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Author SHA1 Message Date
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
aaron 7fc4472e6d A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 
Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 19:35:35 +00:00
chartl 68cb2ee54b Tweaks to parameters for NQS analysis walkers; change to PowerAndCoverage for Jason Flannick (can input the number of alleles to compute power for - i.e. doubletons, tripletons; rather than statically checking singletons. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1757 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 19:11:27 +00:00
ebanks 7249fade05 updated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1756 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 18:10:34 +00:00
ebanks 53a4bd7f51 A better understanding of what's going on means no need for clearing the cache 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1755 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 18:07:46 +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
hanna 2309d19f6f Bug fix from Michael Ross: mark second read in sequence as second of pair. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1753 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-01 14:34:36 +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
ebanks 303972aa4b Yup, I broke the build... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1750 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:20:43 +00:00
ebanks 841d25cc44 Added ability to set the priors after construction (and requiring a flushing of the likelihoods cache) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1749 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 19:55:49 +00:00
hanna 665951f9f0 Support negative strand alignments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1748 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 18:10:26 +00:00
hanna d3b1732cca Start of refactoring effort. Make construction of alignment object simpler. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1747 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 15:19:31 +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
aaron b1c321f161 Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 21:28:21 +00:00
sjia 9b78a789e2 HLA Caller 2.0 Walkers: 
CalculateBaseLikelihoodsWalker.java walks through reads calculates likelihoods using SSG at each base position
CalculateAlleleLikelihoodsWalker.java walks through HLA dictionary and calculates likelihoods for allele pairs given output of CalculateBaseLikelihoodsWalker.java
CalculatePhaseLikelihoodsWalker.java walks through reads and calculates likelihoods score for allele pairs given phase information

File Readers:
BaseLikelihoodsFileReader.java reads text file of likelihoods outputted by SSG
FrequencyFileReader.java reads text file of HLA allele frequencies
PolymorphicSitesFileReader.java reads text file of polymorphic sites in the HLA dictionary
SAMFileReader.java reads a sam file (used to read HLA dictionary when in another walker)
SimilarityFileReader.java reads a text file of how similar each read is to the closest HLA allele (used to filter misaligned reads)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1744 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 20:45:55 +00:00
chartl 281a77c981 Bugfix. isMismatch() was actually computing isMatch(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1743 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 20:04:59 +00:00
chartl e28b45688c More NQS Related Walkers to play with 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1742 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 20:01:04 +00:00
ebanks 9ef80e3c3c One minor addition: to incorporate Pooled calling (and to be as general as possible), we allow the genotype calculation model to use rods if it wants. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1741 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 17:05:59 +00:00
ebanks 19bfe43173 First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class. 
Some notes:
1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris.
2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878.  Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts.
3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 16:48:15 +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 6134f49e3c Convert de novo SNP caller to run using parent1 and parent2 BAM files (by splitting contexts by reader using getMergedReadGroupsByReaders) instead of geli files providing a large speed-up and obviating the need for large whole-genome geli files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1738 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 06:42:21 +00:00
andrewk 5dab95aa5a Fix getMergedReadGroupsByReaders so that it provides read groups in the same way Picard does so that it works correctly when input read files have no clashes in their read groups and retain their original read group names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1737 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 06:35:50 +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 39598f1f0a switching the concordance walker over to the new Variation system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1735 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-28 15:46:36 +00:00
asivache bce2f0d7cf Now instantiates the list of alternative consenses to evaluate as LinkedHashSet to guarantee iterator traversal order. Old implementation used HashSet and exhibited unstable behavior when two alt consenses turned out to be equally good: depending on the run conditions (including size of the interval set being cleaned??), either one could be seen first as selected as the 'best' one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1734 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-28 06:15:46 +00:00
asivache 663175e868 Bug fix: when jumping onto next contig (chromosome), the walker was erasing last mismatch interval from the previous chr it was still holding without printing it; now it gets printed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1733 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 22:24:34 +00:00
asivache 92c6efabb7 moving IndelGenotyper out of playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1732 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 19:44:49 +00:00
asivache aec61c558b moving IndelGenotyper out from playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1731 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 19:43:53 +00:00
chartl fe6d810515 Some basic commits that I've been sitting on for a while now: 
@ PooledGenotypeConcordance - changes to output, now also reports false-negatives and false-positives as interesting sites. It's been like this in my directory for ages, just never committed.

