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1870 Commits (a8a2c1a2a19febdf9d49b1f4c71e2a4d32da2c41)

Author SHA1 Message Date
depristo a8a2c1a2a1 Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 01:19:58 +00:00
ebanks c29924e7cf Reverting previous change. 
Aaron, it's all yours...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:55:24 +00:00
aaron d21b582b18 memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1880 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:39:42 +00:00
ebanks 761a730758 assertBiAllelic -> assertMultiAllelic. 
Chris, if this breaks an integration test, you get it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:09:46 +00:00
depristo 2a26bb42dd Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1878 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 21:54:53 +00:00
chartl 055a99fb05 Change in ordering for a disjunctions. Walker will no longer try to calculate number of simple mismatches in the pileup if the pileup includes 'N's. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1877 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:24:14 +00:00
chartl 10bde9e77b Integration test for BTT calculator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1876 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:55 +00:00
aaron cfa86d52c2 ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:00 +00:00
chartl 3d50c72d74 Forgot a dumb little System.out.println. You will be flooded with "This read will not be used." statements until, overwhelmed, you give in to my demands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1874 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 16:13:48 +00:00
chartl 225ef52973 Now produces same output as the Scala walker for unconditioned tables (no 2bb, no previous base, etc.) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1873 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 16:10:44 +00:00
chartl f0021a3533 Changes to the BTTC scala walker: 
- Updated to use the unified genotyper rather than ssg
 - Fixed a minor issue where the Unified Genotyper returns null
   and SSG would still return an object. isDefinitelyHomRef() now
   checks for null Unified Genotyper <Call list, meta data> pairs.
 - Tables output survive a diff with previous tables




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1872 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 18:09:25 +00:00
ebanks bb180a23ef Updated MD5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1871 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:30:38 +00:00
ebanks 51f9ec0a5c subtract largest posterior value from all values; this hopefully solves any precision issues 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1870 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:20:15 +00:00
ebanks b9e8867287 -push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures 
-use slightly more stringent stability metric
-better integration test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1869 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 04:22:17 +00:00
depristo d6385e0d88 simpleComplement function() in BaseUtils. Generic framework for clipping reads along with tests. Support for Q score based clipping, sequence-specific clipping (not1), and clipping of ranges of bases (cycles 1-5, 10-15 for example). Can write out clipped bases as Ns, quality scores as 0s, or in the future will support softclipping the bases themselves. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1868 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 22:29:35 +00:00
chartl ad777a9c14 @BasicPileup - made the counts public so they can be used 
@PoolUtils - split reads by indel/simple base

@BaseTransitionTable - complete refactoring, nicer now

@UnifiedArgumentCollection - added PoolSize as an argument

@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model

@GenotypeCalculationModel - instantiates with the new PoolSize argument




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1867 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 21:56:56 +00:00
andrewk bdb34fcf38 Updated integration tests for VariantEval. Hooray for IT! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1866 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 20:00:29 +00:00
aaron 41a95cb3f0 fixing unified genotyper test for change: VCF output now emits no calls as ./. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1865 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:58 +00:00
hanna 85a4fbc256 Bumping version of Picard for firehose compatibility. 
Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:56 +00:00
aaron 8aacc43203 VCF output now emits no calls as ./. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1863 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 18:51:31 +00:00
andrewk d1a4cd2f73 Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval". 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:39:08 +00:00
ebanks 07b134a124 Added some integration tests for multiple samples 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:22:10 +00:00
ebanks 418e007ca6 A cleaner interface: now everyone can use UG's initialize method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1860 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 14:09:16 +00:00
aaron 96972c3a5c a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly. 
Also moved a buch of Lists over to Sets for consistancy.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:57:50 +00:00
aaron a69ea9b57c Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially. 
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:11:34 +00:00
ebanks b82c3b6040 Better error output (and fixed spelling mistakes) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1857 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 01:01:45 +00:00
ebanks 993c567bd8 I had to remove some of my more agressive optimizations, as they were causing us to get slightly different results as MSG. Results in only small cost to running time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1856 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 00:59:32 +00:00
asivache 7d7ff09f54 throw an exception if read has no associated read group 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 18:11:32 +00:00
chartl b9544d3f89 Output formatting change (very slight) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 16:47:29 +00:00
hanna 839c5d66bc Read uints directly into longs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1853 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 16:15:11 +00:00
hanna ce38fa7c81 Breaking the signed int glass ceiling; stage 1: convert critical ints to longs. Code cleanup and documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1852 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 15:28:56 +00:00
kcibul 79993be46c changed blank gene name to UNKNOWN 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1851 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 13:47:00 +00:00
depristo 0c2016c19a Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 12:07:44 +00:00
aaron a9094c835c clean-up and fixes to the VCF input 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1849 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 04:53:59 +00:00
ebanks a32470cea1 Deal with the fact that walkers can call UG's init/map functions directly. 
We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 02:31:45 +00:00
hanna 8dca236958 Base-packed reader cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1847 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 01:26:23 +00:00
hanna 316b30ee56 On the road to human: make sure the suffix array will fit in a Java array. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1846 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 21:45:35 +00:00
ebanks e740e7a7ce Because walkers call UG's map function, we need to move the actual writing out 
to UG's reduce function.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1845 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:49:26 +00:00
kcibul 825e6c7a4d added calculation for bases over 2x,10x,20x,30x plus gene name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1844 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:32:26 +00:00
aaron 727b69fce0 catch null output destinations earlier 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1843 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:07:15 +00:00
chartl 1f66738c8e Fix a hashing function bug. Ignore reads with non-reference bases in the pileup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1842 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:41:26 +00:00
hanna 72c34f11dd Bug fixing for BWA output formats. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1841 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:32:22 +00:00
aaron 60183229ab the oldest java mistake in the book... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1840 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:32:13 +00:00
ebanks 52d2e0ca07 All walkers now use read.getReadGroup() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1839 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:27:40 +00:00
chartl 0a09fa4d5c Rename to distinguish this transition table calculator from the scala version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1838 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:52:21 +00:00
chartl 1d055011bd Getting rid of this so I can rename it without the world blowing up. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1837 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:45:11 +00:00
aaron eb90e5c4d7 changes to VCF output, and updated MD5's in the integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:42:48 +00:00
ebanks 89771fef05 -Use read.getReadGroup() 
-Add another filter for read groups for Chris


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1835 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:08:32 +00:00
ebanks 311ab8da5a A helper class to create the masks for the sequenom design maker. 
This project is now officially done.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1834 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:28:51 +00:00
hanna 3553fc9ec0 Preparing for human -- support bwa output files directly rather than relying on a custom fixed sa interval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1833 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:17:46 +00:00