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Author SHA1 Message Date
ebanks 9b2fcc4711 Refactoring of the annotation system: 
1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong.  Fixed the headers too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:05:51 +00:00
hanna 84563b37e5 Partial flattening of the hanger data structure. Hanger data structure is 
not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3512 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 16:28:49 +00:00
chartl 8f9e3e8ad7 Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 14:21:19 +00:00
hanna c2858c8988 Minor performance enhancement. Checkpoint commit before major performance 
overhaul.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 21:39:39 +00:00
chartl 5ed2818ffb Forgot to commit code i relied upon 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 21:01:35 +00:00
chartl 736098b58d A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 20:47:01 +00:00
delangel de134c226d Removed ability of users to specify annotations to recompute, cleanups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 19:17:59 +00:00
ebanks 4d1a6b3d99 quick changes for G 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 16:33:27 +00:00
delangel 907931c902 a) Update annotations when creating new vcf with Beagle's imputed data. Since genotypes may (will) change based on imputation, several annotations need to be updated. By default, AC, AF, AN and AB will be updated. User can force extra annotaqtions to be updated with -A <annotation> argument. 
b) Several cleanups and beautifications.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3499 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 15:12:04 +00:00
chartl 933133ee28 Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf: 
+ Identifies opposite homozygote sites
 + Identifies the parent from whom it is expected that a null allele was inherited (or whether it was a putative genotype error; e.g. mom=homref, dad=homref, child=homvar)
 + Labels each opposite homozygote with its homozygous region in the child (e.g. region 1, region 2)
 + Labels each opposite homozygote with the size of the homozygous region in which it was found, the number of child homozygotes in the region, and the number of opposite homozygote violations within that region

To come:
 + Classification of sites as likely tri-allelic


Note that this is very experimental



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 03:56:07 +00:00
hanna 199e4208cd Bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 00:30:33 +00:00
hanna 52ab9f2417 Feature parity between LocusIteratorByState, DownsamplingLocusIteratorByState, including pushing mrl / 
the LocusOverflowTracker into LocusIteratorByState.  Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3496 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 22:58:21 +00:00
hanna 5c4d070566 Push Mark's changes in LocusIteratorByState into DownsamplingLocusIteratorByState 
in preparation for merging the two into one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3495 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 17:29:30 +00:00
depristo 6eeb1693ca JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 00:33:02 +00:00
hanna c1ecf75dd5 Update to the latest rev of the picard sharding patch. Includes updates reflecting 
the imminent move of IlluminaUtil into picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 20:33:21 +00:00
delangel c503f01dcf More cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3492 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 17:41:38 +00:00
delangel d4c66d6191 a) Small cleanup 
b) Fix major issue with Beagle likelihood converter: if likelihood triplets from UG end up being too low, then Beagle input file will be produced with 0.00,0.00,0.00 triplet. If all samples at a marker have this issue, Beagle will effectively produce junk. To fix, likelihoods are renormalized before converting to linear space.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3491 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 17:31:59 +00:00
depristo cfa18f6743 Fixing missed update with new Allele in it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 23:56:34 +00:00
depristo 3ea506fe52 No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3489 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 23:03:55 +00:00
delangel ef47a69c50 a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes. 
More doc/info to follow shortly. Issues still to be solved:
a) Walker changes all genotypes based on Beagle data, but annotations on the original VCF are unchanged. They should in theory be recomputed based on new genotypes.
b) Current implementation is ugly, dirty unwieldy and will necessitate a refactoring soon so I can keep my pride. Most aesthetically affronting issue right now is that we read the full Beagle files at initialization and keep them in memory, but a more delicate implementation would just read from files on a marker by marker basis. Issue that currently prevents this is that BufferedReader() instances don't seem to play nice when called from the map() function.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3488 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 20:37:25 +00:00
depristo b811e61ae1 Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3487 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 18:11:38 +00:00
aaron 6482b87741 adding the super experimental, half-broken, generally crippled, awkwardly commented, header ignoring vcf4 code. Don't use this, unless you're a developer for VCF4. If so, remove the exception from the constructor so that it won't always exception out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3486 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 07:38:46 +00:00
aaron 0b03e28b60 updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3485 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 06:34:26 +00:00
hanna 3d055e3d16 Fail fast if users try to parallelize a read walker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3484 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 18:14:33 +00:00
hanna 7d79848f40 Better error message when bam file / list file with wrong extension is 
supplied.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3483 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 17:52:48 +00:00
ebanks 597b3744ab Always use phasing info when converting genotypes to strings 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3482 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 17:50:50 +00:00
depristo e2b41082af GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 22:26:32 +00:00
aaron 8ec091d6d2 re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 17:45:51 +00:00
asivache f0c379dde8 Unconsequential changes in report formatting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3479 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 17:43:25 +00:00
weisburd 3ab936181c Supports the join feature of GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3478 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:29:57 +00:00
weisburd f5f7217413 Implemented joins 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3477 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:28:53 +00:00
weisburd 09c3b15af3 Implemented joins 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3476 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:28:06 +00:00
weisburd e14ae471a0 Refactored some of the small utility methods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3475 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:26:00 +00:00
weisburd 898a78e97d Added toString() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3474 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:24:25 +00:00
weisburd 12c3e3ecda Added back the check for values.size() != header.size(). Now exception will be thrown if number of columns in a record doesn't equal number of columns in the header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3473 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:23:05 +00:00
rpoplin 290771a8c2 Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 15:03:00 +00:00
ebanks 4a555827aa Removing more toUpperCase sanity checks 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 14:38:39 +00:00
ebanks 56e504789a trivial change: toUpperCase no longer necessary 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 14:00:47 +00:00
rpoplin 87fe60fe4f Fix for Sendu. new Process and p.waitFor() don't seem to work on his farm. Throws an IOException. This was a problem way back with AnalyzeCovariates too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 11:37:10 +00:00
ebanks 7f0c638653 Fix for the indel cleaner: I forgot to "unclip" the cigar string (even though the clipped bases were removed) before using it as an alternate consensus in a particular instance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-01 02:07:20 +00:00
depristo 2b02324587 Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-30 18:00:12 +00:00
ebanks eb25e41111 minor update to new tribble name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3462 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 20:23:25 +00:00
ebanks ffeb3fd80d Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the 
priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3461 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 19:28:26 +00:00
rpoplin 522dd7a5b2 Adding the variantrecalibration classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3459 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 18:21:27 +00:00
rpoplin 2014837f8a VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3458 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 18:20:18 +00:00
aaron 871cf0f4f6 Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of: 
@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFCodec.class))

you'd say:

@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class))

Which is more in-line with what was done before.  All instances in the existing codebase should be switched over.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3457 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 14:52:44 +00:00
depristo cc2bf549c8 Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3455 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 14:10:48 +00:00
depristo 6485e8383d Trivial change to retrigger broken build that really isn't broken 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3453 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 23:33:46 +00:00
depristo f2e7582cfc Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 23:16:00 +00:00
aaron e1b0aefb29 fix for parallelism bug 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 22:16:14 +00:00
aaron cded9ec985 adding a command line option, -etd (enable threaded debugging), that uses a custom thread pool class to catch exceptions thrown inside of a thread. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3450 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 21:57:56 +00:00
ebanks e2674671e7 The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 19:22:47 +00:00
chartl ff4a0764df Read error rate is now parallelizable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3447 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 19:00:09 +00:00
depristo dfc36c1e95 Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 22:12:25 +00:00
delangel 3873dccb35 First fully functional (though preliminary) version of walker that takes an input VCF and outputs a Beagle .bgl file that can be used for missing genotype calls/haplotype imputation. For now, only supported input format is likelihood format for unrelated individuals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3444 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 21:03:23 +00:00
chartl f9efc1248c VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3443 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 20:03:14 +00:00
chartl 0265199ce4 First pass at an IndelLengthHistogram module for variant annotator. Off by default. Will be tested shortly (have to commit, so I can check out in another directory, so that compiling won't kill all my jobs running on LSF) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3440 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 15:04:39 +00:00
aaron a2fab07258 fixed the build problem: there were two copies of the AnnotatorInputTable Codec and Feature in two different spots. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3439 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 14:47:15 +00:00
depristo 5928047d8b Optimization of reference window calculation to us bytes not char and no uppercasing since reference and read bases are always uppercase now. Should remove some ~5% of runtime of UG. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3438 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 14:10:26 +00:00
chartl 88a06ad81f Changes to Depth of Coverage: 
- For speedup in large number of samples, base counts are done on a per read group level, then
   merged into counts on larger partitions (samples, libraries, etc)
   + passed all integration tests before next item
- Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags,
   the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and
   per sample per interval summary files are effected (thus md5s changed for these)

NOTE:

This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 03:39:22 +00:00
rpoplin 062b316881 Better Exception message when can't find annotation value in variant recalibrator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3434 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:15:50 +00:00
rpoplin bf530d23de Variant Recalibrator now makes use of a prior on known/novel status as well as on allele frequency spectrum. The VariantOptimizer walker now clusters with all variants but gives more weight to knowns / hapmap / 1KG / MQ1 sites. The weights are all optional command line arguments. We no longer assign default values to annotations that are malformed. The walkers will crash with exception so as to not cover up potential issues. We only produce titv-less clusters now, and so the titv argument in VO was removed and the WithoutTiTv string that gets added to the cluster file is removed. The wiki is updated to show new example commands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3433 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:08:31 +00:00
ebanks ae6c014884 Fixed UG parallelization bug. Better integration test to catch this in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3432 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:03:45 +00:00
ebanks 772f558ae0 Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code. 
Small change for Ryan to get hard-clipped reads working for the recalibrator.

PLEASE DO NOT RELEASE THIS WEEK.  I still have some more testing to do and need Mark to run WG jobs.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 20:04:33 +00:00
aaron f3e2aae570 add experimental support for tabix files (for any of our Tribble rod types), as long as they end in .gz and can be read by the tabix reader. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3429 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 04:44:46 +00:00
weisburd 8db7c97c4d Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3427 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:38:54 +00:00
weisburd 4aa749c709 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3426 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:38:07 +00:00
weisburd aca3bcb193 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3425 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:37:17 +00:00
weisburd 64ed770250 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3424 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:36:28 +00:00
hanna ee3f2eb1d0 Don't output traversal reduce result in the logger. In many cases, the reduce 
result is tangential to the product of the analysis and having the logger always
emit it can confuse the output (such as in the new reduceByInterval 
DepthOfCoverage walker).  If users want to emit it, they can choose not override
onTraversalDone, or override onTraversalDone and write results to the output
stream / logger / whatever their choice.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3422 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-23 22:41:43 +00:00
hanna a40e64e47b A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads, 
passed in as a Tribble SAM text feature.  If the generated pileup contains a valid set of reads according to
the downsampling rules, the test passes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3421 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-23 21:49:54 +00:00
delangel a280a0ff0d a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated. 
b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 22:25:17 +00:00
hanna b10950c691 Simple performance optimization -- cache the number of reads in the locus hanger. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3417 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 19:26:16 +00:00
delangel 355396109b Bug fix to avoid build failure (class changed under me??) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 18:48:56 +00:00
delangel 1753d07b02 Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 18:31:34 +00:00
chartl 7fb3f2d3eb Annotator now buffers indel calls (prevents double-output from double-calls to map) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 16:34:34 +00:00
chartl 4e834b5e35 VFW now uses a ref window and thus is compatible with indels. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3412 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 15:59:42 +00:00
chartl 88cb93cc3c Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass. 
Homopolymer Run now does the "right" thing (e.g. single bases are represented as HRun = 0 rather than HRun = 1) for indels. AlleleBalance now does something close enough to correct.