@NQSExtendedGroupsCovariantWalker - change for formatting.

@NQSTabularDistributionWalker - breaks out the full (window_size)-dimensional empirical error rate distribution by the window. So if you've got a window of size 3; the quality score sequences 22 25 23 and 22 25 24 have their own bins (each of the 40^3 sequences get one) for match and mismatch counts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1730 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 19:35:50 +00:00
sjia f7684d9e1b ImputeAllelesWalker fills missing portions of HLA dictionary based on best allele matches 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1729 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 18:51:46 +00:00
sjia 235de38c2e Updates to FindClosestAlleleWalker and CreateHaplotypesWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1728 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 16:41:58 +00:00
aaron 130a01a40a delete the integration test temp files when the test is over 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1727 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 16:34:08 +00:00
aaron 2b7d39035a switched over the FastaAlternateReferenceWalker to the Variation system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1726 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 16:09:43 +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
depristo 392152f149 1000x performance improvements to MSG for crisis control 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1723 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 23:44:33 +00:00
hanna 44879c81b0 Add in weights. Massive performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1722 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 23:19:15 +00:00
hanna 3b79f9eddc Support 'N's and other mismatch characters in the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 21:41:30 +00:00
hanna 08e8d2183a Indels supported. Variable gap penalties are not yet taken into account. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1720 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 21:03:02 +00:00
aaron d2af26e81f Pooled EM SNP Rod converted over to the Variation interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1719 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:33:11 +00:00
ebanks 97105ac001 We need to return a null RODRecordList when the default value is null (as opposed to a list with a single null value), because that's what everyone is expecting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1718 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:23:12 +00:00
ebanks d4b40bc06f Filter for reads with missing read groups so we can safely assume all reads have valid read groups 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1717 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:10:26 +00:00
ebanks 90de2e0cde Added ability to specify whether you want to use a point estimate or fair coin test calculation; for now you can use either but fair coin test is still experimental as it needs to be parametrized correctly. This job will hopefully be done by the future Bioinformatic Analyst... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1716 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 15:29:50 +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
sjia 1ee8ba590c Reads cigar files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1713 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 03:14:10 +00:00
sjia 9422156e09 Finds closest allele for each read in bam file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1712 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 03:12:20 +00:00
sjia 5c5151c4e7 Creates ped file from reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1711 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 02:48:29 +00:00
hanna b0ec7fc144 More comprehensive testing of BWT (mismatches only) module, and lots of bug fixes. 
Limitations:
1) Can't handle RC alignments.
2) Can't handle indels.
3) Can't handle N's in reference bases.
4) Stops at first hit.

