depristo
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a10fca0d5c
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Genotyper now is using bytes not chars. Passes all tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3406 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-20 21:02:44 +00:00 |
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depristo
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727822adb4
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BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-20 14:05:13 +00:00 |
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depristo
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6ce3835622
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Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3399 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-20 12:38:06 +00:00 |
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depristo
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504103bd15
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Misc. additions to correct utilities
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-07 21:34:18 +00:00 |
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depristo
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b8ab74a6dc
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Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-28 21:45:22 +00:00 |
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depristo
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4dd7c5972c
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Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2997 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-14 21:08:14 +00:00 |
chartl
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6759acbdef
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Coverage statistics now fully implements DepthOfCoverage functionality, including the ability to print base counts. Minor changes to BaseUtils to support 'N' and 'D' characters. PickSequenomProbes now has the option to not print the whole window as part of the probe name (e.g. you just see PROJECT_NAME|CHR_POS and not PROJECT_NAME|CHR_POS_CHR_PROBESTART-PROBEND). Full integration tests for CoverageStatistics are forthcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2924 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-04 15:00:02 +00:00 |
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depristo
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956b570c8e
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V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-28 18:37:17 +00:00 |
ebanks
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1dd9996f3a
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New realigner now completely uses bytes, plus misc fixes. Still not ready for use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2719 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-28 04:17:20 +00:00 |
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depristo
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592749a7c1
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isNBase method
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2513 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-06 15:01:51 +00:00 |
rpoplin
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6fbf77be95
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Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2394 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-17 20:07:26 +00:00 |
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rpoplin
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1d5b9883db
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Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2276 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-07 14:26:27 +00:00 |
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depristo
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6231637615
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fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 15:41:35 +00:00 |
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depristo
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03342c1fdd
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Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
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2009-11-25 03:51:41 +00:00 |
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depristo
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be333da9c0
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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
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2009-10-27 21:52:23 +00:00 |
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depristo
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d6385e0d88
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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
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2009-10-16 22:29:35 +00:00 |
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depristo
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0093482c62
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N reference base fix for SSG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1572 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-09 21:19:36 +00:00 |
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depristo
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a639459112
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Trival consistency change from char in to char out, not char in to byte out
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1466 348d0f76-0448-11de-a6fe-93d51630548a
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2009-08-27 23:37:37 +00:00 |
asivache
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144b424933
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Added : String reverse(String s) - reverses a string
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1416 348d0f76-0448-11de-a6fe-93d51630548a
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2009-08-12 20:16:22 +00:00 |
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depristo
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9c12c02768
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AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-22 17:54:44 +00:00 |
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ebanks
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5be5e1d45f
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added conversion from iupac format and new rod to deal with FLT file format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-15 18:34:41 +00:00 |
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depristo
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7d281296a7
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Finishing checking for building
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-17 14:12:40 +00:00 |
kiran
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681e67c72c
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Added some methods to generate random bases or random base indexes, optionally disallowing the generation of a specified base or base index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@943 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-09 00:47:54 +00:00 |
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asivache
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3b4dc6e7b5
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added sequencePeriod(String seq, int minPeriod) - finds smallest period equal to or greater than minPeriod for the specified text string seq; this is a trivial (hopefully correct) back-of-the-envelope implementation for a well-known and well-studied problem; there should be more efficient algorithms in the wild
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@925 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-06 23:05:24 +00:00 |
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depristo
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7e7c83ddca
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fixing insidious bugs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 18:33:45 +00:00 |
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kiran
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454a6d1df7
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Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 19:32:20 +00:00 |
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depristo
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7a979859a9
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Intermediate checking for evaluation -- now supports transition / transversion evaluation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 17:05:06 +00:00 |
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depristo
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dc17a5661d
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Better accessors for dealing with second base prob pileups
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 22:25:16 +00:00 |
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kiran
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83e1454a11
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Added a method to determine the fraction of a sequence that's taken up by the most frequent base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@781 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 20:35:31 +00:00 |
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kiran
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1a9d5cea29
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Added a method to reverse-complement a String object, preserving 'N' and '.' bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 19:39:39 +00:00 |
andrewk
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0219d33e10
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QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 18:30:45 +00:00 |
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kiran
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68c9455c0f
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Moved the base complement method to BaseUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 18:57:48 +00:00 |
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kiran
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ca66cccd2f
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Privatized constructor to prevent instantiation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@506 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-23 17:45:39 +00:00 |
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kiran
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5b2a7c9c23
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Added some methods to complement a single simple base ([AaCcGgTt]) and reverse-complement a byte-array of bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@483 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 22:25:33 +00:00 |
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kiran
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40ea22eb17
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Added some methods to return the cross-talk partner base of a given base or base index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 14:49:12 +00:00 |
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kiran
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5e96ab6161
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Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@373 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 00:46:23 +00:00 |