Added a convenience method to VariantContext that will return the indel length (or lengths if a site is not biallelic).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3409 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 13:02:01 +00:00
depristo 6faf101c6c Minor improvements to Callable Loci for public consumption 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3408 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 12:50:11 +00:00
hanna 388dd8d64d Fixing bugs in downsampler introduced when I added Ryan's dup eliminator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3407 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 02:53:12 +00:00
depristo a10fca0d5c 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
 2010-05-20 21:02:44 +00:00
hanna 7389077b3b A few misc usability fixes: 
- Clarify the message emitted when -XL is supplied so I don't spend another half day chasing a bug that doesn't exist.  
- Crash with a helpful message when running -nt with non-TreeReducible walkers.
- Crash with a helpful message when running -nt with reduceByInterval walkers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3405 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 19:02:02 +00:00
aaron b543dd4ac4 more aggressive checks for the locking, and some more documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3404 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 16:16:36 +00:00
depristo 1ab00e5895 Retiring multi-sample genotyper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3401 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 14:10:56 +00:00
depristo 727822adb4 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
 2010-05-20 14:05:13 +00:00
depristo 6ce3835622 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
 2010-05-20 12:38:06 +00:00
depristo 5abac5c057 A few more char -> byte cleanups 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 00:02:06 +00:00
depristo 8a725b6c93 Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 23:27:55 +00:00
aaron 02cc1afdc8 remove RodBed and all it's dependencies. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 19:12:30 +00:00
chartl ffb1b46166 Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3395 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 18:49:51 +00:00
aaron 0036df7b03 adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 17:40:20 +00:00
aaron ca386439be only emit a warning if the tribble index is out of date, don't remove and replace it for them. Added a test case where the log4j appender checks the logging messages for the appropriate output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3393 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 15:12:48 +00:00
hanna 017ab6b690 Experimental versions of downsampler and Ryan's deduper are now available either 
as walker attributes or from the command-line.  Not ready yet!  Downsampling/deduping 
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 05:40:05 +00:00
weisburd 46ba88018d Updated to the new readHeader(..) api 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 04:06:34 +00:00
weisburd 984c51efd3 Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:42:12 +00:00
weisburd 42ee16f256 Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3389 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:41:37 +00:00
weisburd d8469e2fba Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:40:47 +00:00
weisburd d65b2d32d1 Removed AnnotatorROD which has been ported to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:39:34 +00:00
weisburd b82116f488 Removed AnnotatorROD which has been ported to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3386 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:39:20 +00:00
weisburd 6b96f025f5 Tribble integration for indexing the AnnotatorInputTable format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3385 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:37:54 +00:00
weisburd 2f3933148d Added fast split(str, delimiter) methodf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:37:26 +00:00
hanna aedb9f6734 Bring SAMPileupCodec into compliance with new interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 01:23:29 +00:00
aaron 7cfb9ff3dc updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 19:34:45 +00:00
chartl 635f61c22d Clone the other guy too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3381 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 18:56:01 +00:00
rpoplin 9e15299475 Misc cleanup in variant recalibrator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3380 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 17:37:01 +00:00
chartl eb200e4cce Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 17:13:44 +00:00
chartl e016491a3d Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3377 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 16:58:13 +00:00
weisburd 3c022e4b0c Improved command-line-arg validation at startup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:46:17 +00:00
weisburd 35b4bba35e Refactored so it could be used for knownGene and CCDS as well as refGene 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3372 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:44:10 +00:00
weisburd bb86c0e03a Improved error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:43:13 +00:00
weisburd 68719615be For multiple matches, shifted counter to be 1-based 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:41:50 +00:00
hanna 73e2e32837 Fix typo. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:04:00 +00:00
chartl ebd0fabf86 First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:02:13 +00:00
hanna 0791beab8f Checking in downsampling iterator alongside LocusIteratorByState, and removing 
the reference implementation.  Also implemented a heap size monitor that can
be used to programmatically report the current heap size.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:00:44 +00:00
chartl b7d21627ab Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 17:23:00 +00:00
kiran 4235164359 Removed the confusionMatrix column (of *course* this is a confusion matrix... what else would it be?!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3365 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 21:55:37 +00:00
kiran 95b29f608b Specify default values. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 21:42:53 +00:00
rpoplin 6efd05831b Encapsulating annotation decoding function in order to use same fixed random seed in both VariantOptimizer and ApplyVariantClusters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3363 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 20:03:38 +00:00
ebanks 32389dc0a9 Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 19:17:46 +00:00
depristo 1538dc0144 optimizer now uses -an arguments instead of exclude and force for clarity. command-line length reduced by 50% 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 15:41:44 +00:00
hanna 3e9ad4bbd0 Porting SAM pileup ROD to Tribble as a case study. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 00:22:59 +00:00
aaron 6839c194cb although holding on to memories can be fun, it's bound to hurt performance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 19:26:58 +00:00
aaron cac98ba5ef a couple of small documentation fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 17:40:27 +00:00
depristo 3f07611187 Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 13:36:31 +00:00
aaron 2c55ac1374 fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 06:13:26 +00:00
hanna 6868ce988f Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an 
indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 17:31:19 +00:00
ebanks 572b383fe2 Make VA annotate dbsnp again 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 14:06:53 +00:00
rpoplin b09e7231d1 A quick implementation of the experimental covariates for the TGen folks to work with. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 01:08:52 +00:00
kiran aec5f7b630 Can now threshold results based on minimum base and/or mapping quality. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3343 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 19:58:07 +00:00
kiran 13fd182b7c For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 15:17:05 +00:00
kiran 4a7902bb8e Bases 'A' and 'a' (etc.) no longer considered different. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:53:38 +00:00
kiran ec543b7b62 The Complete Genomics confusion matrix rates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:52:10 +00:00
kiran b223b04331 Don't list '.' as an alternate allele, dummy! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:51:18 +00:00
kiran 98718d0faa Computes the error rate per cycle 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3336 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:50:22 +00:00
kiran 7527f950d1 Computes the quality score distribution per readgroup (one column per readgroup) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3335 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:49:38 +00:00
kiran c111c15072 Computes the distribution of insert size per library (for now, one output file per library) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3334 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:48:35 +00:00
ebanks a51bd57566 First version of the smart batch merging tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3333 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 02:18:48 +00:00
rpoplin 33a9549896 Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-09 16:48:07 +00:00
hanna 76efa757f0 Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder 
which improved startup time 5-10x when dynamically merging many BAMs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-08 14:12:22 +00:00
depristo 504103bd15 Misc. additions to correct utilities 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:34:18 +00:00
depristo 64ccaa4c6a Walkers and integration tests that calculate and compare callable bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:33:47 +00:00
depristo d070554329 A walker that calculates read lengths, number and size of clipping events 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:32:51 +00:00
chartl 1749a49042 Mapping and base quality thresholds for DoC default to none 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 18:08:13 +00:00
aaron 7d2df3f511 example windowed ROD walker for Kristian, and updates to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 17:12:50 +00:00
ebanks 44de92e09d Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 12:31:56 +00:00
ebanks 18f1d31a22 Moving to and organizing in core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 04:05:36 +00:00
aaron 06ea65e60b again for JIRA GSA-320 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3319 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 03:47:58 +00:00
aaron ac9b32db88 a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3318 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 03:31:43 +00:00
hanna 4e0019b04f Repair code that sorts and merges intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 22:37:25 +00:00
aaron 72e030a670 require that snps be biallelic before we pass them to the TiTv calculation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 22:33:00 +00:00
rpoplin 7cecec7d00 Removing zero no-calls restriction in AC stats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 18:55:07 +00:00
ebanks 0e58fb7cc0 Moved over to be a walker inside the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 18:28:03 +00:00
aaron 78409dca0d turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 16:36:58 +00:00
ebanks bacc507a48 Don't worry about sorting anymore in the liftover tool. That will come later. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3311 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 15:00:30 +00:00
ebanks 5df0361bd2 trivial removal of unnecessary comments 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 03:51:14 +00:00
ebanks 2975e3a4e8 picard Intervals don't sort right - switching to GenomeLocs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3308 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 03:50:28 +00:00
ebanks 1a99fb9318 First pass at liftover tool. Passing buck over to Aaron... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 20:38:19 +00:00
aaron a0d71540df speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 20:19:42 +00:00
aaron 6bbcc47b5d removing some out-of-date RODs and some unused genotype writer formats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 19:07:13 +00:00
aaron c998c48a23 adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 17:55:36 +00:00
aaron a68f3b2e9c VCF moved over to tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 17:28:48 +00:00
asivache 0338345bee Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 15:42:27 +00:00
ebanks 64640d6b17 Complete the switch statement to deal with all possible cigar operators for Kris. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 13:41:05 +00:00
aaron f75e54e3f7 fixes for new package names in tribble 74 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 05:47:04 +00:00
chartl 617542853f Walker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3296 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 02:55:01 +00:00
chartl 354262eabe New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 02:54:18 +00:00
ebanks 03bea70f3a Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-04 16:49:21 +00:00
kiran 510b3efcc2 Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 18:46:33 +00:00
sjia 94b51de401 HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3290 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 14:54:52 +00:00
rpoplin 97fdd92e7b Clean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3289 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 13:30:20 +00:00
aaron f497213933 DbSNP moved over to tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 06:02:35 +00:00
rpoplin 9d01670f62 Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-02 19:21:23 +00:00
weisburd a318b1871d Removed unused column 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3285 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 21:29:34 +00:00
ebanks 9dff578706 Added PG tag to bam header to let people know it's been cleaned. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 17:30:30 +00:00
ebanks 0e10359a5e Okay, finished up the ability to cap a base's qual by its read's mapping quality. 
This is experimental - I have not tested its performance on SNP calling, or even played around with it.  If you want to test it out, go nuts.  But don't come running to me if your results are not good.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 16:58:30 +00:00
ebanks 850f36aa61 Changes to the Unified Genotyper's arguments: 
1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 16:44:24 +00:00
weisburd 8b2ce128b5 Optimized the join(..) method. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 15:55:07 +00:00
hanna 8bb15ef812 Checking in the reference implementation of the downsampler for back comparison. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 15:41:13 +00:00
ebanks 1714c322c2 Reorg of UG args; checking in first before upcoming changes that will break integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 14:48:46 +00:00
weisburd ba78d146ec Finished implementing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3273 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 14:14:31 +00:00
weisburd 5d5c7f9d34 Changed short code of stop codon to 'stop' 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3272 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 13:55:52 +00:00
aaron cbed0b1ade Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 22:50:17 +00:00
aaron 7fbfd34315 adding the GELI ROD validation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3270 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 21:43:00 +00:00
chartl 82818a417b Allow header fields to come in any order... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 18:33:10 +00:00
hanna 4617abf1ff Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 20:42:04 +00:00
chartl e2ff4167af Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 18:38:33 +00:00
depristo 5dce16a8f1 Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 13:10:11 +00:00
aaron 64c5f287c5 fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3264 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 17:46:46 +00:00
aaron c647153b10 Adding Jama for Ryan. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 14:30:36 +00:00
aaron f6468f9143 a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 04:49:49 +00:00
aaron 68bdac254b a utility walker for validating changes made to the underlying ROD system in the transistion to Tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3258 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:21:24 +00:00
ebanks d9bf441391 Have UG emit calls at sites from one or more 'trigger' tracks when provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:04:43 +00:00
ebanks 8f2bfac7a6 Bug fix for NullPointerException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:02:09 +00:00
ebanks f5a3b128c8 Fixing bug that's not caught by integration tests: 
If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics.  Instead, just check that any eval's no-call count is 0.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 02:40:34 +00:00
depristo 29ab59a7b3 Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-24 21:31:03 +00:00
aaron c8d09a29ed some quick changes to the VE output system - more to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 21:55:08 +00:00
depristo 7f4d5d9973 Ti/Tv by AC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 17:56:29 +00:00
ebanks 42bcca1010 Pulling out the left-alignment code for indels so that other walkers can use it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 16:12:34 +00:00
weisburd 9e28e4eb42 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3250 348d0f76-0448-11de-a6fe-93d51630548a 2010-04-23 15:50:09 +00:00
weisburd 10bcd72593 1st attempt to implement extra columns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3249 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:49:37 +00:00
weisburd a72a5a7b1a Data object for representing a single amino acid 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3248 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:49:06 +00:00
rpoplin e7c0ded40e Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:48:41 +00:00
ebanks e0b51d0df0 Trigger cleaning of duplicate reads. Also beeter debug output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:12:28 +00:00
ebanks 3adf7fbf64 bug fix for known-indels used as consenses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 13:52:51 +00:00
aaron 536f22f3bd adding VC adaptor for GELI, along with unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 05:28:39 +00:00
depristo 3d2c836db6 Bug fix for case sensitivity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3242 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 03:08:58 +00:00
ebanks 8c94df6f00 Bug fix for Chris: deal with sites that have "semi-deletions" 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 18:34:41 +00:00
chartl 121163dd49 interim commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3240 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 13:44:45 +00:00
weisburd f0fe2ea530 A simple codon -> AA lookup table 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3239 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:18:00 +00:00
weisburd e643a9e7a5 Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3238 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:11:19 +00:00
weisburd 653e08c0b6 Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3237 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:11:03 +00:00
weisburd 20379c3f82 Added location-caching optimization, temporary attributes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 11:35:45 +00:00
ebanks 84ebceb9a6 Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 02:05:10 +00:00
chartl e7334ec11f Checkin for Eric (IndelDBRateWalker is a prelude to a VariantEval module for comparisons for indels) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3234 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 00:40:27 +00:00
hanna 32d86cf457 Rev the reservoir downsampler to support partitioning through a functor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 19:50:26 +00:00
asivache ef6d900eb8 for now, set log error to -1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 19:21:06 +00:00
ebanks e9e844fbf5 1. Reverting: dbsnp automatically is a comp 
2. Fixing logic for min Qscore calculation


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 18:51:35 +00:00
asivache 1373fee278 Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change. 
VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument. 

SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 18:19:03 +00:00
hanna ab34397d2e Continuing to stamp out the non-ASCII copyright virus. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 14:50:45 +00:00
chartl 84f1ccd6ac Two dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations). 
ERIC -- does the IndelAnnotator (the RefSeq lookup code I stole from IndelGentoyperV2) want to be its own Annotation inside VariantAnnotator? Is Andrey already doing this as part of adding indel calling to UG?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3226 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 14:04:10 +00:00
depristo 2fdc1cf490 Bed ROD track support 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 13:22:42 +00:00
depristo 51b3998082 deleting unused code from VariationFiltration 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 13:22:19 +00:00
ebanks 4abd3b0b7b Fixing known/novel calc now that dbsnp isn't a default comp track 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 05:43:59 +00:00
ebanks 114819d980 Allow user to set min confidence score for comp tracks too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 05:09:09 +00:00
ebanks 3db73e0791 Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 03:00:43 +00:00
ebanks 3b5673d967 1. Removed -all; by default all modules are used; use -none for no modules. 
2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 02:46:42 +00:00
asivache 6fda78f93f Always return deleted bases in upper case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3218 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 19:17:40 +00:00
asivache 52a570637d Always keep event bases in upper case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3217 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 19:16:39 +00:00
aaron 80c4f88a72 removing the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 18:56:45 +00:00
asivache 7d952a34ae Fixing copyright note 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3215 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 18:28:57 +00:00
asivache cdc175f7e3 Synchronizing version to make sure everything compiles; this model is not operational yet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:41:52 +00:00
asivache 4437456bb5 Pass array of ref bases to callExtendedLocus() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:41:13 +00:00
asivache 5d2fab93f4 Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:40:30 +00:00
asivache 01e6492ba9 Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:38:09 +00:00
asivache 4723cad1be New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase()) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:35:09 +00:00
asivache cac125b35c Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T') 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:37:28 +00:00
rpoplin f4977965b6 Removing debug statements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3208 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:22:40 +00:00
rpoplin 124b7a2a58 Moved ApplyVariantClusters over to VariationContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:20:25 +00:00
asivache 200d3e2c47 added copyright note 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3205 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:44:26 +00:00
asivache 546dfb629e A draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3204 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:38:16 +00:00
hanna c1e53d407d The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 
unicode quote characters embedded in it.  These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset.  Fixed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:26:32 +00:00
aaron b5f6f54968 Almost done removing any trace of the old Variation and Genotype interfaces. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 14:52:15 +00:00
hanna 818a95ea6e Test of new copyright message without unicode characters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3200 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 14:14:54 +00:00
rpoplin 00feb3eee0 Moving over to VariationContext in CountCovariates. Removed references to class Variation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3199 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 13:26:22 +00:00
hanna 1bc26f69e9 An attempt to cleanup the Utils directory. Email to follow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 23:00:08 +00:00
hanna c08936d6f4 Added a reservoir downsampler which can sample elements in an iterator uniformly 
from a stream (see Vitter 1985).  Thanks to Eric and Andrey for the pointer.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3197 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 20:48:14 +00:00
ebanks abf48cee05 Moving over to VariantContext from Variation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 06:56:29 +00:00
ebanks d73c63a99a Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it. 
Also, adding some more useful integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 05:47:17 +00:00
aaron 131703d9db more clean-up: moving AlleleBalanceInspector to archive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3192 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 20:53:33 +00:00
ebanks 534f24177a Move to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3191 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 20:09:48 +00:00
ebanks 8c32bb8f0a Complete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3190 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 19:41:42 +00:00
aaron 821e8b1c5f more cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3189 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 19:16:16 +00:00
aaron e11ca74eb5 removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3188 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 18:59:29 +00:00
ebanks d5e5589b8f No longer used 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3187 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 17:57:39 +00:00
aaron 4d75b26b7a Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 06:17:31 +00:00
asivache 6dc1275cfb Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3183 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 00:15:57 +00:00
ebanks f4673efd2f Moving to archive as it's no longer supported 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 22:10:42 +00:00
ebanks 02a6f4c401 Moving over to VariantContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 22:07:28 +00:00
ebanks 7adff5b81a Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 20:36:19 +00:00
ebanks e702bea99f Moving VE2 to core; calling it "VariantEval" (one more checkin coming) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 20:25:47 +00:00
ebanks ac9dc0b4b4 Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 19:53:02 +00:00
ebanks 3330e254a9 Standardize the dbsnp track name in preparation for case-sensitivity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 19:41:57 +00:00
ebanks 5f7564bf0a Better naming of output columns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 18:08:07 +00:00
aaron e682460c1f add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 16:31:43 +00:00
aaron b54031fc86 adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 06:09:27 +00:00
ebanks 04909fa6ad Removing arbitrary selects 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 17:46:39 +00:00
ebanks f1189bac5a Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 16:58:55 +00:00
weisburd c0f4695902 Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:42:19 +00:00
weisburd 74ec72d1ac Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:39:50 +00:00
weisburd 77a6608784 Changed a variable name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:38:18 +00:00
weisburd 7b8056099c Fixed 'N' reference-base handling, changed some comments, var names 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:37:25 +00:00
ebanks dde092fb61 Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run. 
Heads up everyone: by default, *no* modules are run.  Please add "-all" to your scripts to maintain the previous behavior.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 22:15:58 +00:00
ebanks 0b575596f8 Fix for concordance: samples found only in truth no longer kill it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 21:33:49 +00:00
hanna 8573b0bc6f Refactoring intervals, separating the process of parsing interval lists, 
sorting and merging interval lists, and creating RODs from intervals.  This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 15:50:38 +00:00
weisburd d0123956bc Modified comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 15:41:59 +00:00
chartl 7b05091c04 DoC now does not require a -o argument. (Change for Matt) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 13:58:17 +00:00
ebanks e413882302 Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 20:42:18 +00:00
hanna 14b8101d45 Error message fail. Failed to supply one of the valid interval file types. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:19:01 +00:00
hanna 60d54e69f3 Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:11:27 +00:00
ebanks 3434a61146 Don't trigger when ref=N (which can happen when a dbsnp track is provided) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 02:59:11 +00:00
ebanks 961ca05abc Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 01:43:07 +00:00
ebanks 0cc6d0fbbb One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:48:36 +00:00
rpoplin c2a37e4b5c Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:36:06 +00:00
ebanks e73e6a4fb0 Significant memory improvements to plink code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 16:12:38 +00:00
rpoplin f1b1e70612 Bug fix for multisample calls in ApplyVariantClusterWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 12:01:15 +00:00
ebanks 3f2455e346 Better error message as suggested by James P 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:52:53 +00:00
ebanks fba48b515a Heads up everyone: 
For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:37:25 +00:00
ebanks e286623f6f Use byte[] instead of String in an attempt to cut down on memory usage 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:32:54 +00:00
chartl 7025f5b51d Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 19:37:17 +00:00
aaron e148a3ac61 added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option. 
Using this feature, sites covered by the target ROD will be iterated over.  This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.

WARNING: for very large ROD's this can be costly.  Consider this experimental for now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 05:14:41 +00:00
aaron 20cc2a85a4 removed the hashmap from Genotype Concordance, moved it into a table 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 21:24:48 +00:00
aaron e55f27b3b1 forgot a file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:51:13 +00:00
aaron 9ca8e345fc by-by old junk. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:41:48 +00:00
aaron 8fd59c8823 Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:39:55 +00:00
depristo 918b746798 More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 16:38:28 +00:00
ebanks e7dad728df Trivial output changes for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 14:47:43 +00:00
depristo 058e7d3d12 Bug fix for Gregory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 00:21:35 +00:00
rpoplin 7b44e6bd55 ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3126 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 19:47:29 +00:00
rpoplin 60c227d67f Added new VE2 module to create a plot of titv ratio by variant quality score 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3125 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 15:19:27 +00:00
asivache 3530ef5a41 Explicit type cast fixed in order to work with new ROD implementation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 15:02:56 +00:00
rpoplin 2d002c56c3 Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3123 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 13:48:31 +00:00
aaron 12e4f88ca7 a little bit more clean-up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-05 20:49:06 +00:00
aaron df7e7921ce removing some unused code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-05 19:30:08 +00:00
ebanks 56eb15f91f Error checking for bad input (thanks, Aaron). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-04 03:17:01 +00:00
weisburd 705b28e90d First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 21:52:26 +00:00
weisburd d78e7f6c0a Added documentation. 
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 2010-04-02 21:51:28 +00:00
aaron 8017fb123f changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 20:55:19 +00:00
weisburd 6b7b07f178 First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3114 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 17:49:42 +00:00
rpoplin 642c969896 reverting optimizer changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3112 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 16:59:13 +00:00
chartl f7d1b8f5de CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive. 
Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:27:23 +00:00
aaron 585cc880a2 changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:23:14 +00:00
hanna d00bde22db Reverting one of Brett's changes that should not have been committed. Will 
address with Brett separately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3107 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:10:46 +00:00
bthomas b4f6f54502 Reorganizing the way interval arguments are processed 
Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java: 
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java

New restrictions: 
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 12:47:48 +00:00
aaron c3c6e632d1 support for two new VCF header info field value-types, Flag (for fields that are just boolean truths), and Character (for single charatcer info fields). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3105 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 03:11:32 +00:00
aaron 3d3d19a6a7 the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date. 
a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects.  This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc.  This layer is needed so we can integrate Tribble tracks (which don't natively have names).  Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).