Ran BWT over a test suite of 800k Ecoli reads.  After removing alignments with indels / reads with Ns, the remaining reads were aligned with quality 'equal to' that of the alignment stored in the BAM file.  In this case 'equal' quality is <= mismatches to the reference as the existing alignment stored in the BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1710 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 23:44:59 +00:00
sjia b446b3f1b6 CreateHaplotypeWalker now gives correct output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1709 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 21:13:52 +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
sjia 3916e165fb New walker to output haplotypes for each read (for SNP analysis or imputation, etc) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1707 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 20:26:43 +00:00
ebanks 423a3ee894 Added a sequenom rod to empower Carrie to convert 1KG validation SNPs to sequenom format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1706 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 20:22:09 +00:00
chartl 63f3d45ca4 fixing the build 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1705 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 20:04:09 +00:00
chartl 540e1b971f And we fix one boneheaded mistake, which was actually causing the problem; though the last change was still correct. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1704 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 19:26:45 +00:00
chartl 124ca68fa8 And an IMMEDIATE minor fix (want neighborhood quality > base quality to be represented correctly) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1703 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 19:21:09 +00:00
chartl 8cdb78ebee More sophisticated version of the NQSCovariantWalker - modified to be more explicit about how much higher the 
quality score of a particular base is than the quality score of its neighbors. The granularity of the binning
jumps from 32 groups to 860 groups.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1702 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 19:18:24 +00:00
hanna 856bbd0320 Let Picard specify the default compression level. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1701 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 19:01:48 +00:00
aaron f783cb30e0 adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1700 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:24:05 +00:00
hanna ebfbe56b43 Make sure compression level always gets pushed into SAMFileWriterFactory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1699 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:20:26 +00:00
asivache fa87dd386d Now uses rodRefSeq in its new reincarnation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1698 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:19:36 +00:00
asivache bf7cd66d53 New, simpler rodRefSeq. Fully relies on the ROD system standard mechanisms. Multiple transcripts over a given location will be now returned by the ROD system itself as RodRecordList<rodRefSeq>; and yes, rodRefSeq does represent a single transcript record now and implements Transcript interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1697 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:18:25 +00:00
asivache 8fa4c93f5a Transcript is now simply an interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1696 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:13:31 +00:00
asivache fe36289e44 Noone needs this, probably... Old experimental code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1695 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:11:50 +00:00
asivache 1bd4c0077c Now that ROD system supports overlapping RODs, we do not need rodRefSeq to be too smart and read in all the overlapping records (transcripts) on its own; leave it to the generic ROD mechanism. 
PARTIAL commit; new, simpler rodRefSeq will reappear in a seq.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1694 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:11:16 +00:00
sjia aa66074a0e Compares each read to the HLA dictionary and outputs closest allele, as well as other stats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1693 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 16:17:23 +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
ebanks b0fa19a0b2 Fixed recal integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1689 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:22:32 +00:00
ebanks 0748d80baa Added a convenience method in rodDbSNP to deal with Andrey's changes to the rod. Now you can just ask for the first real SNP rod from the list and not have to think about how it works. 
CountCovariates uses it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1688 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:15:40 +00:00
ebanks 6780476fb5 updated to deal with new dbSNP rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1687 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 19:46:32 +00:00
hanna 14477bb48e Unidirectional alignments with mismatches now working. Significant refactoring will be required. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1686 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 19:05:10 +00:00
sjia 22932042ea Combined Scores, bug fixed for printing HLA-C 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1685 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 18:28:16 +00:00
ebanks 682b765536 bug: need to upper case chars so that == works throughout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1684 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 18:20:43 +00:00
asivache d7d0b270d1 now supports blacklisting lanes (with -BL option will ignore reads from any of the specified lanes) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1682 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 16:46:57 +00:00
asivache 57d31b8e9b Filter that discards reads from specific lanes; and also its friend that helps blacklisting a set of lanes from GATK command line a one-liner. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1681 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 16:46:06 +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
ebanks b1dc6d65e4 interval merging is now blazingly fast 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1674 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 21:15:04 +00:00
asivache 15135788ca OK, let's bite the bullet. Now rodDbSNP objects are 'isSNP()' only when they are annotated as 'exact', not a 'range'. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1673 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 19:25:16 +00:00
asivache 8ad181f46f Note to myself: do 'ant clean' now and then or old versions of the code that suddenly became invalid will stick around. The world is not perfect, and neither is automatic dependency resolution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1672 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:40:52 +00:00
asivache fb09835ef8 Changed to accomodate new ROD system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1671 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:10:56 +00:00
asivache d2d1354199 Now uses BrokenRODSimulator class to pass the test. CHANGE the code to use new ROD system directly and MODIFY MD5 in corresponding tests, since a few snps are seen differently now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1670 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:03:49 +00:00
asivache f4d270cba4 These classes now use BrokenRODSimulator class to pass the test. CHANGE the code to use new ROD system directly and MODIFY MD5 in corresponding tests, since a few snps are seen differently now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1669 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:03:15 +00:00
asivache 29adc0ca1c Little class that can be used to simulate the results returned by the old ROD system. This is needed to keep couple of tests from breaking. All the code that uses this class must be changed urgently to accomodate the data as returned by new ROD system, and the corresponding tests (MD5 sums) have to be modified as well since some data as seen through the new ROD system is indeed different. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1668 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:58:56 +00:00
asivache a6bd509593 Changing the carpet under your feet!! New incremental update to th eROD system has arrived. 
all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1667 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:55:22 +00:00
asivache 4c67a49ccb Removed unused imports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1666 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:45:22 +00:00
hanna e7f44ada98 Make unpackList public static so that Doug can use it in the scatter/gather framework. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1665 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 15:32:49 +00:00
ebanks 7b627fd622 Check for empty interval lists to merge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1664 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 04:34:26 +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
depristo 4318f75910 tiny cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1660 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 21:04:25 +00:00
depristo 3a341b2f06 Fixes for VariantEval for genotyping mode 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1659 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 21:01:43 +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
sjia 83e6e5a3e4 Calculates Probability for each allele combination (using likelihood score and allele frequencies only) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1656 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 18:46:38 +00:00
ebanks b19fd4d45c Damn unit tests have a null Toolkit()... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1654 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 17:10:49 +00:00
ebanks 90626c843d oops - we don't need reference bases, but we still need reference 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1653 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 16:24:45 +00:00
ebanks 2b2df4e1ba - Fix the CleanedReadInjector to deal with -L intervals correctly. 
- Some walkers don't use the ref base, so speed up traversals by not requiring it


