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Author SHA1 Message Date
ebanks e96b1791ab Need to check for biallelic snp or exception gets thrown. 
Also, update to new tracker calls.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1913 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-27 02:43:43 +00:00
aaron 3fb3773098 a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1912 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 20:18:55 +00:00
hanna a1e8a532ad Support for initialize() and onTraversalDone() output from parallelized walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 20:18:31 +00:00
chartl 62c1001790 BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1910 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 19:24:18 +00:00
sjia 24c7f694e6 Handles allele frequencies for any specified population, changed user input for mismatch filter options 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1909 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-25 22:51:56 +00:00
chartl db9419df49 @ Hack to allow output from onTraversalDone() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1908 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-25 15:19:04 +00:00
ebanks 75ad6bbef7 Check that map isn't being called passing in null arguments. 
(This seems wrong; see JIRA entry GSA-211)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-25 02:30:36 +00:00
depristo b4f55df600 Bugfix for Jason F 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1906 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-24 22:09:27 +00:00
hanna 65b98470f3 Temporary fix: have RodLocusView manage and close its RODs. Really the 
relationship between these two classes needs to be rethought; see JIRA
GSA-207.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 16:00:12 +00:00
aaron ad1fc511b1 intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1903 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 06:31:15 +00:00
ebanks 6c338eccb8 Joint Estimation model now emits calls in all formats. 
The whole GenotypeCall framework needs to be changed, but this will work for the time being.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1902 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 03:07:28 +00:00
chartl a6dc8cd44e BTTC is now Tree Reducible allowing for parallelization. 
Integration test comment changed to reflect actual date of last md5 update.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 23:19:29 +00:00
hanna 2e552eb5a1 Validates intervals against sequence dictionary header bounds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1900 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 19:31:15 +00:00
ebanks 54c61c663c -Cleanup of the Joint Estimation code 
-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 15:25:29 +00:00
asivache 2cab4c68d4 Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1898 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 14:55:07 +00:00
chartl af761fb9bd Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 21:18:26 +00:00
ebanks 55fa1cfa06 -Renamed new calculation model and worked out some significant xhanges with Mark 
-Allow walkers calling the UG to pass in their own argument collections


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1896 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 20:49:36 +00:00
chartl 8e3f72ced9 BTTJ - Code refactoring (major) - passes integration test 
VariantEvalWalker - whoops, wrote PooledGenotypeAnalysis rather than PooledAnalysis, now passes tests again

- PooledFrequencyAnalysis - don't bother initializing matrices if this isn't a pool




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1895 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 19:04:51 +00:00
depristo 15a1849758 notes for chartl 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1894 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 18:31:31 +00:00
chartl 77863d4940 @PowerBelowFrequency 
+ Changes to doc

@ BasicPoolVariantAnalysis
    + use char rather than ReferenceContext
    + calculate # alleles

@ PooledFrequencyAnalysis
    + breakdown of call metrics by estimated number of alleles in pool

@ VariantEvalWalker
    + add PooledFrequencyAnalysis to analysis set

@ PooledGenotypeConcordance
    + correctly calculate maximal allele frequency for output




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1893 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 15:17:11 +00:00
chartl 967128035e Make command like args default to false. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1892 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 13:59:35 +00:00
ebanks 9b9744109c Mark's new unified calculation model is now officially implemented. 
Because it doesn't actually use EM, it's no longer a subclass of the EM model.

Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger).  I need to deal with general UG output tomorrow.  Hold off until then, Mark, and then you can go wild.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 02:39:23 +00:00
depristo caa3187af8 Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1890 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 23:31:13 +00:00
chartl 4a8a6468be Use read group as a condition for confusion tables. With an integration test. 
Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 19:39:32 +00:00
chartl b83df5616a Change for lower-case references (always compare upper case bases) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1888 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 17:36:31 +00:00
chartl 3b1fabeff0 Major code refactoring: 
@ Pooled utils & power
   - Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
     flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
   - Removed a number of PoolUtils variables and methods that were used in those walkers or simply
     not used
   - Removed AnalyzePowerWalker (un-necessary)
   - Changed the location of Quad/Squad/ReadOffsetQuad into poolseq

@NQS
   - Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType

@ BaseTransitionTable
   - Added a slew of new integration tests for different flaggable and integral parameters
   - (Scala) just a System.out that was added and commented out (no actual code change)
   - (Java) changed a < to <= and a boolean formula


Chris



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 14:58:04 +00:00
aaron 4be6bb8e92 added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums. For some reason my check-ins from home wouldn't work last night, so this is the actual changes for 1884. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1886 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 14:15:33 +00:00
depristo 449a6ba75a Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 12:23:36 +00:00
aaron d749a5eb5f added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1884 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 04:56:51 +00:00
ebanks b8ab77c91c Don't filter out reads without proper read groups. Instead, allow the user (or another walker calling UG) to specify an assumed sample to use (but then we assume single-sample mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1883 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 01:30:53 +00:00
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
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
ebanks d89bc2c796 This class no longer outputs in sequenom format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:16:36 +00:00
ebanks 0c95d6906f Merge both versions of the Sequenom assay design maker: use Jared's base code and add in indels. [Jared, this still emits the same output for SNPs as your original version) 
Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:11:45 +00:00
ebanks 49af5269e5 Jared: feel free to change or revert, but until we move over to UG version... 
Only print out positions with at least one non-ref call