Sorry for the inconvenience!  More changes to come, but this is by far the largest (as has the greatest effect on end users).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 22:39:56 +00:00
hanna 4fcee248f9 For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read. 
Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 20:46:44 +00:00
rpoplin d58fe70708 Correctly ignore filtered calls and indel calls in the truth sets 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3101 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 14:33:01 +00:00
hanna b60197ae10 Another round of cleanup and simplification in Picard -- Picard's unit tests 
are now passing for my branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 01:02:59 +00:00
depristo 40f8e7644c Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 23:57:36 +00:00
depristo f992f51a3b Deleting incorrect sampling genotype likelihoods from the codebase 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3098 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 23:56:35 +00:00
kiran b9d3fc3fbb Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 22:40:17 +00:00
hanna 400684542c Revisions to take into account finalization of Picard patch: naming changes, better definition 
of public interfaces.  This won't be the last Picard patch, but it should be the last big one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 19:28:14 +00:00
aaron b00d2bf2bc fixing an annotation that was breaking the error log output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3095 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 15:34:04 +00:00
aaron a6e8687d71 implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 04:20:19 +00:00
ebanks babb9fb825 snp cluster filter should ignore ref calls when determining the clusters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 17:57:33 +00:00
chartl 24461a2503 Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:59:01 +00:00
chartl dc802aa26f Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:32:00 +00:00
ebanks 1e8b3ca6ba Fare thee well, oh LocusWindowTraversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:17:26 +00:00
depristo 8ea98faf47 Deleting the pooled calcluation model -- no longer supported. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 11:44:27 +00:00
hanna 85037ab13f Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of 
Picard patch, including move of some of the Picard private classes we use to Picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 03:21:27 +00:00
depristo a45ac220aa Removing unnecessary printing routines 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-28 22:34:54 +00:00
depristo b8ab74a6dc 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
 2010-03-28 21:45:22 +00:00
kshakir e9e53f68ab Filter lists can now end with .list or .txt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-27 17:41:24 +00:00
aaron 074ec77dcc First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be 
specified with the reportType command line option in VE2.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3083 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-27 03:59:32 +00:00
kiran 85f4f66180 Updated to use VariantContext. Output has been reformatted: variant and genotype concordance are emitted for every coverage level per variant. If the requested sampling level is higher than what's available, the maximum available coverage at that locus is used. This makes it much easier to make plots indicating the percentage of comparison callset recovered at a certain sampling depth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3082 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 21:02:43 +00:00
kiran 391e5843e4 If the annotation engine has not been supplied, don't try to annotate anything. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 20:52:21 +00:00
kiran 8048b709a0 Selects a single sample on which to operate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3080 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 20:50:58 +00:00
kshakir 20e3ba15ca Added an optional argument -rgbl --read_group_black_list to filter read groups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3079 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 19:38:57 +00:00
ebanks 73a14a985b Moving VariantsToVCF to core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 18:55:12 +00:00
ebanks 14bf6923a8 HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3077 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 18:34:59 +00:00
hanna 78af6d5a40 New sharding system is going live again for on-the-fly merging. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3076 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 18:39:04 +00:00
hanna 46c14ec63f New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation 
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 17:41:22 +00:00
ebanks 4398a8b370 Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3074 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 04:53:31 +00:00
ebanks 2373a4618f bug caused by a misprint: context != contexts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3073 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 03:08:24 +00:00
ebanks 3176715c74 1. Alignability mask returns null when not available. 
2. --list now prints out the available classes/groups too.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3072 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 20:49:07 +00:00
rpoplin 06a212e612 Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 19:43:10 +00:00
ebanks 47e30aba92 Rods for reads hooked up into the cleaner 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 18:17:56 +00:00
aaron 5079f35e40 better method names for read based reference ordered data access. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 16:13:31 +00:00
ebanks 49117819f5 For the cleaner to clean, it must beat the entropy produced by the aligner (and not just the raw reads). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3068 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 15:21:58 +00:00
aaron 60dfba997b added some sample annotations to VariantEval2 analysis modules, and some changes to the report system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3067 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 05:40:10 +00:00
hanna 1f451e17e5 Changing preloaded index to only "preload" reference sequences on demand. 
Results in drastic lowering of startup cost when multiple BAM files are 
merged.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 22:02:28 +00:00
hanna 884a577013 Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 16:48:11 +00:00
aaron 7462a0b2d1 cleaned-up of VariantContextAdapter tests, fixed the double comparisons in equals() in RodGeliText (nice MathUtils.compareDoubles Kiran) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3064 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 15:18:30 +00:00
aaron a69b8555dd Geli to variant context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3063 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 06:45:29 +00:00
aaron eafdd047f7 GLF to variant context. Added some methods in GLF to aid testing; and added a test that reads GLF, converts to VC, writes GLF and reads back to compare. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3062 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 03:43:25 +00:00
hanna 3767adb0bb Processing intervals as they stream in means much lower memory usage and 
quicker runtime.  Making change as minimal as possible to avoid conflicts
with BT's incoming patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 22:04:45 +00:00
ebanks 0097106938 VariantFiltration can now filter specific samples. 
This is *NOT* an ideal implementation.  One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL.  For now, though, this will have to do.
Docs coming tonight.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 20:45:11 +00:00
asivache 543aefc3d7 Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 19:20:34 +00:00
asivache d2944461ef We also have to allow the window to be (partially) outside the bounds and trimming to the contig size is not enough (thanks to shards). Now we trim to the current bounds too (i.e. if the interval is not completely within current bounds, we create reference context that contains only bases from the overlap between the interval and the bounds). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3057 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 17:36:29 +00:00
asivache 9053406798 LocusReferenceView: If the locus a view is requested for spans beyond the reference contig ends, create the actual window bounded by contig ends (so that the locus will not be fully contained in the window!!). 
ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3056 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 15:59:15 +00:00
aaron 439c34ed38 clean-up before annotating VariantEval2 for output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3055 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 07:39:20 +00:00
depristo 076d21d394 Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3054 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 02:47:09 +00:00
hanna 6cd97b78ab An additional safety check to ensure that we only walk over coordinate-sorted 
data when doing locus traversals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3053 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-21 23:31:45 +00:00
hanna b4b4e8d672 For Sarah Calvo: initial implementation of read pair traversal, for BAM files 
sorted by read name.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3052 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-21 23:22:25 +00:00
hanna c0eb5c27ea Lower memory support for merged sharding. Merged sharding is still not available. 
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
	 distribute picard-private.jar.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 22:03:47 +00:00
ebanks 4d4db7fe63 Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:45:01 +00:00
ebanks 4c4d048f14 Moving VariantFiltration over to use VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:35:23 +00:00
ebanks c88a2a3027 Fixing/cleaning up the vcf merge util 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:13:32 +00:00
rpoplin cdec84aa8f Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3046 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:07:32 +00:00
depristo d8ff552311 Support for EXPERIMENT sampling-based genotype likelihoods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3044 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:40 +00:00
depristo 7b17bcd0af Refactoring a few useful routines for detecting mendelian violations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3043 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:01 +00:00
depristo 56092a0fc2 Slight cleanup for mathutils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:18:08 +00:00
depristo b221ce94ce Still being tested trio-aware genotyper that calculates P(de novo) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3041 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:11:39 +00:00
ebanks 03480c955c And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 04:58:37 +00:00
ebanks e757f6f078 Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3038 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:56:27 +00:00
ebanks 0311980668 The VariantAnnotator can now officially annotate genotype (FORMAT) fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:30:14 +00:00
hanna 9b61d95d9c Khalid found an out-of-memory condition with the new sharding system when 
merging lots of BAMs, and the fix is taking longer than I thought.  Disable
experimental sharding when merging until the fix is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 02:43:46 +00:00
ebanks b8e8852b4f Better interface for the Annotator in how it interacts with VariantContext. 
Also, added a proof of concept genotype-level annotation (not working yet, almost there).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3035 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 20:41:57 +00:00
hanna 96662d8d1b Moving from GATK dependencies on isolated classes checked into the GATK 
codebase to a dependency on a jar file compiled from my private picard branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 17:43:42 +00:00
aaron 8a5f0b746e some cleanup for the output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:54:39 +00:00
rpoplin c78fc23ec5 Minor updates to output of variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:46:47 +00:00
ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 05:38:32 +00:00
rpoplin 58a31bab6a Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 20:41:42 +00:00
hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 
now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 19:39:30 +00:00
aaron 182f1061ff Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3025 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:56:48 +00:00
ebanks 5e29d0c219 Be smarter about dealing with infinite quals for ref calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:35:23 +00:00
rpoplin 1bb4394aa9 Adding a skeleton for the second step of the variant optimization process. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3023 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:03:40 +00:00
ebanks ded4ba8966 Let's make artificial reads that actually adhere to the specs... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:51:42 +00:00
bthomas 5b34bb9ab0 Adding three minor new features: 
+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:24:10 +00:00
ebanks 4340601c26 -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 
-Better integration test


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3020 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:00:10 +00:00
ebanks 76d14d17dc oops, need to update class names too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3019 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:01:31 +00:00
ebanks 85a030069d renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3018 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:00:28 +00:00
ebanks af5fd99444 Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 13:53:42 +00:00
hanna 2cc040aa1c New sharding system is live. Disable with -ds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 03:32:45 +00:00
ebanks 1fd909cdaf Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 00:20:15 +00:00
hanna 849bd1f451 Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 22:01:23 +00:00
rpoplin 933823c8bc Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 19:45:02 +00:00
hanna 59045ccb28 Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3011 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:23:37 +00:00
hanna 6dd5f192e7 Performance improvements for RODs in conjunction with new sharding system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 14:54:12 +00:00
kiran f20f78d77f Don't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3009 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 04:00:04 +00:00
aaron 10e76abbbc adding some VE2 report infrastructure; work-in-progress. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3008 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 03:57:42 +00:00
ebanks 586f87fa35 Quick fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:59:26 +00:00
ebanks 202231141c -Push the --use_original_qualities argument into the engine. 
-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:06:11 +00:00
ebanks 035d4170aa fix bug in read clipper: output bam can be null, so check for it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:49:26 +00:00
ebanks 411d25c8d1 -Integration tests for walkers that use original quals. 
-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:46:31 +00:00
aaron e365d308d4 add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 16:00:55 +00:00
kcibul 9f519af06d new method to filter out overlapping PE reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3002 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 15:40:09 +00:00
hanna 45f70de6df Fixed bug that failed to reset an accumulator when crossing contig boundaries, 
meaning that in special cases of shallow coverage, an interval might get dropped.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 04:45:55 +00:00
depristo 4dd7c5972c 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
 2010-03-14 21:08:14 +00:00
ebanks e367a50e9b Added genotype concordance module. Not at all finished, but needed to give something to Aaron to look at for help in printing the output nicely. 
Also misc cleanup and fixes (e.g. perform evalulation even when no comp tracks are provided).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2996 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 19:02:24 +00:00
aaron ecb59f5d0d removed old tests and old code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2995 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:57:01 +00:00
depristo e7eae9b61d High performance, correct implementation of -XL exclusion lists. Enjoy. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2994 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:39:20 +00:00
aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:35:49 +00:00
depristo b39b5edca8 Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:23:12 +00:00
aaron 1eb5f97255 fixed dropping single base intervals from deleteRegion, moving onto performance fixes. 
(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:14:21 +00:00
hanna 7aa7a5f9b8 Bug fixes for edge cases and filtration in the earlier performance fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 04:46:08 +00:00
hanna 5e8654fcdc Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 23:19:42 +00:00
asivache d804bdf210 New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:15:03 +00:00
aaron 661a043cef adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:13:39 +00:00
depristo 18ba9929f9 notes for eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2983 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:34:54 +00:00
hanna cbd529d544 Better chopping up of data for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2982 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:13:26 +00:00
hanna a7ba88e649 Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 
with less memory consumption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 18:40:31 +00:00
ebanks 4a05757a2a Fixed strand bias calculation because of -Infinity issues. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2980 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 16:05:51 +00:00
aaron dde9fd8a15 some rods-for-reads cleaning and performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:54:58 +00:00
depristo 4f4555c80f PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:28:31 +00:00
depristo 486bef9318 Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 16:25:16 +00:00
ebanks c85ed1ce90 Plumbing is now in place to emit indel calls from the UnifiedGenotyper. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2975 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 04:30:12 +00:00
ebanks 5c35be39ef Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:14:06 +00:00
ebanks 1a576525e9 misc improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:00:28 +00:00
ebanks 6e855809e1 Renaming and moving relevant tools into a sequenom directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 02:31:10 +00:00
asivache c638c29eea In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 22:18:44 +00:00
ebanks bc3761dc16 allow clipper to use original quals if requested 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2969 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 21:50:31 +00:00
ebanks f096a958d6 Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2967 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:13:01 +00:00
chartl 0a49dffa8f Row/Column names are now R-friendly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:01:03 +00:00
ebanks 0e360ea8af Alleles now hash correctly. 
Special thanks to Matt & Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2965 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 18:09:44 +00:00
ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:16:47 +00:00
hanna cdce639bae Partially reclaim performance lost during integration test fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2961 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 12:36:11 +00:00
ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 03:41:07 +00:00
hanna 02f48b6457 Fix bug that's been in the GATK for a very long time: update nReads (as well 
as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'.  While
I'm in there, update TraversalStatistics to store longs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 22:44:54 +00:00
chartl 21bf8b4b93 Odd, what I saw on IntelliJ hadn't saved to sting before committing. Here's the actual change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2956 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 15:54:41 +00:00
rpoplin fe8a8b9199 Hooked up both optimization models via command line arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2955 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:49:59 +00:00
chartl cc6a714c09 Handle excess coverage in interval output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2954 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:40:05 +00:00
rpoplin ca2a0266dc Converting annotation values that are set to Double.Infinity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2953 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:04:33 +00:00
rpoplin b42e0a398e Bug fix in variant optimizer for when there are more novel variants than known variants in the callset. Changing the magic numbers related to the starting sigma values for the gaussian clusters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2952 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 13:02:08 +00:00
hanna e4360bac6a More comprehensive support when sharding for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 11:25:20 +00:00
hanna eb165ca844 Celebrate the fact that the new sharding system works with integration tests 
by removing the scary debug line.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2950 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 23:40:56 +00:00
hanna 9e107513d0 In the new sharding system, if no read group is present, hallucinate one. Added 
for test compatibility, but not sure whether we still need this feature.  TODO: Poll the group about this feature.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 23:01:34 +00:00
hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding 
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
   shards.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 21:01:25 +00:00
hanna dd6122f682 Fixed another bug in the original sharding system. Updated integration tests 
as appropriate.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 15:32:18 +00:00
hanna ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by 
awking output of BamToFastq vs. samtools until the outputs matched exactly.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-06 18:52:53 +00:00
hanna 1ef1091f7c Cleanup and simplification of read interval sharding. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2944 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 23:34:38 +00:00
ebanks 7fa0f77721 add output for number of variants that validated as true 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2942 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 18:57:44 +00:00
chartl 037ac9c9af Actually calculate base counts by read group when "both" is specified. Modified integration test to cement the now-correct "both" behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2941 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 18:31:48 +00:00
chartl 8738c544f1 Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 17:06:52 +00:00
rpoplin 95d560aa2f More incremental updates to the variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2939 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 16:42:42 +00:00
hanna 7a7e85188c Better eagerDecode default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2938 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 16:42:23 +00:00
depristo 33cefddf55 Better INFO field annotation for Mendel violations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2937 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 15:22:04 +00:00
ebanks 9f7ebe1e1c - add name to vcf od field 
- don't do HW calculation if everything is a no-call


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2936 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:43:01 +00:00
hanna 7104a3a96c Fix for accumulator exception when running reduce by interval walkers without 
intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:04:08 +00:00
ebanks 9eb122924f misc cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2933 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:34:13 +00:00
chartl 706d49d84c Commit for Aaron 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:29:07 +00:00
ebanks c20d3e567e Now outputs fully spec-compliant VCF with proper annotations. Emits statistics as to number of good/bad records. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2931 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:28:17 +00:00
hanna adea38fd5e Sharding system fixes for corner cases generally related to lack of coverage 
in the BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2928 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 18:59:21 +00:00
chartl a4d494c38b Add option to adhere to the PlinkRod naming convention [ProjectName]|c[Chrom]_p[Pos] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2927 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 18:31:27 +00:00
ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. 
We almost completely support indels. Not yet done with plink stuff.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 17:58:01 +00:00
aaron c8077b7a22 Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 16:02:21 +00:00
chartl 6759acbdef 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
 2010-03-04 15:00:02 +00:00
hanna 023654696e First pass at handling SAMFileReaders using a SAMReaderID. This allows us to firewall 
GATK users from the readers, which they could abuse in ways that could destabilize the GATK.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2923 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 00:59:32 +00:00
rpoplin b241e0915b Incremental update to VariantOptimizer. Refactored parts of the clustering code to make it more clear. More comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2922 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 20:33:35 +00:00
asivache 073fdd8ec7 Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2921 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 17:34:30 +00:00
chartl 6ca6c98980 Can just give PickSequenomProbes a dbsnp rod to mask 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2920 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 16:50:58 +00:00
aaron ca2cd9d4f5 a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 16:31:45 +00:00
aaron 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 15:56:44 +00:00
ebanks 0e9a6826b0 Update to VCF code to get it up to spec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 06:12:42 +00:00
ebanks 317fac8dff Better error message for --assume_single_sample_reads screw up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2916 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 01:03:10 +00:00
hanna 104f4f7383 Mediocre implementation of reader pooling within the SAM data source. Will fix this week. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2915 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 22:35:02 +00:00
ebanks 5f3c80d9aa 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. 
2. Significant refactoring of Plink code to work in the rods and use VariantContext.  More coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:26:40 +00:00
ebanks 6ceae22793 utility methods for genotype counts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2912 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:23:41 +00:00
kcibul 7578678f99 refactored to provide a sum of mismatch quality scores capability as well (used by Cancer) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2911 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 16:40:03 +00:00
aaron 232fcf829a removing the unsupported VCF validator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2909 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 15:45:33 +00:00
hanna 1b572b192a Stopgap fix for temporary problems sharding when indexless. A more compelling solution will come later this week. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2908 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 02:59:14 +00:00
hanna 75a541b479 Fix nasty issue where shard boundaries aren't properly clipped during locus traversals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2907 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-01 23:31:58 +00:00
rpoplin af6e476df5 Copyright compliant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2905 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-01 15:29:34 +00:00
rpoplin 3a863d3e8c Initial check in of VariantOptimizer in playground. There is a Gaussian Mixture Model version and a k-Nearest Neighbors version. There is still lots of work to do. Nobody should be using it yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2904 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-01 15:26:18 +00:00
hanna 6133d73bf0 Locus (non-intervalled) traversal with new sharding system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2903 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-01 01:58:44 +00:00
hanna 80f5d2829d Support for read interval sharding with proper filtering. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2902 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-27 20:26:34 +00:00
aaron d8fedd59be docs, cleanup, and some improvements to the iterators. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 22:36:04 +00:00
hanna b69c2d0f70 Cleanup. Remove some unnecessary methods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2900 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 21:50:48 +00:00
hanna 30eb28886b Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so 
the mode of operation is currently queryOverlapping rather than queryContained.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 21:41:55 +00:00
chartl cfff486338 This commit is for Kiran 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2898 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 18:18:38 +00:00
chartl 87f8fb7282 Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2897 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 16:39:47 +00:00
aaron 622554d7bd disable a part of the ROD for Reads code until the rest of the system goes live 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2896 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 16:15:42 +00:00
chartl 496ecc8186 Change in how overall coverage and means are stored in the DOCS object; change from keeping track of sample mean coverage to keeping track of sample total coverage (calculate means at the end) 
This is a mid-way commit for Aaron



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2895 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 15:51:12 +00:00
hanna 1017a38f38 Initial refactoring of read traversal to make it easier to drop in intervalled reads traversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2894 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 15:09:09 +00:00
depristo 9a6b384adb Support for no qual fields in VCF; better support for Mendelian violation calculations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 00:29:17 +00:00
aaron 246fa28386 RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 22:48:55 +00:00
chartl 591102a841 Don't close the output stream if we're printing to stdout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2891 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 21:50:58 +00:00
chartl 10cc71ceb0 Another midway commit for teh engineerz 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2890 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 21:24:02 +00:00
hanna 3289826892 Fix chartl's issue -- reduceInit() is sometimes called unnecessarily at the 
end of a traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2889 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 21:02:18 +00:00
chartl 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] 
Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output).

Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 20:25:07 +00:00
hanna 553d39bb00 Clean up the code a bit following the introduction of reduceByInterval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 01:20:22 +00:00
hanna 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a 
simplification of some of the locus traversal code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 00:16:50 +00:00
asivache 2572c24935 We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2885 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 23:13:23 +00:00
aaron fef1154fc8 starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 22:11:53 +00:00
chartl 5df37968de Simplification of code segments; slight alteration to per-locus tabulation; added to-do items for cosmetic changes (mostly binning options and settigns) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2882 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 05:20:18 +00:00
asivache 27d3ef9458 Got rid of annoying commented printouts; no functional changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2881 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 05:12:30 +00:00
asivache d73bc490c2 Do not build alt consensuses from insertions that have an N in the inserted sequence. Seems to cause problems rather than solve any 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2880 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 03:00:26 +00:00
asivache 94d74d4f78 Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored. 
in class Consensus: 
1) use Arrays.equals() to compare java arrays!!
2) if object overrides equals() it also MUST provide appropriate hashCode() (thanks, Matt) 

As a side effect, a number of commented out debug prints are committed, still need them...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2879 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 02:09:50 +00:00
chartl 1f673e9fab Float the bins with the given lower bound 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2878 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-23 20:48:53 +00:00
chartl 119d449b46 Formatting changes 
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 2010-02-23 20:43:15 +00:00
chartl 173956927b Summaries generated for firehose from DoC output have been migrated to its own walker to calculate aggregate coverage statistics in a parallelizable and fast way. This is an initial commit, bug-fixing and testing is upcoming. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2876 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-23 18:41:02 +00:00
hanna 491b30e8de Eliminate a few stray loci that weren't being filtered out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2875 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-23 18:00:52 +00:00
hanna fff15944fe Bug fix. Stopping condition of recurrence stopped too soon in some cases where an interval *contained* zero reads but *overlapped* with some reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2874 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-23 15:58:54 +00:00
hanna a0e8de40cf Bug fix: at one locus in the dataset, two reads were dropped. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2872 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 23:54:52 +00:00
aaron 5546aa4416 adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2871 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 22:27:39 +00:00
hanna 88d0677379 Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2870 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 22:19:06 +00:00
ebanks 8b555ff17c Killed the old cleaner code. Bye bye. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:49:58 +00:00
kshakir 3738b76320 Added a playground concordance analyzer for summarizing VariantEval across a group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2867 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:28:52 +00:00
ebanks a640bd2d79 ignore uninteresting extended events 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2866 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 19:55:46 +00:00
rpoplin 32e5dceef9 Moving comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2865 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 19:27:31 +00:00
alecw b236714c8a Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2863 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 17:35:25 +00:00
ebanks 32d14d988e Overload parseIntervalRegion() to allow for the interval merging rule to be passed in (so one is not required to use the value from the GATK arg collection). 
Now the IndelRealigner can use this functionality without being forced to merge  abutting intervals (which was actually causing a problem with the cleaning).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2862 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 04:13:54 +00:00
hanna cc09f48cd8 Correctness fix: index can concat chunks around shard edges, and my code didn't account for that. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2861 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 21:44:33 +00:00
chartl 0e05a3acb0 Adding depth of coverage features to firehose summary tools 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2860 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 19:47:16 +00:00
hanna 71f18e941f Significant performance improvements made by subtracting out the contents of the prior highest-level bin. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2859 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 16:46:16 +00:00
rpoplin 7f19ff1fa1 Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2857 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 15:25:23 +00:00
aaron b1a4e6d840 removing non-ascii characters from my Copyright and from VariantEval2Walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2856 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:54:36 +00:00
aaron 33ae256186 a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2855 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:43:52 +00:00
ebanks bbbad79f8c Forgot to remove debugging code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2854 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:12:58 +00:00
ebanks 7669eaaeb3 Optimizations to the cleaner algorithm; reduce total runtime by almost 20%. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2852 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:10:56 +00:00
ebanks 79ab7affda - Change sortOnDisk option to sortInMemory 
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 20:52:57 +00:00
ebanks 2520889cb3 Check for bad intervals and don't emit them 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 21:42:36 +00:00
aaron 653f70efa2 added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2846 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:35:35 +00:00
chartl 01af3d0663 Update an error message :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2842 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 23:24:06 +00:00
jmaguire 81313d9452 added class VCFMerge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2840 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 14:41:50 +00:00
jmaguire 0ef50bcae7 - update to match recent changes in the VCF parser 
- compute Het Error Rate in VCFConcordance
- changes to the frequency-specific optimizer




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2839 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 14:27:01 +00:00
depristo 8072e9aed5 should never commit without running intergration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 23:42:37 +00:00
depristo a1a3d5fcb0 Support for reading in table of rsIDs -> dbSNP builds to back generate a dbSNP build X from a single file. Very useful indeed. dbSNP -> VC now captures the rsID in the context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2837 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 22:40:55 +00:00
kcibul 28f24ca2ae made some private member/methods protected to allow for subclassing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2836 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 21:16:00 +00:00
hanna 232d884578 Got back most of the performance lost when I fixed the dropped reads problem. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2835 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 19:59:56 +00:00
chartl 04a2784bf7 Initial commit of tools under development for data QC through firehose. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2834 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 19:13:24 +00:00
hanna 77af5822d4 Correcting my incomplete understanding of how the BAM file index actually works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2833 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 16:15:19 +00:00
depristo 5f74fffa02 Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2832 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:26:52 +00:00
ebanks c6f6948f9d Haiku: 
Eric is a fool.
Matt found his really dumb bug.
Eric is humbled.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2830 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 04:51:56 +00:00
rpoplin ecebf0bc62 Bug fix for null pointer exception in AnalyzeAnnotations if -name argument isn't specified 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2828 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 18:39:26 +00:00
mmelgar ad608d0e9d Cleaned up documentation on SecondaryBaseTransitionTableWalker and added Read Group and Allele Balance to the info. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2827 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 17:20:35 +00:00
hanna 34e566c90d Fixed bug where new sharding system wasn't grabbing the reads that start at the end of a bin. Caused by what I currently believe to be a bug in Picard -- will verify with Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2826 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 17:00:04 +00:00
ebanks 96fee7cf7a Disabling input of known indels for use as alternate consenses. When we get rods in a read traversal, it will be trivial to hook it into the cleaner (the code is already there). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2825 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 15:52:21 +00:00
ebanks a4a2c9b172 Deal with bad input; also N-way out isn't default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2823 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 03:44:56 +00:00
hanna dc885ba386 Fix for some correctness bugs found during early performance testing, phase 1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2822 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 22:32:25 +00:00
depristo c66861746a improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 16:12:29 +00:00
rpoplin 3de72daa88 Removing an accidently added import statement. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2818 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:54:24 +00:00
rpoplin 0b1e243a7b CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:52:20 +00:00
ebanks 6652b992f7 The new cleaner can now use known indels to create alternate consenses for cleaning. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2816 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 04:39:15 +00:00
hanna 0250338ce7 Basic use cases for merging BAM files with the new sharding system work. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2815 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 22:14:37 +00:00
depristo 934d4b93a2 VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 19:02:25 +00:00
andrewk 369cc50802 Added playground walker that does a basic concordance check between two VCF files - an eval and a truth file - across all samples in the eval file. Produces per-sample, per-locus debug info and simple concordance stats. This is not meant to be extended, but rather used for validating the HapMap to VCF conversion in preparation for retiring GFF-based HapMap data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2813 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 02:41:18 +00:00
depristo 94f892ad42 VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:22:05 +00:00
depristo 457568485a simple Beagle input ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2811 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:21:04 +00:00
hanna 57b8c9a53c Supporting infrastructure for merging SAM files. Not yet integrated into the datasource. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2810 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 23:59:38 +00:00
kshakir fc810a1800 Updated VCF Reader to parse VCFs according to the VCFv3.3 spec. Column headers are tab separated since sample names might have spaces. 
Updated test files in /humgen/gsa-scr1/GATK_Data/Validation_Data/*.vcf to remove spaces except for when they are supposed to be in the sample name.
Added @Test before VCFReaderTest.testHeaderNoRecords()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2809 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 22:55:59 +00:00
chartl 935e76daa1 Minor changes to oneoff walkers. PlinkRod altered but still commented. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2808 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 18:49:56 +00:00
hanna 21369869b7 Extend regex that supports every 'word' character to use any printable character except ':'. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2807 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 03:29:55 +00:00
ebanks 4fe851a83d Optimization: don't keep scoring an alternate consensus if it's already worse than the best alt seen so far. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2806 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 05:06:32 +00:00
ebanks ca1917507f Various improvements and fixes: 
In indel cleaner:

1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.

2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header.  This entailed some reworking of the datasources code.

3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses.  Not done yet.

In UG: fix bug in beagle output for Jared.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 04:21:04 +00:00
depristo 3b1ab86d11 Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-06 16:26:06 +00:00
depristo 995d55da81 now uses the new RMDT getVariantContext() functions instead of doing the work itself. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2802 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-06 16:23:06 +00:00
depristo 33760834d6 commented out inactive (due to string ==) but actually incorrect code. Sometimes two wrongs do make a right 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2801 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-06 16:22:26 +00:00
hanna c7e006a996 Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes 
basic tests for small and large intervals and intervals that cross bin boundaries.  Currently works
only with a single BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2800 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 21:47:54 +00:00
asivache a1d5a384f4 Reverting the last reversal. bestConsensus points to something also kept in a set, so just reassigning it will NOT automatically destroy the underlying data; explicit clearing of unneeded data reinstated. STUPIDO!!! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2796 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 18:08:53 +00:00
asivache cf7e6d0c0b Memory-saving change, same as in old IntervalCleaner (if alt consensus does not beat the best one, destroy its data immediately) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2795 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 18:05:04 +00:00
asivache df0be25afb ooops, no need to destroy old best's data explicitly, it will be done automatically of course 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2794 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 18:03:16 +00:00
asivache 9f44018b7d Reducing memory footprint: if alt consensus does not beat the best alt observed so far, destroy its data immediately, instead of keeping them around. If new alt is better than the old best, then destroy the old best right away instead. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2793 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 17:58:54 +00:00
rpoplin be33d1852c Reverting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2792 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:57:09 +00:00
depristo af8c47fc2f Fixing up testVariantContext for integration tests for variant context. Printing of VCs and genotypes now stable using sorting. Cleaned up comments in quality score by strand. RefMetaDataTracker now directly allows walkers to obtain VariantContexts using the simple Collection<VariantContext> getAllVariantContexts(GenomeLoc curLocation, EnumSet<VariantContext.Type> allowedTypes, boolean requireStartHere, boolean takeFirstOnly) function. VCF and dbSNP VariantContexts now officially supported. Other importan types can be added to the adapator system in refdata package. Integration tests later today 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2791 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:42:54 +00:00
rpoplin 0d8d6e0a14 Ti/Tv module in VariantEval shows known and novel ratios if possible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2790 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:37:40 +00:00
depristo c6d86da4b8 almost managed to move things around perfectly in move go 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 14:18:26 +00:00
depristo e0af3bf761 updating back names 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2786 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 13:53:45 +00:00
depristo 777617b6c7 managed to actually move the files too! Damn you svn 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2785 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 13:47:19 +00:00
depristo 8938a4146d moving varianteval2 to it's own dir 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2784 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 13:37:04 +00:00
depristo 69132c81aa Documentation. Plus nicer structure to adaptors. Intermediate checkin before move into core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2783 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 13:33:27 +00:00
hanna e53432d54d Checkpoint for combining adjacent intervals into the same shard. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2782 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 02:48:02 +00:00
asivache 0d347d662a More plumbing: if after the shift window contains indel(s) at the first position, do not throw an exception, just print the warning (we can not deal with this situation!!) and discard those indels without trying to call them. This situation will most probably arise after forced shift over a messy region anyway. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2781 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 21:06:28 +00:00
depristo 1d86dd7fd1 Interface changes following Matt's advice. VariantContexts are now immutable, and there are special mutable versions, in case you need to change things. AttributedObject now a InferredGeneticContext and package protected. VariantContexts are now named, which makes them easier to use with the rod system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2780 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 20:55:49 +00:00
asivache e7b710791f OK, we finally ran into a messy dataset where we can not find a place to shift the window to: there's an indel at every position. Don't panick, don't throw an exception, just ignore the whole window completely, we do not want to call there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2779 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 19:49:56 +00:00
asivache 152f65b362 Do not die in --cycleOnly mode when the lane is not paired end, just count all single end basequals into the first column and leave the second column filled with 0s 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2778 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 19:48:12 +00:00
asivache a3cd56897d moving older versions of the oneoff project to archive, bye-bye 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2777 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 19:46:27 +00:00
asivache f7e7bcd2ef Oneoff project, totally unrelated to anything 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2776 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 19:44:50 +00:00
hanna 334da80e8b Fixed Mark's bad checkin. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2775 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 12:40:58 +00:00
depristo 1ce0f06216 temp checkin for reorganization 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2774 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 11:10:24 +00:00
ebanks 83b9d63d59 1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files. 
2. Used said mapping to implement N-way-in,N-way-out functionality in the new indel cleaner.  Still needs more testing (to be done after vacation but preliminary tests look good).
3. Fixes to VCF validator: ignore case when testing VCF reference base against true reference base and allow quals of -1 (as per spec).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2773 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 04:12:49 +00:00
rpoplin 210c4c9913 AnalyzeAnnotations now makes plots for the value in the QUAL column as if it were an annotation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2771 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-03 20:33:15 +00:00
hanna 3f35e181d5 Add an alternate implementation of the BAM file reader that keeps the entire index in memory. Initial revision of BAMFileStat, a tool to inspect BAM file BGZF blocks and index entries. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2769 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-03 19:48:15 +00:00
depristo c89ba7b1a4 improvements to variant eval 2. Now has titv calculations and mendelian violation detect support. we only make ~80 mendelian violations in 380K calls for the YRI trio, in case you are interested 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2768 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-03 16:03:19 +00:00
depristo fa2cd432fd better printing in VE2. Added support for TiTv analysis 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2766 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 21:20:29 +00:00
depristo cbbc0e98d2 fix for broken imports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2765 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 15:20:27 +00:00
depristo 681c196097 V2 of VariantEval2. Framework is essentially complete., very simple and clear now compared to VE1. Support for any number of JEXL expressions. dbSNP% evaluation added to show paired comparison evaluation. Pretty printing output tables. Performance is poor but can easily be fixed (see todo notes). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2764 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 14:18:46 +00:00
hanna 9dbdfff786 Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 00:22:15 +00:00
asivache 4ddbaeed07 In attempt to reuse: --pairCountsOutput is now optional, if not specified then only per-locus statistics is collected; --silent - do not echo results into stdout; --minMapQ - count only bases coming from reads mapped with specified quality or better; --blacklistedlanes - do not count reads/bases coming from specific lanes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2761 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 22:05:19 +00:00
chartl 2c4f709f6f Bunch of oneoff stuff that I don't want to lose. Also: 
VCFRecord - "." dbsnp-ID entries now taken into account (thought these were represented as null; but I guess not)
VCFGenotypeRecord - added a replaceFormat option; since intersecting Broad/BC call sets required genotype formats also be intersected (no changing on-the-fly)
VCFCombine - altered doc to instruct user to give complete priority list (was throwing exception if not)




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2760 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 21:35:10 +00:00
asivache 421282cfa3 Convenience method: getMappingFilteredPileup(int minMapQ) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2759 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 21:19:53 +00:00
ebanks 506d39f751 The UG calculations are now driven by an independent engine. 
This completely separates the genotyper walker from other walkers.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2758 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 20:57:31 +00:00
hanna d8e75cf631 Fix for Kiran's memory issue running UG...turned out to be a particularly bad interaction between @By(Reference) traversals and TreeReduce. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2757 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 20:27:06 +00:00
depristo d9671dffba Documentation for VariantContext. Please read it and start using it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2756 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 17:49:51 +00:00
asivache 990af3f76e Will now work with simplest tabular format - genotype string ("+ACTT") does not have to be followed by ':' 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2755 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 15:40:01 +00:00
ebanks e0808e6c37 Moved old EM model to archive 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2754 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 02:55:32 +00:00
rpoplin 64fc76e4bf Added an option to AnalyzeCovariates to set the max value of the histograms to make them easier to directly compare. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2753 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-31 23:13:57 +00:00
ebanks f6da57dc79 1. For Matt: JIRA GSA-270. Other walkers needing to call into the Unified Genotyper now use static methods (e.g. runGenotyper()) instead of calling initialize and map. 
2. Set the default confidence cutoff to 50 (instead of 0).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2752 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-31 21:14:57 +00:00
ebanks ce9d3dcefb Removing deprecated version of indel genotyper (putting it in archive in case we need to reproduce original 1KG indel calls for some reason). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2749 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-31 14:05:36 +00:00
depristo 3d45457595 VariantEval2 test framework implemented; Kiran is experimenting with the system. Not for use by anyone else. VariantContext appears to work well; I'll release it next week for general use following docs of the functions. Removing newvarianteval and other classes to avoid any future confusion. Update to TraverseLoci and RodLocusView to simplify a few functions and to correct some minor errors. All tests pass without modification. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2748 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-30 20:51:24 +00:00
chartl 236764b249 Major (and useful) changes to MultiSampleConcordance: 
1) Now cares about Genotype filtering. If it is flagged as filtered, it can count as a FP/FN/TP; but goes into a "non-confident genotype" bin, rather than het/hom.

2) Can give it a Genotype Confidence flag (-GC) which will automatically filter genotypes in the way above for quality > Q for "-GC Q"

3) Can give it an -assumeRef flag. For sites only in the truth VCF (that don't even appear in the variant VCF), that locus will be treated as confident
   ref calls for all individuals in the variant VCF; and the calculators updated accordingly.

*** Important: Default behavior is that sites unique to the truth VCF are considered no-call sites for the variant. This flag can help get aroudn that;
    however the safest way to run this is to have a variant VCF with calls at each and every locus, if that is possible.