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1652 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 16:17:58 +00:00
ebanks 7da9ff2a9e Put back the check that both chip and variant are not null. 
Also, sanity check that ref is not 'N'.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1651 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 16:03:54 +00:00
asivache 94618044e8 Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe. 
The main reason for the change is that there can be (and are!) multiple RODs overlapping with a single reference base position in a single track. There can be two "trivial" RODs at the same location (e.g. samtools pileup will have two point-like records at putative indel sites: one for the reference, the other one for the indel itself). Or there can be one or more "extended" RODs (length >1), eg. dbSNP can report an indel at Z:510-525 AND a SNP at Z:515.

The ReferenceOrderedDatum object (and children) will not be changed, but it is now explicitly interpreted as a single data *record*, possibly out of many available from a given track for the current site. As long as single data record occupies one line in a data file, the new ROD system will take care of loading and keeping multiple records, including extended (length > 1) ones, and will automatically drop the records when they finally go out of scope. For one-line-per-record, multiple-records-per-site RODs, there is no need anymore for the hack used so far that involved passing ROD's own implementation of iterator through reflection mechanism (though it will still work)

* RODRecordList: 
the ROD system (its iterators) will now always return a LIST of all RODs available at current position or at current query interval (see below). This class is a trivial wrapper for a list of ROD objects, with added location argument for the whole collection. The location of the RODRecordList is where the ROD system is currently sitting at: a single, current base on the reference (if next() traversal is performed), or the location of the query interval when returned by seekForward() (see below). The ROD objects themselves will have their locations set according to the original data in the file. Hence, perusing the above example of a dbSNP indel at Z:510-525 and SNP at Z:515, when moving to the position Z:515 the ROD system will return a RODRecorList with location Z:515, and with two ROD objects packaged inside, one with location Z:510-525, the other with Z:515.

*RODRecodIterator:
Almost identical to old SimpleRODIterator used by ReferenceOrderedData; this is a low-level iterator that walks over records in the data file (with a callback to ROD's ::parseLine() to parse real data)

*SeekableRODIterator:
a decorator class that wraps around Iterator<ROD> (such as RODRecordIterator) and makes the data traversable by reference position, rather than record by record. This is reimplementation of the old RODIterator.  SeekableRODIterator's ::next() moves to the next position on the ref and returns all RODs overlapping with that position (as a RODRecordList). This iterator also adds a seekForward(loc) operation, that allows fast forwarding to a specified position or interval. Length > 1 query arguments (extended intervals) are fully supported by seekForward(), the returned RODRecordList wil contain all RODs overlapping with the specified interval, and the location of the returned RODRecordList object will be set to that query interval. NOTE: it is ILLEGAL to perform next() after a seekForward() query with length > 1 interval. seekForward() with point-like (length=1) interval reenables next().


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1650 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 15:58:37 +00:00
ebanks 66a4de9a1d Genotype check should be case-insensitive 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1649 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 03:23:30 +00:00
hanna c186a49d55 Time for a reorganization. Repackage generally useful alignment classes lower in the package structure, and create a subpackage for bwa-specific code. Repackage BWA alignment code away from BWT representation. Isolate byte- and word-packing streams in another package that will ultimately be killed off en masse. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1648 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 23:28:47 +00:00
hanna b4df089b59 Putting some of the required data structures together for imperfect lookup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1647 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 22:43:11 +00:00
hanna 355136928e Play nice with other jobs in this VM -- don't close stdout / stderr. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1646 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 18:55:08 +00:00
sjia 0e73b2ba8e Use population allele frequencies to distinguish between top candidates 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1645 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 15:49:19 +00:00
chartl 534486a254 Output formatting changed: 
- summary output now reported as a percentage rather than proportion; 2 sigfigs
  - fixed minor bug where FNR was calculated over total calls rather than total variant sites
  - column headers are_now_contiguous_strings
  - spacing fixed
  - "No Call" separated from "Ref Call" as its own column