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1830 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:08:57 +00:00
chartl f5a2e6dd50 Fix! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1829 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 16:15:20 +00:00
ebanks f2886d88e0 We now emit genotype calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1828 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 02:49:56 +00:00
ebanks 1b214c0de5 Fixed logic: throw exception if contigs are NOT equal 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1827 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 02:48:44 +00:00
ebanks aeca14d052 On our side of 5CC, we spell multi M-U-L-T-I. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1826 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 01:41:25 +00:00
ebanks c9c8fd1fef Added the discovery LOD score to the meta data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1825 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 01:24:06 +00:00
ebanks 0c06bf9dbc Explicitly set output to GELI now that default is VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1824 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 22:12:03 +00:00
hanna a76fac4687 Cleanup existing speedups. Minor performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1823 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 21:51:18 +00:00
hanna 837ae1d33a Optimization: from 22k reads/min - 30k reads/min. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1822 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:59:29 +00:00
ebanks 96b8499a31 Remodeled version of the UnifiedGenotyper. 
We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases.  Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1821 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:27:01 +00:00
ebanks b28446acac Multi-sample calls now have associated meta-data (SLOD, allele freq), which wil 
l soon actually be used...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1820 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:08:43 +00:00
hanna db642fd08b Optimization: from 10k reads/sec - 22k reads/sec.. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1819 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 18:07:15 +00:00
aaron 77499e35ac fixes for GSA-199: Need easier way to write binary outputs to standard output. GLF and VCF now have stream constructors, and can get dumped to standard out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1818 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 15:50:20 +00:00
hanna f37564e63a Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1817 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 15:50:04 +00:00
chartl 8d0e057d83 I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure 
I have  previous revision to revert back to.


This is a calculator that will calculate:

P[ True base is X | read base mismatches, secondary base is Y, previous K bases are Z1,Z2,...ZK ]

where the number of pervious reference bases to take into account is user-defined. The secondary base is optional as well.

--usePreviousBases k

tells the walker to use the k previous reference bases in the transition table

--useSecondaryBase

tells the walker to use the secondary base at a locus in the transition table

these can be used together.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1816 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 02:55:29 +00:00
ebanks be92a1e603 Don't try to close if the lazy initialize hasn't triggered 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1815 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 01:20:25 +00:00
chartl ec83bc6ec5 This somehow didn't make it into subversion the last time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1814 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 21:11:13 +00:00
chartl ecbb11e017 Modified PowerBelowFrequency to ignore reads below a user-defined mapping quality. Request from Jason Flannick. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1813 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:59:24 +00:00
chartl ec68ae3bc5 Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1812 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:58:37 +00:00
chartl 0d73fe69e7 Recalibrator by NQS. Had this puppy running all afternoon. Thing had got through 100,000,000 reads before I decided to delete my sting tree. *sigh*, a little more delay. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1811 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:55:02 +00:00
chartl ee0afba0af Recalibration stuff... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1810 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:51:39 +00:00
ebanks caf689821f added method to get normalized posteriors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1809 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 02:33:22 +00:00
ebanks cf7a26759d -use the getReadGroup() function that was added to picard for us 
-clean up some include lines


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1808 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 01:39:32 +00:00
hanna d844d1c496 SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 19:16:46 +00:00
hanna da084357db Fixed minor typo in output message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1806 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 18:56:54 +00:00
aaron 62c484b57a Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work. 
Also a little playground walker that changes the sort order flag of a BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 18:11:32 +00:00
hanna 32d55eb2ff Fix issue Eric was seeing with java.lang.Error in unmap0. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1804 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 17:46:56 +00:00
ebanks 9f3482ef11 VCF is both a multi- and single- sample format, so we shouldn't be throwing an exception when used for SS 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1803 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 17:43:26 +00:00
jmaguire d9f5a314ac avoid an out of memory error by no putting more than 5000 reads in the cache. on pilot1 at least those are crazy loci anyway. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1802 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 14:56:55 +00:00
hanna f4b6afb42c JVM issue id 5092131 (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131) 
was causing OOM issues with the new mmapping fasta file reader during large jobs.
Temporarily reverting the reader until a workaround can be found.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1801 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 04:45:46 +00:00
chartl 6d7f4481e4 Changed traversal type slightly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1800 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 04:11:48 +00:00
ebanks a9f3d46fa8 Your time has come, SSG. 
Fare thee well.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1799 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 20:27:56 +00:00
jmaguire 8fdb8922b8 now output in the exact format that works with sequenom software. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1798 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 20:06:27 +00:00
aaron 98e3a0bf1a VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:50:04 +00:00
hanna 95f24d671d Fixed 'visualization' of reads that didn't match bwa's alignments exactly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1796 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:45:30 +00:00
kiran 29ad6cd876 Made redundant by BCMMarkDupes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1795 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:47:20 +00:00
kiran 94d82d1915 Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1794 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:32:37 +00:00
ebanks 15bf014e0b logger.info -> logger.debug (don't want to risk filling up my log on genome-wide calls) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1792 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:53:11 +00:00
ebanks df8ea8f437 UG integration test. This was the old SSG test with MD5s updated. 
I'll need to add some multi-sample tests in a bit...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:43:58 +00:00
ebanks 008455915a One way of making the integration test stop failing is to remove it... 
[waiting for Matt to cringe...]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1789 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:08:41 +00:00
chartl f89a89ffe3 Use of AlleleFrequency as an input to PowerAndCoverage is deprecated by the new walker. Reverting to the standard "power at 1 allele" calculation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1788 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 16:07:45 +00:00
chartl ae05f5c7ad Fixin the header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1787 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 15:49:28 +00:00
chartl 11ff1e09b8 A new power walker for the user to feed in a number of alleles. Call that number k. Output is: 
Locus Power_for_k_alleles  Power_for_k-2_alleles  Power_for_k-2_alleles ... Power_for_1_allele