VCFGenotypeRecord -- added an isFiltered() call to automate looking up the FILTERED flag for VCF v3.3

SimpleVCFIntersectWalker - basic outline for a walker I'm working on tonight.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2747 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-30 01:18:31 +00:00
jmaguire ea7e737441 Two new annotations: 
1. LowMQ: fraction of reads at MQ=0 or MQ<=10.
	2. Alignability: annotate SNPs with Heng's (or anyone else's) alignability mask.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2746 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 23:23:00 +00:00
chartl 97f60dbc4b Moving stuff around. ( core;playground ) ----> ( oneoffs ). I've been a bad boy, sullying the core codebase. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2745 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 22:50:03 +00:00
rpoplin 16da5011c0 Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2744 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 21:58:31 +00:00
hanna 668c7da33d Bug fix in custom override of queryOverlapping. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2743 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 21:35:59 +00:00
rpoplin c6cc844e55 Added -name argument to AnalyzeAnnotations that allows one to specify the name of the annotation to be used on the plots. Instead of seeing AB and DP, one can add -name AB,AlleleBalance -name DP,Depth 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2742 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 20:48:53 +00:00
depristo 62a80f2b6f fixed out of date tests. Also, tests uncovered a subtle bug in new implementation that was also fixed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2741 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 20:03:48 +00:00
rpoplin 4f29a1d4f6 AnalyzeAnnotations now plots true positive rate instead of percentage of variants found in the truth set. Committing GCContentCovariate to help people experiment with correcting the pilot3/Kristian base calling error mode in slx. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2740 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 20:01:56 +00:00
aaron ac2a207b0b added a wrapper exception for anything that goes wrong in VCF parsing; this way the problematic file line is emitted, no matter what happens. Makes debugging a lot easier, especially in large files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2739 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 19:58:51 +00:00
hanna e7f5c93fe5 Cleaning up the inheritance hierarchy from the previous commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 19:13:36 +00:00
depristo 88495a39d4 better formating 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2737 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:38:21 +00:00
depristo 1993472b38 Just like VariantFiltration but lets you match info fields out of the VCF instead of annotating them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2736 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:38:03 +00:00
depristo 0a7426c29c Computes SNP density over the genome. Doesn't work with intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2735 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:36:49 +00:00
depristo 9decd20f46 Fix to priors to allow lower het values for mouse guys; no intergration test changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2734 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:36:12 +00:00
chartl d57a86ad41 Not nearly as badass as it looks. The problem I mentioned yesterday with "bleeding in" of samples comes from VCFUtils and SampleUtils looking for all VCF-class RODs in the tracker, and stealing the name from them. I have introduced a new HapmapVCF - type rod for use 
when you want to protect your VCF header from being infected by the samples in a bound hapmap VCF. Changes are as follows:

VCFRecord - minor change to adapt isNovel() to the case where the dbsnp ID field is empty, but the info field has DB=1

HapmapVCFRod - introduced for the reason at the top

RODRecordIterator - was: catch ( Exception e ) { throw new StingException("long ass message") }
                 is now: catch ( Exception e ) { throw new StingException("long ass message",e) }
                    to permit full stack ejaculation.

RodVCF - Now with more brackets!

ReferenceOrderedData - registering HapmapVCF as a bindable string

VariantAnnotator - There's an extra space on a line. And some new brackets.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2733 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:19:50 +00:00
depristo 5aaf4e6434 VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2732 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 12:13:08 +00:00
ebanks 01e73fc39e Yuck - Picard's SAMRecord Comparator only deals with mapped reads. Adding an extended version that works for all reads. 
After adding some more minor changes to the new realigner it now gets the same exact results as the original version - except that sometimes it doesn't clean when it shouldn't!
More testing coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2731 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 07:49:47 +00:00
hanna 3d922a019f Basic support for very simple index-driven locus traversals. Interface has been changed to 
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 03:14:26 +00:00
asivache 4810e9c9cd And now the DOCS! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2729 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 23:21:33 +00:00
asivache 40262e2070 Now calls single-sample indels too, with all the V2 level stats and bells. This officialy obsoletes IndelGenotyperWalker (V1). In addition, the alignments spanning beyond the contig end are now completely ignored (with a user warning), this applies to both single-sample and paired (somatic) calls. You just wait, Eric, I'll get you the docs with the next commit! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2728 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 22:28:02 +00:00
rpoplin 79c4cc1db7 AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2726 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 21:41:23 +00:00
chartl 7a10c40fb3 Much clearer (and, like, not totally incorrect) implementation of isNovel 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2725 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 21:16:21 +00:00
chartl 8de6a8d246 Lots of changes; all to do something relatively minor. 
1) Changed VCF/RodVCF to allow for inquiries to whether or not the site is novel; isNovel() looks at the ID field, and those members of the info field that indicate membership in dbsnp, hapmap2, or hapmap3; and if none can be found, returns true.

2) Changed VariantAnnotator to annotate hapmap2 and hapmap3, if you bind rods to it with those names. Works in the same way as DBSNP does -- if you give it a rod named "hapmap2" it'll annotate membership in it. -- Passes integration tests

3) Changed UnifiedGenotyper to do the same thing (since it uses Annotations as a subroutine) -- Passes integration tests

4) Changed MultiSampleConcordanceWalker to take a flag --ignoreKnownSites (or -novels) to examine concordance only on sites that are not marked as in dbSNP or in Hapmap in the variant VCF

5) Changed VCFConcordanceCalculator (the object MultiSampleConcordanceWalker runs on) to output Concordant_Het_Calls and Concordant_Hom_Calls separately, rather than combined as Concordant_Calls

6) AlleleBalanceHistogramWalker -- I don't know what i did to this thing. I've been jerry rigging System.outs to do stuff it was never really intended to do; so there's probably some dumb System.out.print("HI I AM AT LOCUS:"+loc) stuck somewhere. It compiles at any rate.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2724 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 21:06:56 +00:00
ebanks 6f11fe442a Sync with Andrey's changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2723 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 20:49:38 +00:00
asivache db429e1096 Some alt consenses may have cigar string starting with an insertion. Not a bug, strictly speaking, since the cleaner had been detecting this and crashing deliberately. Now it knows how to deal with this special case though. Also, uppercase the ref before using it in SW aligner! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2722 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 18:53:02 +00:00
depristo 956b570c8e 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
 2010-01-28 18:37:17 +00:00
depristo 9876645a5d Now drives the walker by reference, not by reads, so we see even loci with no reads. This allows us to accurately calculate the true total callable area 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2720 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 11:12:46 +00:00
ebanks 1dd9996f3a 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
 2010-01-28 04:17:20 +00:00
depristo f6bca7873c V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 04:10:16 +00:00
chartl 23fc9737b4 Added the ability to filter out variant (not truth) calls based on read depth. Using -NLD 5 will not update concordant counts for calls with 0, 1, 2, 3, or 4 reads supporting them. Not to be used with VCF files that do not have DP in the format field. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2716 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 23:28:04 +00:00
chartl 1b9184a1c7 Added a multisample concordance walker which takes the place of the VCF python library I've been using. Takes a truth VCF and a variant VCF and outputs A TSV that looks like this: 
Sample_ID       Concordant_Refs Concordant_Vars Homs_called_het Het_called_homs False_Positives False_Negatives_Due_To_Ref_Call False_Negatives_Due_To_No_Call
NA19381 491     294     2       0       0       0       1
NA19451 489     298     1       0       0       0       0
NA19463 486     289     2       3       1       4       3
NA19376 488     296     1       0       2       0       1
NA19317 489     284     5       3       3       3       1


This walker will be merged with GenotypeConcordance once it's clear how to do so. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2715 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 22:59:17 +00:00
asivache bd11060e72 Ups, I did it again. Fixing the bug introduced in a previous commit: use correct length of the indel event. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2713 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 21:51:54 +00:00
ebanks fddca032bb Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris) 
Cleaned up SW code and started moving over everything to use byte[] instead of String or char[].

Added a wrapper class for SAMFileWriter that allows for adding reads out of order.

Not even close to done, but I need to commit now to sync up with Andrey.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 21:36:42 +00:00
rpoplin b8ae083d1b AnalyzeAnnotations creates a plot of dbsnp rate as a function of the annotations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2711 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 21:08:33 +00:00
rpoplin 3999a8d2c8 IntelliJ no longer complains that my methods are too complex to analyze. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2708 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 20:12:13 +00:00
rpoplin fc4285f9fd AnalyzeAnnotations seems to be popular so I've rewritten the guts to be easier to extend and maintain. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2707 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 19:30:31 +00:00
hanna fa3589e5c5 Update our error messages to point to getsatisfaction.com/gsa. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2706 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 19:16:28 +00:00
depristo 3399ad9691 Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 17:19:37 +00:00
asivache 3edcefb7fb add _gI and _gD to the indel probe names according to the spec (in the hope that wiki is not obsolete); added optional cmd line param -project_id to prefix all probe names with. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2704 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 17:06:49 +00:00
chartl ed9b7edee3 Changed " to ' to stop the 
[javadoc] /humgen/gsa-scr1/chartl/sting/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java:99: warning: unmappable character for encoding ASCII
  [javadoc]      *   if one of the alleles is deleted (?-?).

warnings on compile.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2703 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 15:23:55 +00:00
depristo 40c242d2b8 Fix for overflow issues 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2702 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 13:37:16 +00:00
aaron 8453676b71 added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine. 
Also deleted the FixBamSortOrder package that isn't used anymore.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2701 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 05:17:01 +00:00
rpoplin 4bcdab580c --output_dir has been changed to --output_prefix to give the user more control over the names of the resulting mass of files in AnalyzeAnnotations. The fontsize of the axes is increased. Cumulative filtering plots are removed since the binned filtering plots are much more useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2700 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 04:50:54 +00:00
chartl df112e64b8 Minor tweaks 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2699 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 04:17:47 +00:00
ebanks 476d6f3076 RealignerTargetCreator is officially live 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 03:41:52 +00:00
asivache 1f64c5d41a Do not slurp the whole set of snp mask sites into memory (gets pretty heavy on full dbSNP!); instantiate a privare ROD iterator instead and drag it across the sites we are designing probes for. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2694 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 22:39:46 +00:00
ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. 
- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 21:56:33 +00:00
chartl 2c8d7b0c44 Forgot the onTraversalDone. That was dumb. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2692 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 21:02:46 +00:00
chartl 04e1832968 Added - AlleleBalanceHistogramWalker -- hopefully this'll be able to tell us very clearly whether bad genotype concordance is a result of systematic contamination (consistent wonky allele balances) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2691 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 20:57:12 +00:00
rpoplin a1054efe8a Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 18:47:40 +00:00
rpoplin 0345d9f6a5 Updating the recalibrator to use non-depricated getPileup() method. Adding documentation to AnalyzeAnnotations so that the walker isn't marked as unclean at compile time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2688 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 14:15:09 +00:00
depristo c231547204 Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 13:53:29 +00:00
aaron 2e57bc7879 added a better message for the SO flag error in MergingSAMIterator2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2685 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 22:57:18 +00:00
rpoplin 24d4082925 AnalyzeAnnotations can now process only variants that are found in samples that match the -sampleName argument. X-axis of plots no longer use annoying scientific notation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2684 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 20:52:11 +00:00
hanna 022601b1a5 Warnings for walkers w/o Javadoc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 20:34:50 +00:00
rpoplin 894a2b511b Fixing no platform warning message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2682 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 19:46:50 +00:00
rpoplin 2b51cf18f0 AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2681 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 19:39:18 +00:00
asivache 6cf413e630 Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2680 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 19:23:44 +00:00
ebanks dc170caafc Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2678 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 17:27:12 +00:00
rpoplin 5d2f8aaa54 Updating recalibrator version number after the several emergency changes last week. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2677 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-25 14:35:47 +00:00
jmaguire 588417e17d Don't reference that optimiation library I'm not using anyway. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2676 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-24 20:30:50 +00:00
jmaguire d3e3c1c2e0 don't require that optmization lib that I'm not using yet... (doh) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2675 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-24 20:28:21 +00:00
jmaguire 1d6d2b26f7 tools for optimizing calls. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2674 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-24 20:16:55 +00:00
jmaguire 877957761f lots of new stuff, some generally useful, some one-off. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2673 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-24 19:50:48 +00:00
ebanks 78890c0bee First version of walker that combines the functionality of IndelIntervalWalker, MismatchIntervalWalker, SNPClusterWalker, and IntervalMergerWalker - plus it allows the user to input rods containing known indels (e.g. dbSNP or 1KG calls) for automatic cleaning. Basically, all pre-processing steps for cleaning are now done in a single pass. 
More testing needed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2672 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-24 05:32:38 +00:00
chartl d6b9b788a8 Renamed -- PlinkRodWithGenomeLoc --> PlinkRod 
Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 18:19:28 +00:00
chartl ae22d35212 PlinkRod now correctly parses binary files without indels; unit test added for this behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 17:34:06 +00:00
chartl 94dc09c865 PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files. 
Upcoming: Test that the instantiation is correct, do it for indel-containing files.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 16:13:24 +00:00
chartl 01db93299c PlinkRodWithGenomeLoc now properly handels indels. 
There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 07:34:52 +00:00
chartl 42fb85e7f3 PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 06:19:26 +00:00
depristo c871a0f221 UG map() now returns a VariantCallContext object. Also has a field for confidentlyCalledBases. UG reduce() emits statistics on the confident called % of bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2664 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 23:06:43 +00:00
chartl fbf82526cb Minor renamign changes. 
PlinkRodWithGenomeLoc now supports .bed file parsing (and doesn't require |c#_p# conventions for SNPs -- still requires _g[I/D] for indels)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2663 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 23:06:32 +00:00
rpoplin fd223e955c Reverting the previous solid change. We now refuse to recalibrate if the solid read doesn't contain proper color space information. The exception message has been updated to say this. Also, Tile has been downgraded to an ExperimentalCovariate due to performance issues. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2662 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 20:55:28 +00:00
rpoplin 7732f98e56 Fix for Solid reads that have '.' in their color space field. The recalibrator will just set them to be illumina reads and won't apply color space correction. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2661 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 20:09:16 +00:00
aaron 2ea768d902 ant clean is your friend....fixed test code dependent on an interface change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 20:07:46 +00:00
rpoplin a11503819a AnalyzeAnnotations now breaks out its TiTv plots into novel SNPs, dbSNP sites, and combined. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2659 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 19:00:23 +00:00
aaron cc3b818268 cleanup of the pile-up limit exceeded warning, and a little code cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2657 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 22:17:24 +00:00
ebanks c1e09efb23 - Fixed output for beagle header 
- Better description for QualByDepth annotation



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 21:25:56 +00:00
rpoplin d9df72e1b5 AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2654 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 21:15:11 +00:00
chartl f51cffe220 Alteration of PlinkToVCF to be much more flexible about parsing .ped file headers, which can have one of a number of different standard fields, and be in different orders. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2650 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 18:02:28 +00:00
chartl 5b2a1e483e Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 17:35:20 +00:00
asivache 74779a9a78 First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2648 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 15:28:20 +00:00
hanna d25a2fe120 Better handling of enums by the command-line argument system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2647 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 21:36:46 +00:00
ebanks 9c7b281b4f Set default value for max_coverage to be 100K (since 10K is too small). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 20:15:25 +00:00
hanna 1e9fe2a334 Clean up error output when enums have missing arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2645 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 19:48:26 +00:00
aaron 8d1d37302c a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 19:36:49 +00:00
hanna 908d399670 Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2643 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 19:18:19 +00:00
chartl ab289872e4 Changes: 
- Annotations return null when given pileups with no second-base information

- SequenomRodWithGenomeLoc -- beter handling of indels

Eric; I made two small changes to the new Genotype interface that we should talk about (they basically have to do with allele/genotype representation):

Allele - added a new UNKNOWN_POINT_MUTATION to AlleleType. If I see a sequenom genotype AG; one's got to be ref, one's got to be SNP, but until I have
         an actual reference base in hand, I don't know which is which. That's what this entry is for.