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1644 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 14:00:25 +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
chartl 4ad46590a3 Changes to PooledGenotypeConcordance: 
Additional output & better output formatting. It has now undergone a good five hours of testing; and for pools of size 1 outputs exactly the same statistics as GenotypeConcordance (when GenotypeConcordance is modified to do nothing on reference='N'); and for pools of many sizes outputs close to the expected (by genetics) statistics. Looks like this is working properly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1642 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 21:45:01 +00:00
chartl 386a6442ba Actually deleted now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1641 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 20:28:06 +00:00
chartl 8fce376792 Changes: 
Deletion: PooledGenotypeConcordanceNew

Rewrite: PooledGenotypeConcordance. It works, and is blazing fast compared to the earlier version (1 order of magnitude speedup)! And is now entirely non-hackey, as opposed to before when there were some hacky bits.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1640 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 20:22:16 +00:00
asivache 3e289fcaa4 A little piece that PairMaker needs in order to compile ;) 
Iterates synchronously over two (name-ordered) single-end alignment SAM files with, possibly, multiple alignments per read and for each read name encountered returns pairs<all alignments for end1, all alignments for end2>

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1639 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 19:17:40 +00:00
asivache 2f29cf59ba Very early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1637 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 18:38:18 +00:00
ebanks 5d85bd9671 By default, VF should ask for deleted bases so that they show up in coverage. 
The Strand filter then needs to ignore those bases when determining bias.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 16:46:09 +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
hanna 01a9b1c63b Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 08:33:56 +00:00
aaron eedf55e94d temp fix for a broken test, we'll fix the test tomorrow. We promise, we're engineers, we love our tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1633 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 04:36:42 +00:00
chartl f6bdb47bb6 Addition: 
@PooledGenotypeConcordanceNew - a new version of the pooled genotype concordance test for Variant Eval. Code altered to be more extensible, use a private class for handling the count tables so it doesn't gunk up the code in the test itself, and for easy debugging. The hackier methods from the original were rewritten properly. Currently computes more statistics that it outputs. Code compiles, is never called by anything, and breaks none of the tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1632 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 04:14:58 +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
hanna 9f7cf73411 Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem. 
Sigh.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1630 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 21:06:45 +00:00
hanna 17758b381c Properly initialize redirected output streams in case of out and err. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1629 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 19:47:43 +00:00
andrewk 00dfe014b7 Added option to FastaReferenceWalker to change output FASTA file format's line width and to remove header lines; allows dumping raw sequence using intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1628 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 18:00:30 +00:00
hanna b69eb208a6 Always create output files, even if no output was written to them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1627 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 17:58:14 +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
ebanks 6783fda42a Updated unit test to reflect changes to vcf output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1623 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 01:56:08 +00:00
andrewk fb254759cb Trivial: Don't print reduce result 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1621 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 23:42:20 +00:00
hanna 118071cfd8 Proof-of-concept perfect read aligner, implemented as described in sec 2.4 of BWA paper. Has successfully aligned a handful of reads. Requires significant cleanup and refactoring. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1617 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 21:54:56 +00:00
ebanks 01e7b39c8d 1. Don't print out values in filter field of the VCF. 
2. Fix ratio printouts (for params file)
3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1616 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 21:03:39 +00:00
ebanks 436f543b3b I owe Doug a beer for finding this: 
don't print out intervals to be merged if they're not within the global -L intervals


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1615 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 20:22:30 +00:00
chartl 7d6d114ab5 Additions: 
@NQSMismatchCovariantWalker - Walks along the gene calculating the table     
    # NQS
    # Q score
    # mismatches at non-dbsnp sites
    # total number of bases at non-dbsnp sites

And prints it out at the end.

Changes:

@PooledGenotypeConcordance now works. Takes a path to a file listing a bunch of hapmap IDs in whatever pool we want to check, reads those in, and checks for concordance by name.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1614 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 20:12:04 +00:00
sjia 9be1832d7b Phasing version 1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1613 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 16:10:37 +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