 
@Deprecated constructors from AlignmentContext.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4142 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 16:12:05 +00:00
ebanks bfcac33e80 Cleaning up playground utils and tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4136 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:25:47 +00:00
ebanks 4979dcc9a7 Finishing up the playground cleanup (for now) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4135 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:19:37 +00:00
ebanks 0452b1ab68 archiving, removing, or promoting to core from playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4134 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:07:42 +00:00
ebanks dfae48cee0 Moving supported tools to core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4127 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 13:56:19 +00:00
ebanks e06b2c90ef Cap the default size of join tables; this can be modified with the --maxJoinTableSize argument. Also, misc cleanup of the comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4125 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 05:21:26 +00:00
ebanks 79cd716671 More cleanup of the Genomic Annotator. Also, we now require join tables to have unique entries for the column keyed on the join. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4124 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 04:43:52 +00:00
fromer 39da567d48 Changed ReadBackedPhasing to be a RodWalker (corrected to By(READS)) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4120 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 20:53:04 +00:00
ebanks 4678613893 Significant fixes for the Genomic Annotator. 
1. Rip out all of Ben's code intended to circumvent the stable VCF Writer output system in multi-threaded mode (I threw up a little when 
I saw this code).  This will improve memory consumption when running with -nt.
2. Don't annotate indels or > bi-allelic sites.
3. Fix bug where not all records were making it into the output VCF.
4. General code clean up.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4118 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 20:16:50 +00:00
fromer 41e53d37e1 Changed ReadBackedPhasing to be a RodWalker (more efficient, since it is ROD-focused) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4117 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 19:43:57 +00:00
fromer aa8cf25d08 Implemented fully symmetric sliding window read-backed phaser 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4104 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 21:12:32 +00:00
ebanks 90aef66ec5 Minor fixes for my last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4090 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 23:25:29 +00:00
ebanks ef795825fd Yet more argument consistency updates 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4089 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 20:52:30 +00:00
ebanks ccda4f6ec1 More output consistency changes (updating wiki docs as I go along). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4086 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 18:46:08 +00:00
ebanks 55a8306a0d Update the @RMD tags to look for VariantContext.class instead of ReferenceOrderedDatum.class. Since the test for rod type is broken this won't affect anything right now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4084 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 17:49:37 +00:00
aaron 35b9883dd6 vcfwriter is in tribble now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4083 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 17:01:04 +00:00
kiran 295472bf69 Simple change to handle a no-call (must avoid asking for the second allele, which will be be null in this case). Also, added a hack to deal with input VCFs where there are no genotype likelihoods (needed in order to process Hapmap and 1KG VCFs). In this mode, called genotypes are assigned a likelihood of 0.96, and alternative genotypes are given 0.02 each. I know Beagle actually takes genotype data without likelihoods, so this might not be the right way to do this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4081 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 05:13:09 +00:00
hanna b80cf7d1d9 Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4077 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-22 14:27:05 +00:00
depristo b6989289fc Potential bug fix for bad references where some codons may have Ns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4075 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-21 12:09:33 +00:00
ebanks 165dc6d3b0 Ryan, what did you decide about supporting this tool? Is it still useful? 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4073 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-20 19:16:14 +00:00
fromer 1c4784999a Updated to work exclusively in log10 space 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4069 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-19 21:31:07 +00:00
fromer 3af4e618cc Fixed precision issues with PQ (phasing quality) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4068 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-19 20:34:47 +00:00
fromer effeedf1a3 Updated Bayesian phasing method to output per-site phasing statistics (and to not cap PQ at 40) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4064 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-19 19:55:47 +00:00
fromer 1336ea17a3 quality-scored-based Bayesian phasing algorithm implemented 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4055 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-18 21:17:46 +00:00
kiran 3d63302b70 Deprecated. Use SelectVariants instead. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4043 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-16 15:07:50 +00:00
fromer dfe2922b5e First working version of statistical haplotype phaser 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4031 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-13 21:29:45 +00:00
ebanks f36c0ed613 Stop building obsolete VCFTools and CGUtilities 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4030 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-13 19:28:36 +00:00
hanna cb144734c0 Getting rid of GenotypeWriter interface. Of note: 
- GATKVCFWriter deleted, to be replaced if absolutely necessary when VCF writing goes into Tribble.
- VCFWriter is now an interface, for easier redirection.
- VCFWriterImpl fleshes out the VCFWriter interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4026 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-13 16:33:22 +00:00
kshakir f39dce1082 Exposed CommandLineFunction defaults to the Queue.jar command line (see -help). 
Added ability to skip up-to-date jobs where the outputs are older than the inputs.
Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names.
Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile
Moved Hidden from the GATK to StingUtils.
Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7
Added Queue to javadoc and testing build targets.
Added first Queue unit test.
Another pass at avoiding cycles in the DAG thanks to all function I/O being files.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4017 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 21:58:26 +00:00
ebanks 419a36f74c Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3994 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-10 02:16:05 +00:00
kiran 9aa70d9c7c Replaced by SelectVariants 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-08 07:07:42 +00:00
ebanks 637a1e5055 Updating to use the new VA interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3975 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-08 05:31:01 +00:00