Genotype - added an enum class StandardAttributes for dealing with things like deletion/inversion length. This is probably not the way we want to
         represent indels, so we should talk about this. Plus now that there's a direct link between my ROD and the genotype; when we do decide
         how to deal with indels, we'll be forced to alter the SequenomRodWithGenomeLoc accordingly.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2642 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 16:45:17 +00:00
aaron a1b4cc4baf changes to intelligently log overflowing locus pile-ups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 08:09:48 +00:00
ebanks 4ac9eb7cb2 - Smarter strand bias calculation 
- Better debug/verbose printing



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 03:01:26 +00:00
depristo ff66023d83 Trivial change to support filter field in VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2636 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 22:56:22 +00:00
asivache 4625261d79 Bug fix: alignments ending with 'I' were not counted into the overall coverage which resulted in inaccurate stats, and in rare occasions outright messed up ones. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2635 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 22:12:16 +00:00
hanna 8dafd26100 Print out the current version number in the application header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2633 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:58:36 +00:00
depristo 9e0ae993c7 -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:33:13 +00:00
rpoplin c98df0a862 Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:18:02 +00:00
chartl 53352e1bb4 First pass at a sequenom ROD. Nothing uses it; currently undergoing testing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2629 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 17:09:36 +00:00
hanna 1488578617 Working with Aaron to get svnversion running within the build system. This change will break the build. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2628 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 16:55:42 +00:00
rpoplin bca436578f Added the -maxQ argument to the list of arguments in the PG tag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2627 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 15:55:23 +00:00
rpoplin d61cafd19f Make the formatting of the list of args in the PG tag consistent. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2626 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 15:31:37 +00:00
rpoplin a12465b6d5 The recalFile argument is no longer added into the PG tag of a bam produced by TableRecalibration. Based on a request from the Sanger. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2625 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 15:25:57 +00:00
rpoplin ba19afd529 Draft version of AnalyzeAnnotations which creates plots of cumulative TiTv ratio versus filter value per each annotation in the input VCF rod. Minor cleanup of recalibration walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2623 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-18 20:47:10 +00:00
kiran ff6877a15e Added a forgotten column label 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2622 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-18 01:00:52 +00:00
kiran dd6d5aadf9 Computes empirical confusion matrices, optionally with up to five bases of preceding context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2621 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-18 00:55:12 +00:00
ebanks 12453fa163 Misc cleanup of UG args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-17 04:38:52 +00:00
ebanks b8cdf64c20 Better descriptions for max reads/downsampling args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2618 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-17 02:30:27 +00:00
depristo 64225b28fd Convenience methods for getting the VCFReader and VCFRecord 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2614 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:22:31 +00:00
depristo d0af7f6c7b Now analyzes filtered SNP like all, novel subsets; support for selecting a single sample to analyze from a multi-sample VCF, support for trivial selection of records with INFO field key/value pair. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2613 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:22:04 +00:00
depristo 8ae8e120f8 New annotateUnion operation -- provides clearer annotations on where a call came from when unioning two VCF call sets 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2612 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:20:37 +00:00
depristo 41392f8ff5 functions for setting gentoype records and alternate bases; function for getting all rods implementing VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2611 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:19:43 +00:00
hanna ac4756db20 Add the svn version on the fly to the version number properties. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2607 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 00:28:01 +00:00
hanna 420cef4094 Added version numbers to the help doclet extractor. Since the help system is behaving 
more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 23:31:29 +00:00
rpoplin 4de7d6a59b Initial checkin of skeleton code for AnalyzeAnnotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2605 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:52:34 +00:00
hanna 930082314a Put a major.minor version into the GATK Javadoc for reading. Also, 
update some straggler packages to the new package-info.java format introduced in 1.5.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2604 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:48:30 +00:00
mmelgar 3063224446 SecondaryBaseTransitionTableWalker now breaks by genotype and read group, is javadoc annotated, and is compatible with ReadBackedPileup's methods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2603 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:43:39 +00:00
asivache 7a991421f7 -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2601 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:11:14 +00:00
asivache c8c5c176cd -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2600 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:07:49 +00:00
asivache a12933a26d Bug fixed: now the length of an insertion is determined correctly. Thought I committed this... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2599 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 20:58:48 +00:00
asivache 404b95183f This is a LocusWalker, not a RodWalker (thanks Mark!!). RodWalkers currently are not capable of attaching alignment contexts (reads) to the ROD-annotated loci they traverse over... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 20:33:41 +00:00
rpoplin 7078219b89 Updating outdated comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2595 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 19:17:52 +00:00
rpoplin ba2acda406 Clarifying the comment regarding differentiating between first and second of pair in CycleCovariate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2594 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:36:14 +00:00
ebanks b911b7df82 Fixing the AC annotation to be in line with the VCF spec 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:28:52 +00:00
rpoplin f2e539c52f As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:18:59 +00:00
asivache eae1b73945 Fixed a bug in left-adjusting the indels introduced in previous commit :-/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2591 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 17:41:23 +00:00
rpoplin df998041a8 Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 16:31:25 +00:00
rpoplin 70df30fc1b Added method to AlignmentUtils which takes a read's cigar and the refBases char array given to a ReadWalker and returns the aligned reference char array. Bug fix in solid_recal_modes to use this aligned reference array. Recalibrator version number is no longer separate for each of the two walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2589 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 15:36:59 +00:00
ebanks 2a116bb5d6 Made the VCF validator a simple rod walker instead of having it be in a separate package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2588 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 06:39:06 +00:00
hanna b19bb19f3d First successful test of new sharding system prototype. Can traverse over reads from a single 
BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 03:35:55 +00:00
aaron db9570ae29 Looks bigger than it is: 
* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations.  You can now specify:

"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 00:14:35 +00:00
kiran 04fdbbfa65 This is the beginning of a new version of VariantEval that can cut VCF files up in a variety of ways with JEXL expressions, select one sample out of a multi-sample VCF, and can load analysis modules dynamically. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2584 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:45:58 +00:00
asivache df63f51253 No changes, just sync-ing; only some commented out debugging prints are added... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2583 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:45:15 +00:00
asivache d85461c463 MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2582 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:43:36 +00:00
asivache c0891d512f added: peekNextLocation(); it's quite hard (and probably unnecessary, ever) to make seekable iterator a peekable one, but it is quite easy and useful to be able to peek just the next location the iterator will jump to after next call to next() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2581 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:38:19 +00:00
ebanks a082b948a3 Support throughout for S and N cigar elements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2579 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 03:45:42 +00:00
chartl 424d1b57f7 Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 23:22:37 +00:00
rpoplin 49c44e7b36 PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 20:09:10 +00:00
hanna 05575e2e56 Better bounding for the locus window. Don't make the locus window calculation blow up if the GenomeLoc ends 
up being outside the reference.  Force the blowup elsewhere.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2573 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 17:03:54 +00:00
ebanks 8ca5bba738 We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test). 
SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:40:27 +00:00
chartl 6d1107a4ed Update to SequenomToVCF 
Output changing slightly so integration test disabled temporarily



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:32:05 +00:00
ebanks f99586f91b Added integration test for beagle and verbose output in UG. 
Minor cleanup of VCFRecord code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 03:55:24 +00:00
hanna 02e23e2d9c Threading support for beagle output files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2569 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 02:42:16 +00:00
aaron 0513690416 two fixes in the new cached DbSNP code: 
-isBiallelic would incorrectly say triallelic sites are biallelic.
-getAlternateAlleleList was broken, since the new cached list is immutable, we couldn’t remove list items.

Also added a dbSNP validating walker to the one-offs, for testing the new b37 130 dbSNP rod.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2568 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 00:27:34 +00:00
asivache a138bad95a A rare but not-so-subtle bug fixed: a funky alignment (a kind that should not have been generated in the first place) could make the indel left-adjusting method to overshoot read start and build a cigar like -3M6I... 
also, few minor fix-ups.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2567 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 21:29:50 +00:00
rpoplin b51f4aae11 Updating the recalibrator to make use of StingSAMFileWriter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2566 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 20:58:27 +00:00
rpoplin c8ad025ad0 cleaning up unused import statements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2565 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:52:37 +00:00
rpoplin 189829841b The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:50:39 +00:00
aaron 16777e3875 more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:47:43 +00:00
hanna 35a4fcc481 Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2562 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:39:41 +00:00
ebanks 03b7d5f5c7 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. 
2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly).  Untested so they're still experimental.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:33:53 +00:00
hanna 58999a8e9d Enhance the I/O management system to support custom headers and set the presorted flag 
from the initialize() method (or at any time before the first SAM record is written).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2560 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:21:42 +00:00
aaron 3c5f5177b1 check to see if the parsed interval list is empty, since we now allow interval files that are empty. If so, make sure we default to a non-interval based traversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2559 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 17:52:27 +00:00
ebanks 040fdfee61 Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter. 
I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 21:42:12 +00:00
ebanks 42aff1d2c3 Annotator in general should be able to annotate monomorphic or tri-allelic sites. 
It's up to the individual annotations to decide whether they want to annotate or not.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 19:52:18 +00:00
rpoplin 11f91b3c95 Reverting Eric's previous change because it killed the PG tag in the output bam file header. Added a new -compress command line argument to set the compression level of the output bam file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2555 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 19:02:56 +00:00
chartl dfa3c3b875 Added: 
SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.

Modified:

VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call

Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 17:17:21 +00:00
rpoplin 62dd2fa5be Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 14:28:52 +00:00
ebanks 971834ca90 Added a walker to the vcf tools compilation: one that combines vcf records. Both merges and unions are supported (see documentation... when it gets written this week). 
Also, moved some code that pulls samples out of rods from VCFUtils into SampleUtils.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2552 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-10 06:45:11 +00:00
ebanks 80af0f2f54 Changed the OUTPUT_BAM_FILE argument from String to SAMFileWriter and removed the call to close(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2551 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-10 03:45:54 +00:00
hanna 7893aaefe9 Updates to chunk iteration. Includes the return of the dreaded *2.java files; 
hopefully I can find a way to kill these off before the Picard patch is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2550 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 20:20:56 +00:00
ebanks fcce77c245 Added -beagle option to emit likelihoods file for use with the BEAGLE imputation engine; still experimental. 
(Also converted getPileup -> getBasePileup)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2549 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 18:41:04 +00:00
rpoplin 9cbae53ee1 Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2548 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 15:19:22 +00:00
ebanks d5ab002449 Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 06:02:01 +00:00
ebanks b468369dfa -UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one) 
-MQ0 annotation is now standard again
-Added AC and AN annotations to VCF output



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 05:40:42 +00:00
rpoplin f587ff46af Tile is now a standard covariate. By default the TileCovariate returns -1 if tile can't be derived from the read's name. Added a new command line option -throwTileException which will force TileCovariate to throw an exception if tile can't be derived for a read. Singleton covariates, such as any read group without tile info, must be skipped over in TableRecalibration so that the sequential formulation doesn't apply the same correction more than once. TileCovariate class has been added to the Early Access package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2544 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 22:51:41 +00:00
asivache d01bde36a4 Make sure that reference view holds enough bases to pass full-length deleted sequence to the walker's map() function in extended event mode (this addresses the problem of a deletion crossing the shard's boundary, so that an attempt to extract deleted bases results in a crash) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2543 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 22:37:22 +00:00
asivache e9bc85c188 Now has methods that allow to 1) check if a location is within the bounds of the reference view; 2) expand reference view (i.e. expand the bounds and reload the reference sequence) in order to accomodate specified location. The second method can be called directly since it performs a check and if the location is already within the bounds, then returns immediately. The costly ref sequence reloading occurs only when the location is not fully contained within the current bounds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2542 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 22:35:17 +00:00
asivache 7f91b4d824 Bug fix. It would be nice if we could extract ROD annotations for the whole length of an extended event (indel), and we tried... But alas, it does not work with the current ROD system (after extracting length on ref > 1 ROD data for a deletion, rod iterator crashes on the attempt to re-load annotations for next reference base) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2541 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 21:30:55 +00:00
rpoplin 5f58492401 A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 21:17:39 +00:00
ebanks c7a8dffa89 Check for division by 0 in annotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2539 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 19:27:15 +00:00
ebanks 9a658e6b18 -Fixed VCF header line bug 
-Added useful trim() method for Strings for characters other than whitespace


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2538 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 17:51:41 +00:00
ebanks b643a513bb Minor interface change for VCFGenotypeRecord. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 16:48:09 +00:00
andrewk 431e9c2c8b Add dbSNP ID to VCF output records 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 15:30:04 +00:00
depristo 076481f786 Fixes to mergeVCF -- now correctly supports merging of filter fields. Also removed incorrect hasFilteringCodes() function. Updated intergration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2535 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 14:50:13 +00:00
rpoplin cea544871d Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 13:50:30 +00:00
ebanks 6c739e30e0 1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease. 
2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext.  This is by no means complete - further updates coming tomorrow.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 05:51:10 +00:00
depristo a9245a58e2 Fix for incorrect exception throwing in VCFRecord. It is reasonable to ask for the non-ref allele freq at all ref sites. Was only passing in tests because isReference was broken 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2532 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 01:18:30 +00:00
depristo 7215526810 Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2531 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 00:03:29 +00:00
andrewk 6c4ac9e663 Updated HapMap2VCF to use the VCFGenotypeWriterAdapter interface; fixed bug in VCFParameters that affects VariantsToVCF and HapMap2VCF when reference is lower-cased; added integration test for HapMap2VCF that checks for the lower-case issue by testing against Hg18 region that has lower-cased bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 21:27:11 +00:00
aaron 576594eda2 clean-up of the GATK paper genotyper, and better output formatting for the simple call format we emit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2529 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 20:54:56 +00:00
chartl 7e3e714d3c Moving experimental annotations from core to oneoffs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2528 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 19:34:10 +00:00
chartl a32245f7d2 Modifications: 
QualityUtils - Stole the BaseUtils code for flipping reads around and applied it to quality scores
SecondBaseSkew - Nothing's really different, just a commented line

Additions (experimental annotations for future development of second-base annotation)
** I DO NOT INTEND FOR ANYONE TO USE THESE **
- ProportionOfNonrefBasesSupportingSNP
- ProportionOfSNPSecondBasesSupportingRef
- ProportionOfRefSecondBasesSupportingSNP
  + I hope these are self-explanatory
- QualityAdjustedSecondBaseLod
  + Adjust lod-score by 10*log10[P[second bases are as observed]]

Added walker:

QualityScoreByStrand - oneoff project that's being saved if i ever need it



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2527 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 19:18:07 +00:00
asivache eb899741e1 reverting last changes. no cacheing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2526 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 18:59:37 +00:00
asivache a17d725c35 Cache pileup bases and mapping quals after first call to getBases() and getMappingQuals(), respectively. Subsequent calls to these method will return cached arrays. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2525 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 18:05:00 +00:00
ebanks d6fb19bb67 Don't hard-code base qual max 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2524 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 17:21:44 +00:00
rpoplin 75809100c6 Use inheritance so that shared code isn't duplicated between the RecalDatums 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2523 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 16:45:16 +00:00
ebanks fdd14e1a01 Proposed interface for VariantContext. It's currently an interface so it doesn't break the build... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2521 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 16:31:39 +00:00
rpoplin e011a1b6f8 Cut the memory footprint of the RecalDatum in half to improve performance of CountCovariates when run with many covariates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2520 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 16:12:27 +00:00
rpoplin 370a365147 Small runtime improvement in TableRecalibration. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2519 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:51:12 +00:00
ebanks b745c2f8d7 Fix for Jared: don't blow up if there are no samples in the input (since that's allowed) - but warn the user just in case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2518 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:37:06 +00:00
depristo 1e462419da trivial code restructuing, and commented out failed attempt to support sample selection with VCF. VariantEval2 go go go 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2516 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:04:27 +00:00
depristo f857159343 useful convenience function to get a genotype associated with a particular sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2515 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:03:07 +00:00
depristo 34519b3e3b Better printing support for false positives and false negatives in concordance tables 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2514 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:02:40 +00:00
depristo 592749a7c1 isNBase method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:01:51 +00:00
depristo 5ce11c3dad toString method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2512 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:01:20 +00:00
rpoplin 1c90e6a954 More informative error message in AnalyzeCovariates and cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2511 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 14:56:29 +00:00
depristo bca3d1b943 useful convenience function to get a genotype associated with a particular sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2510 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 14:53:56 +00:00
depristo ec774f62be Some checking to protect the BasicGenotype 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2509 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 14:53:24 +00:00
rpoplin 71ecbe75d7 AnalyzeCovariates would crash with 'too many open files' exception when spawning Rscript jobs for every read group at once. It now waits for some to finish before spawning the rest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2508 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 14:19:02 +00:00
depristo 21a50eedb5 Simple extension to VariantEval: --includeFilteredRecords will now keep filtered VCF records so you can see what the entire call set looks like. Looking forward to VariantEval v2 from Kiran. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2506 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 12:59:09 +00:00
depristo 8d13597a27 Temporary command-line support to enable rod walkers, if you know what you are doing this is safe. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 12:15:36 +00:00
ebanks d8351cb9fc Give Annotations access to rod data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2504 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-05 18:53:01 +00:00
ebanks 8b087305f3 Added back the MQ0 annotation - however, it's not yet standard (since mq0 reads are filtered out by default in the genotyper). But it'll work when using the Annotator as a standalone. 
While I'm at it, change getPileup to getBasePileup to remove all of the deprecation warnings.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2502 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-05 17:07:19 +00:00
hanna a4b69d0adf Misc bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2501 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-05 14:48:19 +00:00
depristo c209ba55aa More informative error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2499 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-05 13:55:20 +00:00
rpoplin 0a6bd5a270 CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 20:52:15 +00:00
ebanks ed2fff13aa -Misc improvements to VCF code 
-Small fix to callset concordance


