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466 Commits (2748eb60e14503a2f7e9cea739c35b718d01ebf9)

Author SHA1 Message Date
ebanks bf935a6ab1 1. Fixed bug in PrimaryBaseSecondaryBaseSymmetry code (not checking for null before trying to access object's methods) which was causing Integration Tests to fail. 
2. Retired allele frequency range from UG, which wasn't very useful.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 01:31:48 +00:00
aaron 33dcfc858d updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing. 
Also a 250% improvement in the getBases() and getQuals() of BasicPileup, which was nearly all of the runtime for the genotyper (using primitives instead of objects when possible).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2097 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 23:06:49 +00:00
aaron 6ba1f3321d Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord. 
Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 18:17:47 +00:00
ebanks a70cf2b763 A bunch of changes needed to make outputting pooled calls possible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2073 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 18:42:57 +00:00
ebanks 0a35c8e0ba 1. The joint estimation model now constrains genotypes to be AA,AB,or BB only (i.e. to use a single alternate allele). Note that this doesn't work for the old models (point estimate or SSG) because calculations aren't divided by alternate allele. 
2. Allele frequency spectrum is not emitted for single samples (since it doesn't make sense).
3. If in pooled mode, throw an exception of pool size isn't set appropriately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2072 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 17:43:15 +00:00
depristo 6fe1c337ff Pileup cleanup; pooled caller v1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2070 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 17:03:48 +00:00
chartl 43bd4c8e8f Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2058 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 17:20:13 +00:00
aaron aece7fa4c7 a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2057 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 16:50:01 +00:00
ebanks 4558375575 Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 
VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper.  UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).

This is a fairly all-encompassing check in.  It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout.  All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.

Stage 2 of the process will happen later this week.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 02:41:20 +00:00
depristo cff31f2d06 comments for eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2035 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 14:19:31 +00:00
aaron 234bb71747 changed the toVariation() method to take a reference base, instead of using the reference base loaded from the underlying data source (if it was reference aware). Also changed some isVariant() methods which weren't using the passed in ref base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2034 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 06:54:38 +00:00
ebanks 555fb975de 1. Print out allele frequency range (from joint estimation model only). 
2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 03:59:13 +00:00
ebanks 61b5fb82ce 2 major changes: 
1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.

2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:51:49 +00:00
mmelgar 3742a05760 Now can read E2 or SQ tag. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2027 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 15:18:21 +00:00
aaron c3c001e02e cleanup of the traversal output code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 06:18:10 +00:00
ebanks 697d7e02c8 Remove the lazy initialize functionality. When no calls are made by the genotyper, we still want a vcf file to be output with valid header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2024 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 02:14:50 +00:00
depristo 6c9f86bb4d Removed unnecessary output and added debugging print() routine 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2020 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 18:37:36 +00:00
hanna 2cf9670d1e Allow users to directly specify filters from the command-line, applicable to 
any walker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2012 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 18:40:16 +00:00
ebanks 6a37090529 Output changes for VCF and UG: 
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 16:31:31 +00:00
depristo 7e30fe230a oops, missing file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:25:18 +00:00
aaron 2ed423ed56 print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 05:57:01 +00:00
ebanks c9c3cf477a Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2005 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 02:41:37 +00:00
ebanks 3793519bd4 -Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields 
-Don't restrict info fields to 2-letter keys
[about to move these to core]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:52:51 +00:00
ebanks 74751a8ed3 -Some minor fixes to get accurate vcf record merging done 
-Improvement to snp genotype concordance test

And with that, it looks like I get revision #2000.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 06:40:55 +00:00
ebanks bc6f24e88f Added VCFUtils which contains some useful VCF-related functions (e.g. ability to merge VCF records). 
Also, various minor improvements.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1998 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:53:32 +00:00
ebanks cff645e98b convenience method to deal with genotypes that are unsorted (e.g. CA vs. AC) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:45:49 +00:00
ebanks 6fdfc97db6 Added optional field DP to VCF output for Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 20:03:22 +00:00
depristo 5d5dc989e7 improvements to VCF and variant eval support of VCF -- now listens to the filter field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1963 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 12:09:30 +00:00
ebanks 3a33401822 2nd stage of the genotyper output refactoring is complete. 
Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 22:43:08 +00:00
hanna 5a510e6d98 New PackageUtils interferes with the packaging utility. Revert until Aaron and 
I can get together to make this work.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 19:14:14 +00:00
aaron de6ae51f7e Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 06:02:41 +00:00
ebanks af6d0003f8 -Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out). 
-Make rods return the appropriate type of Genotype calls from getGenotype().