This was a request from Jason Flannick & the T2DB group.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1786 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 15:35:35 +00:00
ebanks 04fe50cadd *** We no longer have a separate model for the single-sample case. *** 
For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input.  For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.

The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you.  More on that in a separate email.
Other minor cleanups added too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 14:08:57 +00:00
jmaguire 32128e093a misc. changes to get the numbers back to the baseline while keeping the speedup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1784 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 12:27:07 +00:00
jmaguire d38a0d04b9 fix a snp mask offset error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1783 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 12:25:40 +00:00
kiran 829e99413b Rescores a variant after removing duplicates (defined very strictly as reads with the same start points). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1782 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 03:07:36 +00:00
hanna fcb6a992c8 Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than 
the loop-with-small block size.  Performance improvements in loading refs are extreme;
segments can be loaded in <1ms.  chr1 in its entirety can be loaded in 1.5sec (down
from 30sec).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 00:07:15 +00:00
jmaguire 02d2492d68 Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 23:46:41 +00:00
ebanks 1905b5defa Hash by chromosome for now to reduce memory. This is a temporary solution until we decide how to reture the Injector for good. 
Also, with Picard's latest changes, we need to make sure we don't double-close the sam writer.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1779 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 20:06:25 +00:00
ebanks f9a1598d75 Reformatting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1778 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 20:03:34 +00:00
ebanks 203c626fc2 A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper. This wrapper incorporates both strand-based likelihoods and a combined likelihoods over both strands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1777 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 19:57:37 +00:00
sjia 5bdcc2b4dc Included HLA class 2 genes in CreatePedFileWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1776 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 18:46:51 +00:00
sjia 8f896b734f Included HLA class 2 genes in CreatePedFileWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1775 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 18:28:01 +00:00
aaron f9a0eefe4b GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1774 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 18:20:34 +00:00
chartl 225b9bccc1 Modifications to NQSClusteredZScoreWalker to output empirical mismatch rates on bins by both Z-score and reported Q-score, rather than averaging over all Q-score bins for each Z-score. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1773 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 13:45:12 +00:00
depristo 8dd0924b37 Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1772 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 23:40:30 +00:00
aaron 4554ca1b28 more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 19:09:27 +00:00
aaron 3aec76136f Removing the AllelicVariant interface, which is replaced by the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 17:44:24 +00:00
depristo 1bd0c3c145 variant eval allows non Variation rod objects 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 13:04:26 +00:00
aaron 66fc8ea444 GSA-182: Adding support for BED interval files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 02:45:31 +00:00
hanna aec83b401d SSG multithreading doesn't play well with some I/O changes made since I last svn up'd. Reverting until I can find the reason. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1766 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 19:48:57 +00:00
hanna 8a503c86b6 Code supporting SSG proof-of-concept shared memory parallelism. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1765 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 18:56:16 +00:00
ebanks fb619bd593 -Refactoring: make GenotypeCalculationModel constructors empty so that they don't have to be updated every time we add a new parameter; instead put that logic in the super class's initialize method (making everything protected so that only the factory can access them) 
-Adding initial version of Multi-sample calculation model.  This still needs much work: it needs to be cleaned up and finished.  Right now, it (purposely) throws a RuntimeException after completing the EM loop.

Also:
-Fix logic in GenotypeLikelihoods.setPriors
-Add logger to the models for output






git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1764 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 18:10:36 +00:00
sjia 98076db6b4 Modified CreatePedFileWalker to output PED file given HLA allele names 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1763 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 03:06:42 +00:00
hanna 56bc4fa21a Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-04 18:20:20 +00:00
hanna 05aa928e3e Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1761 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-03 21:55:18 +00:00
chartl 7605ee500c Idiocy! All tests were being disabled because I forgot the instanceof 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1760 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 20:04:56 +00:00
chartl 88d0890cc3 Made PooledGenotypeConcordance a standard test in VariantEval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 20:03:31 +00:00