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2497 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 02:28:47 +00:00
hanna 29c129aced Added very primitive read fishing walker with lots of hard coding. Fixed 
bugs encountered when testing read fishing in Ecoli.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2496 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 00:54:57 +00:00
ebanks 7b702b086f You don't need to be bi-allelic to have a non-ref alt allele frequnecy, but you do have to be a variant. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2495 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-03 22:02:39 +00:00
ebanks b668d32cf1 Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-03 21:31:04 +00:00
hanna b6ecc9e151 Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out 
and the data backing it up deleted without my knowledge.  Unfortunately, since the data was deleted, I had
to regenerate the data and a new md5.  Hopefully the aligner output is still correct.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-02 20:19:14 +00:00
asivache 46362ce532 In extended event lines, now prints deletions in verbose format as well (e.g. "-AAT") 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2490 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:57:20 +00:00
asivache a18e31f5b8 If alignment context at the locus holds extended event, get rod metadata and (importantly) reference bases for the whole span of the event (if it is a deletion that is, insertions still have length 0 on the ref!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2489 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:56:25 +00:00
asivache a41cb0701b Now can generate verbose String representation of deletions (e.g. "-AAT") if reference bases are provided as an argument to getEventStringWithCounts(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2488 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:54:50 +00:00
asivache 89791d730e Compute and cache the length of the longest deletion observed at the site; ReadBackedExtendedEventPileup now has a getter to access that value. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2487 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:19:39 +00:00
asivache 8932e67325 Removed sanity check that required GenomeLoc argument to be strictly 1-base long. We need to relax this in order to be able to pass around a reference context containing full-length chunk of deleted reference bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2485 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 20:14:08 +00:00
hanna 497ae700c4 A rethink of the existing BAM block extraction code: rather than working in 
chunk space directly, stream data in block space, converting to chunk space
on demand.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2484 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 18:19:51 +00:00
rpoplin 80658fd99e AnalyzeCovariates gets the same performance improvements as the recalibrator. NHashMap class is removed completely. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2483 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 18:10:10 +00:00
rpoplin 9b2733a54a Misc clean up in the recalibrator related to the nested hash map implementation. CountCovariates no longer creates the full flattened set of keys and iterates over them. The output csv file is in sorted order by default now but there is a new option -unsorted which can be used to save a little bit of run time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2482 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 16:58:04 +00:00
asivache c928347c0c Extended event pileups are more verbose now: following a sequence of 'D','I', and '.' symbols, actual distinct events are listed along with their counts (example: +AAA:3,+AAC:1 for the total of 4 indel observations with 3 reads showing +AAA and one read showing +AAC) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2480 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 22:44:18 +00:00
asivache 8330058216 method added: getEventStringsWithCounts() 
Returns list of Pairs <String,Integer>, where each pair consists of a unique indel event observed at the site and the total number of observations of that event. String representation for insertions is verbose (e.g. +ACT), while deletions are represented as "5D" (since read backed pileup has no reference information, so we can not get actual sequence of deleted bases)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2479 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 22:41:58 +00:00
asivache cf3e59eb4a back to archive 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2478 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 22:00:38 +00:00
asivache 295d16572e synch; will go back to archive in a sec 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2477 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 22:00:03 +00:00
asivache e286313b67 Fix for reads that have insertion as their last (mapped) cigar elements (i.e. not followed by M) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2476 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 21:13:16 +00:00
hanna 05deb8796b Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2475 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 21:06:20 +00:00
rpoplin 96c4929b3c Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 21:01:32 +00:00
asivache bfd6bf9ec5 PileupWalker just got a new option: --showIndelPileups. When this option is used, two lines are printed for every genomic location that has indels associated with it: first line is a conventional base pileup, the second line is an "extended event" (indel) pileup. The refence base in that second line is always set to "E" (for Extended), and the pileup string contains I,D,. symbols for insertion, deletion, noevent, respectively. Only this simple short format for indel pileups is implemented so far. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2472 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 20:16:34 +00:00
asivache 9652692019 Modified to enable locus traversals firing additional calls to walker's map() with alignment context filled with extended events (indels). Walker should override generateExtendedEvents() to return true, and it should make sure that it catches those additional indel pileups and processes them differently, as needed. If there are indels associated with a specific reference base, TWO map() calls will be issued in locus traversal at that location: first one will have a context filled with a regular base pileup, the second call will provide the context filled with indel pileup (pileup elements will have insertion, deletion, or noevent type associated with them and will also carry information about the full length of the event and inserted bases). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2471 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 20:13:25 +00:00
asivache 06eb576924 Can now be constructed with either base pileup or extended event (indel) pileup; has query methods checking what kind of pileup is served by the context, and getter methods return the appropriate pileup. TODO: while it is impossible right now to create a context that contains both types of pileups simultaneously, this restriction is only weakly enforced through the lack of appropriate constructor. Either we keep it this way, or some getters may become ambiguous and have to be fixed! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2470 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 20:07:29 +00:00
asivache f445745c56 Pileup element and corresponding container class tweaked for representing pileups of extended events (indels) at a given locus. There's some redundancy with PileupElement and ReadBackedPileup (should we rename them to BasePileupElement and ReadBackedBasePileup?), so that abstracting a basic interface/abstract base from these classes can be considered in the future 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2469 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 20:03:39 +00:00
depristo 87e863b48d Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2468 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 19:46:29 +00:00
depristo 29f94119d1 Fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2466 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 18:08:41 +00:00
ebanks 5fdf17fccb Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 17:30:47 +00:00
hanna e32174fbc4 UnifiedGenotyper now works without -varout or -vf set. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2464 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 16:46:24 +00:00
hanna b125571a98 Intermediate check in: transfer responsibility of wrapping the GenotypeWriter around the output stream to the output 
management code.  Currently, will not work when neither -varout nor -vf are specified, but should work in all other
cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2463 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 16:11:11 +00:00
ebanks aeb34758e6 Adding a validation stringency to the VCF writers (which defaults to STRICT). If set to SILENT, it will not throw an exception for (reasonable) off-spec requests but will instead ignore such requests and silently move on. 
This change allows the pooled calculation model to work correctly with multiple threads.  Boys, the Genotyper is now officially parallelized.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2462 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 15:33:53 +00:00
rpoplin 29a3d9b47a AnalyzeCovariates also has to skip over NO_DINUC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2461 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 14:36:05 +00:00
depristo fcc80e8632 Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:56:49 +00:00
hanna d4ee999ef9 Creates files supplemental to the reference sequence, consumed by BWA. 
ANN - Alternate form of the sequence dictionary.  Should be created from a sequence dictionary with full contig names.
AMB - A map of 'holes' in the genome, aka runs of non-ACGTacgt bases.  This skeletal implementation always reports no
      holes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2455 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 21:40:44 +00:00
rpoplin fcc52fbcd1 Fixed the build. Added missing import line. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2454 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 21:26:00 +00:00
ebanks 893c9c85fa Added previous optimization to diploid (non-pool) model and shaved off 20% of runtime from it. Moved out some common functionality to joint estimate parent class. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2453 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 21:20:48 +00:00
rpoplin 92e3682991 Moved NHashMap to sting/utils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2452 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 20:57:32 +00:00
rpoplin 562db45fa5 Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 20:19:37 +00:00
asivache 2a704e83df Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2450 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 19:52:44 +00:00
ebanks c8d0e6e004 Optimization to pooled calculation model: stop calculating P(D|AF) if we are beyond the max likelihood such that subsequent likelihoods won't factor into the confidence score. Also, use new Pileup interface. 
Pooled calling now takes less than half the time it used to.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2449 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 18:39:55 +00:00
ebanks b1ac4b81d5 Optimization: look up diploid genotypes from a static matrix instead of creating them on the fly (with String.format); bases no longer need to be ordered appropriately 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2448 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 17:28:51 +00:00
andrewk 57516582c2 Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2447 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 01:36:08 +00:00
ebanks d2770f380c Writing calls to standard out now works again (it got broken when we introduced parallelization) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2446 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-27 04:36:45 +00:00
ebanks 12990c5e7a Added qual-by-depth annotation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2445 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-25 02:30:30 +00:00
ebanks 0571d9dcb9 Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE. 
Also, array size for caches should be max score + 1.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2444 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 20:47:32 +00:00
ebanks 438d21842a The new recalibrator had been mimicking the behavior of the old one in that if there was no dinuc available (following a no-call base or at either end of a read), it didn't try to recalibrate. Now that Ryan has modularized the system, we no longer need to skip the base completely (we just need to skip the dinuc value)... which is good because the Picard people complained after realizing that cycle #1 never got recalibrated. 
The major effects of this commit are as follows:
1. We no longer skip any good bases (of course, this change alone breaks every single integration test).
2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N').

I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 20:41:29 +00:00
ebanks aaf674d9db Cleaned up this annotation. 
Still experimental.  As of now, it's not useful.  More analysis is needed to determine how to handle cases where UG is unsure whether a sample is het or hom.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2442 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 03:06:46 +00:00
ebanks 6df40876a3 Un-reverted Matt's previous changes and fixed integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2441 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 02:47:00 +00:00
hanna 2bd0b1bbf7 After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. 
Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 00:32:33 +00:00
hanna 98c268483e Fixed issues with the integration tests: 
1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 23:12:22 +00:00
aaron b134e0052f added changes to the code to allow different types of interval merging, 
1: all overlapping and abutting intervals merged (ALL), 
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY), 
3: no merging (NONE).  This option is not currently allowed, it will throw an exception.  Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.  

The command line option is --interval_merging or -im


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2437 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 21:59:14 +00:00
alecw 159778416c In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 21:42:36 +00:00
hanna 87ff2b15d4 First step in introducing a patch to Picard: create our ideal interface into the BAM file for sharding. 
This commit can iterate over the BAM file, pulling out information about the blocks in the file without actually loading
or decompressing the reads.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2434 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 21:35:08 +00:00
ebanks dc96879861 2 separate changes which both affect lots of UG integration md5s, so I'm committing them together: 
1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls)

2. Updates to the Unified Genotyper for parallelization:
   a. verbose writing now works again; arg was moved from UAC to UG
   b. UG checks for command that don't work with parallelization
   c. some cleanup



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2432 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 19:03:56 +00:00
ebanks 872a9d1c7b I'm making this change now (as opposed to waiting until Monday) to honor Tim's request. 
The cycle covariate is now first/second of pair aware.  I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do.  We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 16:26:43 +00:00
hanna e29e8e52b9 Multithreading support for the unified genotyper. Tests on a 10Mbase region on pilot 1 show a 6.8x improvement 
when running 8 ways parallel.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2430 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 00:48:06 +00:00
kiran 164a94a3d0 Modified the walker documentation so that the stray punctuation wouldn't cause the GATK to stop parsing the help documenation early (aka I changed one word). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2429 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 20:50:01 +00:00
kiran 4ee6a478e3 Creates a table of reference allele percentage and alternate allele percentage at Hapmap-chip sites in a BAM file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2428 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 20:43:44 +00:00
ebanks 03bf75e335 Now implements TreeReducible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2427 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 17:52:51 +00:00
hanna 0d890e1bf0 Rework Eric's output management code given that the behavior of the UG changes drastically 
depending on its output format.  Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2425 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 00:33:43 +00:00
ebanks f448a263e9 The cleaner now cleans duplicate reads (instead of ignoring them) - although it doesn't include them for scoring ref or alt consenses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2424 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 21:01:55 +00:00
ebanks cf303810d3 VCF reader now creates the correct type of header line for each header type 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2423 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 20:39:06 +00:00
ebanks e06dfe44c4 Check for null platform (even when the read group isn't null) and assign it the default platform if it is 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 07:01:41 +00:00
ebanks 87e5a41964 Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels. 
Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 05:46:16 +00:00
hanna b780ffb34a Add a getFormat() method to get the output format from the writer. The need for 
this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 01:46:26 +00:00
hanna 11cbfcec9c Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple 
source -> single definition mapping sets.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 00:39:36 +00:00
hanna 9e53c06328 First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 19:19:23 +00:00
ebanks 4ff61097cf Trivial change: < -> <= 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2415 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 03:35:27 +00:00
ebanks 566b556b50 Give user ability to turn off max allowed interval size 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 03:20:22 +00:00
ebanks a5f75cbfd4 The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 02:34:41 +00:00
depristo ee8bcdc61d PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-19 23:22:36 +00:00
depristo 9bf2d12c64 Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2411 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-19 23:20:57 +00:00
aaron 7e0f69dab5 Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:54:56 +00:00
hanna 80b3eb85fa Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:52:44 +00:00
rpoplin fdf542c214 The CycleCovariate for 454 data is now the TACG flow cycle. That is, each flow grabs all the T's, A's, C's, and G's in order in a single cycle. This is changed from incrementing the cycle whenever there is a discontinuous nucleotide along the direction of the read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:39:51 +00:00
aaron c39675d2c1 VCFTool.java got left off of the last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 21:33:53 +00:00
ebanks 4ea31fd949 Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 19:16:41 +00:00
ebanks eeddf0d08e Adding sample utils for convenience methods to pull out samples from e.g. SAMFileHeader or Genotype objects 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2405 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 18:51:21 +00:00
chartl 79b997f43d Minor fix to getValue (thanks Ryan!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2404 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 15:45:51 +00:00
aaron 9971a8da9a adding a check to the RodVCF to ensure that records are in-order in the underlying VCF file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2403 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 15:24:45 +00:00
chartl 38563bbc2d The values used to be integers (-1 for unpaired, 0 for unmapped, 1 for first, 2 for second); but i switched to strings before commit so it was more clear. Forgot to update the OTHER getValue method. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2402 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 15:05:14 +00:00
chartl 7b5e332ff3 Added - PairedQualityScoreCountsWalker: counts quality scores (e.g. as a histogram) on first reads of a pair and second reads of a pair. Turns out there's a consistent difference in quality scores; even after recalibrating without the pair ordering as a covariate (there's a bit of averaging -- but not as much as I initially thought). 
Added - A paired read order covariate to use with recalibration. Currently experimental: for instance, what's a proper pair versus just a pair? Nobody should use this one...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2401 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 15:01:01 +00:00
ebanks 4f59bfd513 Updates to the various GenotypeWriters to make them do simple things like write records (plus allow GLFReader to close). 
Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable.  Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault.  We can clean it up later if this whole thing works.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2400 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 07:20:23 +00:00
ebanks 94f5edb68a 1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString) 
2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 04:14:14 +00:00
jmaguire 98839193b7 compatibility with VCF lib's switch to GenomeLoc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2397 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 00:52:48 +00:00
jmaguire 8787dd4c5e Various and sundry additions to VCF tools. Some useful to the general public, some one-offs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2396 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 00:35:45 +00:00
rpoplin 6fbf77be95 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
 2009-12-17 20:07:26 +00:00
ebanks c75ec67f84 When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 19:01:08 +00:00
rpoplin aa86f3710d Updating HomopolymerCovariate to only count the consecutive previous bases. I left in the code but commented out for if somebody wants to worry about carry forward homopolymer problems. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 18:25:09 +00:00
hanna 9143822822 Fix half-hearted attempt to try to move classes from package to package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 17:41:42 +00:00
asivache acb4d477da sync... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 01:03:01 +00:00
asivache ba86508854 remove debug print command 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2386 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 00:00:01 +00:00
asivache d72d332239 1) changed to search specifically for D and I cigar elements (and to process properly/ignore H,S,P elements) and print out only intervals that encompass actual indels. There's still one interval per read (at most) generated, which is the smallest intervals that covers ALL indels (D or I elements) present in the read; 2) if an interval (thus the original read itself and indels in it) sticks beyond the end of the chromosome, the read is ignored and this interval is NOT printed into the output; instead, a warning is printed to STDOUT (should we send it to logger.warn() instead? 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2385 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 23:29:07 +00:00
hanna 5b78354efd Fixed NPE in index check with RefWalkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2384 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 22:37:45 +00:00
hanna e6127cd6c5 Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single 
shard for cases when the index file isn't available.  Works for the case in question, but is not
guaranteed to work in general.  Will be replaced once the new sharding system comes online.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:55:42 +00:00
ebanks bef1c50b3b Some cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2382 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:41:06 +00:00
ebanks bb92e31118 Optimizations: 
1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:39:58 +00:00
andrewk 36875fca89 Update documentation in the new help system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2380 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:33:12 +00:00
hanna ee47eb4367 Make filters used available to the walker via getToolkit(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2379 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:26:04 +00:00
ebanks b626fc0684 Joint Estimate is now the default calculation model. 
Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 19:41:02 +00:00
ebanks e051311e8c Added convenience methods in RodVCF to pull out all of the VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues()) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 17:58:41 +00:00
ebanks bb312814a2 UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). 
Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 17:28:09 +00:00
aaron af440943a4 Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek(). 
Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).  

Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 23:04:40 +00:00
andrewk 1035abc85f Add minimum base quality thresholding to depth of coverage via getBaseAndMappingFilteredPileup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2371 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 22:58:30 +00:00
sjia 2deae95df9 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2370 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:31:47 +00:00
hanna 555976d575 One more walker with formatting to fix. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2369 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:23:13 +00:00
hanna cf46472419 Fix up Sherman's new docs in compliance with javadoc specs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2368 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:20:38 +00:00
sjia df79ed8db1 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2367 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:53:41 +00:00
sjia a80a5f1036 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2366 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:52:08 +00:00
sjia 18f61d2586 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2365 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:45:19 +00:00
sjia 5974c42468 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2364 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:41:35 +00:00
sjia d8cfd707bc Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:35:18 +00:00
sjia 4322beeb35 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2362 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:33:38 +00:00
sjia 4148991d81 Now also encodes amino acids, includes documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2361 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:26:56 +00:00
ebanks 9b0bdbbf29 Fix for homopolymer bug: ref was lowercase, alt allele was uppercase, so alt != ref. Yuck. 
This is a temporary fix - pushed more elegant solution over to Matt.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 19:02:23 +00:00
depristo a810586418 Check-in without javadoc = smackdown 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2359 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 15:32:39 +00:00
ebanks b234019cf5 Readded locus printing suppression to DoC walker 
(and removed unused import from UG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 14:50:56 +00:00
depristo 0d2a761460 Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 14:38:39 +00:00
ebanks bf7bab754e Made getPileupWithoutMappingQualityZeroReads() and getPileupWithoutDeletions() more efficient, per Mark's cue. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2356 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 04:35:21 +00:00
ebanks 874552ff75 Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper. 
[Also, enable Mark's new UG arguments]



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 04:29:28 +00:00
depristo 2cbc85cc7a min mapping quality and min base quality arguments for UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2354 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 03:57:27 +00:00
depristo faa638532a Correct location 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2353 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 02:42:21 +00:00
depristo 1da97ebb85 Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2352 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 02:40:15 +00:00
chartl b42fc905e8 Added - new tests (Hapmap was re-added) 
Modified - Hapmap now takes a -q command to filter out variants by quality
Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions
Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:57:20 +00:00
rpoplin 8e44bfd2ef CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:52:30 +00:00
ebanks c7b23d6ca5 Now that VCFGenotypeRecords implement SampleBacked (as they should), a quick fix was needed to get the GenotypeConcordance working when no direct samples were provided in a samples file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2348 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 04:27:16 +00:00
asivache bd7b07f3f1 added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2347 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 00:15:44 +00:00
ebanks 97618663ef Refactored and generalized the VCF header info code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 21:02:45 +00:00
depristo 05b8782d5f Documentation updates. Moved CountX.java walkers to QC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 18:40:22 +00:00
depristo 92307361a4 In preparation for move 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2344 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 18:28:06 +00:00
ebanks 45199136f0 Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 04:13:30 +00:00
ebanks bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 
1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 02:52:18 +00:00
kiran 2748eb60e1 Added short documentation for each class so that it appears in the walker command-line documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 21:41:07 +00:00
rpoplin 78e94b5a84 TableRecalibration now puts the full list of walker arguments into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the default nback for the HomopolymerCovariate is 8, down from 10. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2339 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 17:29:41 +00:00
rpoplin 014013630f Added hieracrchy to the covariate classes: Required, Standard, and Experimental. Required covariates (rg and reported quality) are added for the user whether or not they are specified in the -cov list. There is now a -standard option in CountCovariates which will add in all of the standard covariates so the user doesn't have to type them all out or even know which ones are the standard. There is logger output to say which covariates are being used of course. The list of covariates used is also added to the PG tag in the bam file produced by TableRecalibration. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2338 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 16:34:05 +00:00
hanna 6955b5bf53 Cleanup of the doc system, and introduce Kiran's concept of a detailed summary 
below the specific command-line arguments for the walker.  Also introduced
@help.summary to override summary descriptions if required.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2337 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 04:04:37 +00:00
hanna cdfe204d19 Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions. 
Also increased the line width as much as I could tolerate (100 characters -> 120 characters).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2336 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 21:59:55 +00:00
rpoplin 4fa4e95fbc Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 21:57:18 +00:00
kiran 38d9f7b903 Renamed ReferenceContext's getSimpleBase() method to getBaseIndex() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2334 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 20:14:39 +00:00
aaron 09811b9f34 Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 19:51:05 +00:00
hanna 0da2105e3c Moving DuplicateQualsWalker to oneoffprojects. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 19:22:32 +00:00
rpoplin 60c3eb4b60 Added help.description to the recalibration walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 19:02:29 +00:00
ebanks 2ea7632b76 The SNP genotype concordance module is now more comprehensive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 18:34:33 +00:00
hanna 590aeee7d2 Documentation for more basic walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 18:15:40 +00:00
hanna d1815f3559 More documentation for walkers that I'm familiar with in the collection of core walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2328 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 18:02:33 +00:00
hanna 956c36a2c8 Help for the qc package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2327 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:32:47 +00:00
hanna 450ea233a5 Docs for the basic walkers: CountLoci, CountReads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2326 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:17:34 +00:00
hanna f97ac939fa Punch up the help documentation for CombineDuplicates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2325 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:09:35 +00:00
aaron 86dc98bfb5 update the documentation for CombineDuplicates for the new help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:01:42 +00:00
aaron 420725441a documentation updates for the new help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 16:15:44 +00:00
hanna 23d96b1d43 Help system content for the alignment module. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 16:01:25 +00:00
ebanks 2de7e1a178 Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample. 
The only major difference is that we are now able to get accurate allele balance ratios.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 05:28:28 +00:00
depristo 8f7554d44f A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2320 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 23:09:10 +00:00
aaron f64a4c66ac some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 22:33:51 +00:00
andrewk a7cd172628 Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2318 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 22:14:44 +00:00
ebanks 2869270c11 Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 21:11:42 +00:00
ebanks 31b1d60d28 Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 19:50:06 +00:00
hanna 0c396f04a2 Fix obvious cut/paste error in output stream management code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2313 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 19:23:13 +00:00
ebanks 11ac7885b0 Pull out StratifiedAlignmentContext code so other walkers can use it. 
This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 19:21:16 +00:00
hanna adb2fdbee7 Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2311 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 19:15:48 +00:00
hanna 5eac510b2f Refactor the code I gave Eric yesterday to output command line arguments. 
Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 18:57:54 +00:00
hanna 74b8055b6a Only show extra walker help if the user didn't specify a walker or specified 
an invalid walker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2309 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 16:43:06 +00:00
ebanks 0fae798b3a 1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls). 
2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2306 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 04:26:06 +00:00
ebanks a45adadf1f VCFGenotypeRecord already defines all the methods needed to be SampleBacked, so let's annotate it as being SampleBacked. This way, when used as a generic Genotype, sample data can be retrieved. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2305 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 04:16:21 +00:00
ebanks 78d5ac9bc2 Don't check het count when there are multiple Genotypes per Variation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2304 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 04:07:47 +00:00
ebanks f7c44ad019 - Read in arguments for the header based on reflection 
- Hook up Variation and Genotype in SSG