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-01 05:35:47 +00:00
ebanks 1c4ca9d383 -Mark just reminded me: actually force the ref/loc to be immutable 
-VCF writer should be blind to the score/confidence/lod value - just print the thing out as is


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1932 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 13:41:53 +00:00
ebanks 5cdbdd9e5b now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 13:27:37 +00:00
ebanks 3091443dc7 Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron. 
Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 03:46:41 +00:00
aaron 5a3bd50537 adding error log reporting to the GATK, and a stream based output method for the argument collection 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1926 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-28 19:56:05 +00:00
aaron 04e9a494e9 removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1924 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-28 18:08:14 +00:00
depristo ef2ea79994 code cleanup and containsStartPosition function 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1919 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-27 21:53:40 +00:00
depristo be333da9c0 charSeq2byteSeq -- convert a char[] to a byte[] for convenience 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1917 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-27 21:52:23 +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
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
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
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
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
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
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
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
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
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
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 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 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
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
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
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
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
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 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
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
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
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
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
aaron e885cc4b21 changes for corrected GLF likelihood output, along with better tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1754 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-01 20:45:05 +00:00
aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:37:59 +00:00
hanna 70e1aef550 Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 22:23:19 +00:00
ebanks 8bd345ba00 Generalized deletions in pileup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1739 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 15:58:43 +00:00
andrewk 5662a88ee1 Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1736 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-28 18:12:32 +00:00
aaron 7ffc1d97ef Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1724 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 04:35:52 +00:00
aaron d262cbd41c changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 15:16:11 +00:00
aaron eeb14ec717 a couple of light changes to GenomeLocSortedSet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1708 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 20:38:53 +00:00
aaron 11c32b588f fixing VariantEvalWalkerIntegrationTest md5 sums, a couple comment changes, and a little bit of cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1690 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:54:47 +00:00
aaron 83a9eebcc4 fixed a bug I checked in that Eric found, for intervals with no start or stop coordinate. Now I owe Eric a cookie, and Milk Street is so far away. Damn. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1679 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 04:34:18 +00:00
ebanks 5ce42cbab3 After thinking about this a bit more, it makes sense to pull this functionality out of my walker and into the GenomeLocParser where everyone else can benefit from it... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1677 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 01:32:35 +00:00
aaron 7bfb5fad27 fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1676 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 23:32:24 +00:00
aaron 39a47491a9 changes to make GenomeLoc string parsing 25% faster 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1675 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 22:37:47 +00:00
hanna 7f5778c966 Update gsadevelopers -> gsahelp. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1663 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-20 23:36:54 +00:00
aaron 3a487dd64e little fixes; also fixed a tyPo 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1662 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 22:38:51 +00:00
aaron b6d7d6acc6 fix for the eval tests, and a change to the backedbygenotypes interface, more changes to come 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1661 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 22:25:16 +00:00
aaron 7b39aa4966 Adding the VCF ROD. Also changed the VCF objects to much more user friendly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1658 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 20:19:34 +00:00
depristo 73bec6f36d Now uses expanding array list for coverage histograms. No hard limit on maximum depth now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1643 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 23:27:25 +00:00
ebanks a7c306f757 -deal with offsets that can be -1 
-added option to have "D"s inserted for deleted bases in pileup strings


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1635 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 16:44:57 +00:00
aaron 542d817688 more cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1631 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 21:42:03 +00:00
aaron b401929e41 incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 04:48:42 +00:00
asivache a009592662 the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1612 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 16:04:19 +00:00
aaron e03fccb223 Changes to switch Variant Eval over to the new Variation system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 05:34:33 +00:00
depristo bd75a8d168 Unused code has been removed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1599 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:12:23 +00:00
depristo 3ad97e4ab4 Easier to print GenomeLoc compareTo() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1597 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:10:35 +00:00
depristo 17ab1d8b25 General purpose merging iterator implementation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1593 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:06:15 +00:00
aaron 296878e8e3 adding a basic implementation of the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1578 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 04:41:13 +00:00
aaron 5a64a80ab5 changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 04:31:33 +00:00