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 21:35:33 +00:00
hanna 408f6f3dee Refactoring of prior commit: better handling of unnamed package within the help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2297 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 20:12:35 +00:00
hanna 1d2151adcf Better handling of nulls output by 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 19:34:56 +00:00
ebanks 40c2d7a4bc Fix all-bases-mode and genotype-mode in the UG and add integration tests for them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 17:41:30 +00:00
ebanks 4e54b91ce4 UG now outputs the FORMAT header fields when there's genotype data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 16:31:07 +00:00
rpoplin 12c49ea485 Added DuplicateReadFilter to filter out reads that are marked as duplicates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2293 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 15:42:53 +00:00
ebanks fb900b12e1 VariantFiltration now details the filters it has used in the header of the VCF it produces. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2292 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 15:36:15 +00:00
ebanks 7a76e13459 Better explanation in the exception being thrown. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2291 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 03:59:36 +00:00
ebanks 8d67d9ade3 -Minor fix in UG for all-bases mode 
-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2290 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 03:49:10 +00:00
ebanks 717eb1de96 - Depth annotation now includes MQ0 reads 
- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 02:53:00 +00:00
ebanks e8822a3fb4 Stage 3 of Variation refactoring: 
We are now VCF3.3 compliant.
(Only a few more stages left.  Sigh.)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-08 21:43:28 +00:00
hanna 9e2f831206 A bit of cleanup in preparation for Picard patch. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-08 16:09:04 +00:00
hanna d3b78338da Get rid of characters in the docs that aren't universally compatible with 
character sets used throughout the group.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2285 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 21:41:07 +00:00
hanna d75d3a361a Clean up some of the walker help output based on additional experience and 
feedback received.  Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 21:33:11 +00:00
hanna a3e88c0b1c Cleanup results of bad merge. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2281 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 19:30:49 +00:00
hanna 10be5a5de9 Move some files around to reflect our growing help infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 19:23:12 +00:00
rpoplin 1d5b9883db 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
 2009-12-07 14:26:27 +00:00
depristo 8f461d3c40 Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2274 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 03:36:38 +00:00
hanna 8089aa3c50 Adding support to override the help text. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2273 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 00:16:26 +00:00
ebanks c0528cd88e Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 11:43:40 +00:00
ebanks b6f8e33f4c Stage 2 of Variation refactoring: 
VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.

Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else.  Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 06:48:03 +00:00
hanna 3b440e0dbc Add a taglet to allow users to override the display name in command-line help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2270 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 04:12:10 +00:00
ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. 
This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers.  I haven't finished refactoring the writers and haven't even touched the readers at all.

The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).

The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 03:12:41 +00:00
hanna b04de77952 First pass at a reorganized walker info display. Groups walkers by package 
and displays walker data extracted from the JavaDoc.  Needs a bit of help,
both in content and flexibility of package naming.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2267 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 23:24:29 +00:00
depristo 07b88621c5 Improved RankSum calculations and RankSum annotation. Much more meaningful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2266 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 22:16:40 +00:00
hanna 4c147329a9 Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 
in GenomeAnalysisTK.jar.  Still no support for actually displaying the archived javadoc.  Also change the approach 
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 20:08:41 +00:00
ebanks 1e8dcc30da -dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data 
-added code to cache the allele list so it didn't need to get recomputed each time it was requested.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 14:56:48 +00:00
ebanks 58937bf9ba You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2256 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 04:45:05 +00:00
ebanks b05e73a914 Finished implementation of the Wilcoxon Rank Sum Test thanks to Tim Fennell (calculating the normal approximation) and Nick Patterson (dithering to break tie bands). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2255 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 04:04:39 +00:00
ebanks 861221d046 - Moved various header line printing into a single method 
- Fixed output for coverage above min depth



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 02:15:43 +00:00
ebanks aef4be5610 Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2249 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:53:36 +00:00
ebanks df4e001a07 Renamed to more accurately describe its function. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:34:49 +00:00
ebanks c2017cc91b PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:23:59 +00:00
ebanks 01cf5cc741 1. Merged CoverageHistogram into DepthOfCoverageWalker 
2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:01:53 +00:00
ebanks 44b9f60735 PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 16:11:09 +00:00
ebanks 126d1eca35 Move to core (qc/) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2243 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 15:45:58 +00:00
ebanks 9da5cc25ad More archiving (with permission from Andrey) plus a move to core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 15:40:27 +00:00
aaron b3bdcd0e60 make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 06:59:27 +00:00
ebanks a88202c3f6 Refactored DoCWalker to output in a more helpful and usable style. It now outputs in tabular format with 2 different sections: per locus and then per interval. 
I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 05:28:21 +00:00
ebanks d7e4cd4c82 Moving some useful and stable walkers to core: 
- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 03:00:45 +00:00
rpoplin 46f3d3e39b Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 23:15:52 +00:00
depristo c776f9fb90 Simple utilities for dealing with Complete Genomics data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2230 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 22:51:41 +00:00
ebanks a09fee2b5e Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:28:07 +00:00
depristo dec0a781c2 Un-reinventing the wheel. --sleep argument removed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:19:28 +00:00
ebanks a3343c75db Move and rename a hybrid-selection-specific coverage calculation to hybridselection/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:11:22 +00:00
ebanks 2c83f2f2bc Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:04:22 +00:00
chartl 6a9e7bea05 Removing experimental annotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2220 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 19:03:55 +00:00
jmaguire c180a76b05 Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it. 
Great for resuming long jobs that died partway through.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 18:56:19 +00:00
ebanks 0a2304eff8 - Rename minConfidenceScore in VariantEval to minPhredConfidenceScore 
- Moved validation walkers to new qc dir
- Killed unused test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:59:19 +00:00
ebanks a5dfc9107d - Cleaned up annotation code some more 
- Use QualityUtils when phred-scaling now



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:45:29 +00:00
ebanks 7055a3ea2d - All annotations are now required to return their VCF INFO keys and descriptions 
- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:24:06 +00:00
rpoplin 67179e2412 Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 16:47:35 +00:00
ebanks 2838629724 -VCF writer now checks whether the allele frequency has been set before trying to write it out. 
-Renamed methods to be more consistent.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 16:25:32 +00:00
depristo 6231637615 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
 2009-12-02 15:41:35 +00:00
aaron d487428468 remove incorrect parentheses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2211 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 06:46:32 +00:00
ebanks b979bd2ced - Optimized implementation of -byReadGroup in DoCWalker 
- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 03:39:24 +00:00
ebanks 7c73496e72 Moved DoC walker over to new pileup system so it no longer moves like it's stuck in molasses. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2208 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 02:46:39 +00:00
ebanks ba8a8febc6 Thanks to Steve Hershman for finding this bug: 
getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled).  Probably we should change the method to be getNeg10Log10PError().  Anyone have strong feelings on this?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 01:59:03 +00:00
ebanks 3303808a8f Yet more walkers moved to oneoffprojects. 
Made hybridselection subdir in playground.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2205 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 21:29:12 +00:00
ebanks 05923f7fba Started transition to oneoffprojects. 
Moved/killed a few other walkers (with permission).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 21:19:02 +00:00
ebanks c36069355e Trivial change to verbose 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2203 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 20:48:10 +00:00
jmaguire 74f6526e09 VCFHomogenizer: A class that extends InputStream and dynamically re-writes pilot1 VCF's to be on-spec. 
VCFTool: A command-line tool with various useful VCF functions (validate, grep, concordance).




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2202 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 17:55:42 +00:00
jmaguire adf8f1f8b3 Add an InputStream constructor, which is immensely useful for various reasons. 
Also a minor performance optimization.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2201 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 17:25:00 +00:00
ebanks e581cceab6 Got Kris's permission to delete these walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2200 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 16:57:28 +00:00
rpoplin 3180fffd43 Eliminated unnecessary boxing of longs in RecalDatum. Changes to RecalDatum in preparation for new AnalyzeCovariates script. Updated TableRecalibrationWalker to make use of these changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2199 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 16:49:05 +00:00
chartl 21a9a717e4 Some minor changes and test: 
- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
  - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
  - A PileupWalker integration test on a particularly nasty FHS site
  - Two second-base annotation related integration tests on that same site
       + outputs were all hand-validated in matlab; within a certain tolerance for the annotations




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 15:15:54 +00:00
ebanks 084337087e Removing deprecated code and walkers for which I had the green light from repository. 
Moved piecemealannotator and secondarybases to archive.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 05:58:20 +00:00
ebanks 2c16c18a04 Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 05:29:00 +00:00
ebanks 7c6c490652 An unfinished implementation of the Wilcoxon rank sum test and a variant annotation that uses it. I need to merge and update this code with Tim's implementation somehow - but that won't happen until later this week, so I'm committing this before I accidentally blow it away. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2193 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 04:56:17 +00:00
ebanks 00f15ea909 Improved performance of deletion-free pileup and added mapping-quality-zero-free pileup convenience method. 
Finished converting genotyper and annotator code to new ReadBackedPileup system.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2192 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 04:50:47 +00:00
rpoplin 6bb864da2a More misc cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2191 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 22:29:07 +00:00
rpoplin b89b9adb2c misc code cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2190 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 21:16:00 +00:00
depristo e793e62fc9 minor code cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2189 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 20:57:20 +00:00
rpoplin 4969cb1957 CountCovariates uses new optimized ReadBackedPileup. It also smarter about re-doing calculations for the dnsnp variation rate sanity check. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2188 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 20:35:40 +00:00
ebanks add2fa7ab4 more use of new ReadBackedPileup optimizations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2187 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 20:04:01 +00:00
rpoplin 817e2cb8c5 Recalibrator makes use of the new GATKSAMRecord wrapper and now no longer has to hash the SAMRecord. Covariate's getValue method signature has changed to take the SAMRecord instead of the ReadHashDatum. ReadHashDatum removed completely. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2185 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 19:59:17 +00:00
ebanks e9a8156cfb Use new optimized ReadBackedPileup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 18:17:18 +00:00
rpoplin d8146ab23d Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2183 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 17:55:23 +00:00
ebanks a184d28ce9 Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine. 
I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 17:39:29 +00:00
depristo af22ca1b47 Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 01:39:01 +00:00
chartl 27651d8dc2 Oops. numReads is now called size 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2175 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-29 06:59:17 +00:00
chartl 21744e024b Quick walker that determines % of bases covered at (user - defined depth)x . I've been maintaining it in my directories alone, but now that i've accidentally deleted it twice, into playground it goes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-29 06:51:19 +00:00
hanna 3300ca906a An iterator for Eric to use when injecting his new wrapping reads -- a stopgap solution for getting additional caching 
functionality into a SAMRecord.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2173 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-27 22:25:52 +00:00
rpoplin 26db15be5c Added SingleReadGroupFilter to only use reads from a specific read group, filtering out all others. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2172 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-27 20:33:59 +00:00
rpoplin 91f5672a32 misc cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2171 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-27 19:56:20 +00:00
rpoplin d1298dda13 Encapsulated the sections of code that were shared by the two Recalibration walkers. This includes both the shared command line arguments and the section of code in the map methods which pull out data from the SAMRecord and stuff it into the ReadHashDatum. Command line arguments are now passed to the Covariates using a new initialize method that all Covariates must implement. Updated the dbsnp sanity check warning message to be less cryptic. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2170 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-27 19:54:10 +00:00
depristo 75b61a3663 Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2169 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 23:30:39 +00:00
alecw ac1b289d55 Add tile to ReadHashDatum, and implement TileCovariate 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2166 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 21:41:42 +00:00
depristo db40e28e54 ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2165 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 20:54:44 +00:00
rpoplin b44363d20a Removed silly casts from Integer to int. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2164 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 19:59:21 +00:00
ebanks d0f673f0c0 Use Math.abs so we don't get (inconsistent) -0's 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 19:08:34 +00:00
rpoplin 6ff8526592 Added arguments to the recalibration walkers so the user can specify the default read group id and platform to use when a read has no read group. There are also options to force every read group and every platform to be the specified values. Added integration tests that use a bam file with no read groups. Added comments to all the covariates to explain what each of the methods in the Covariate interface are used for. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2157 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 15:41:12 +00:00
aaron cfbd9332b0 small cleanups for the GATK paper genotyper; switched to the managed output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 08:04:13 +00:00
ebanks e1e5b35b19 Don't have the spanning deletions argument be a hard cutoff, but instead be a percentage of the reads in the pileup. Default is now 5% of reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2155 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 04:54:44 +00:00
depristo 03342c1fdd 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
 2009-11-25 03:51:41 +00:00
ebanks 2cb3e53b0b Verbose mode shouldn't be printing out 'NaN's and 'Infinity's 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2153 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 22:01:00 +00:00
rpoplin c9ff5f209c Added a CountCovariates integration test that uses a vcf file as the list of variant sites to skip over instead of the usual dbSNP rod. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2152 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 21:51:38 +00:00
ebanks 3484f652e7 1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info. 
2. Killed OnOffGenoype
3. SpanningDeletions is now SpanningDeletionFraction



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 21:47:20 +00:00
ebanks e05cb346f3 GenotypeLocusData now extends Variation. 
Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 21:07:55 +00:00
rpoplin 8b30279edc style update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2149 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 20:56:31 +00:00
rpoplin dffa46b380 BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2148 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 20:53:57 +00:00
aaron 8fbc0c8473 fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 19:19:47 +00:00
andrewk 3fca23cd16 Added a stub treeReduce function for debugging multi-threaded execution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2146 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 18:51:19 +00:00
rpoplin 277e6d6b32 Further optimizations of TableRecalibration. This completes my goal of having the only math done in the map function be addition, subtraction and rounding the quality score to an integer. Everything else has been moved to the initialize method and only done once. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2145 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 18:21:57 +00:00
andrewk e4546f802c Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency. Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points. Outputs R parseable file that has all data in lists and then does some basic plotting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 18:12:34 +00:00
andrewk e5106c9924 Hybrid selection performance statistics now include counts of the number of adjacent baits (0,1,2) using OverlapDetector and optionally include assayed bait quantities input via interval lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2143 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 18:07:23 +00:00
ebanks 87c1860398 I'm not sure I believe it, but JProfiler claims that calling FourBaseProbs.isVerbose() was taking 5% of my runtime... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2142 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 17:00:32 +00:00
ebanks b3f561710f Optimizations: 
1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)

UG now runs in half the time for JOINT_ESTIMATE model.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 16:27:39 +00:00
rpoplin a59e5b5e1a Added dbSNP sanity check to CountCovariates. If the mismatch rate is too low at dbSNP sites it warns the user that the dbSNP file is suspicious. Added option in CountCovariates and TableRecalibration to ignore read group id's and collapse them together. Also, If the read group is null the walkers no long crash with NullPointerException but instead warn the user the read group and platform are defaulting to some values. Default window size in MinimumNQSCovariate is 5 (two bases in either direction) based on rereading of Chris's analysis. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2140 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 16:16:44 +00:00
alecw e5e6d515c3 Fix misunderstanding of GenomeLoc interval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2138 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 15:12:49 +00:00
ebanks cb6d6f2686 Very minor performance improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2137 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 05:21:07 +00:00
ebanks c90bea39a1 read.getReadString().charAt(offset) --> read.getReadBases()[offset] 
[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 04:25:19 +00:00
ebanks ec321abd7b Added ability to filter on the QUAL field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2135 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 04:08:22 +00:00
ebanks 36d493e645 All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2134 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 03:55:12 +00:00
ebanks ee5093d2c6 -Added VariantFiltration integration tests 
-Added integration test for GLFs



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 02:36:27 +00:00
ebanks be6a549e7b Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 02:34:48 +00:00
hanna 4837fe919c Convenience changes. If no -BWT option is specified, pull the BWT location from the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2130 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 22:46:05 +00:00
rpoplin 9e4eadc37c CountCovariates v2.0.2: Added a --process_nth_locus <int> argument to only use every Nth covered locus when creating the recalibration table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2129 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 22:07:38 +00:00
ebanks ed4cf3de57 Check that we're biallelic before calling isSNP() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2127 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:20:48 +00:00
rpoplin 5744a1d968 The covariates don't care about SAMRecord's anymore - Cleaning up the import statements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2126 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:10:12 +00:00
chartl 23983b2fd8 New annotation: ResidualQuality 
Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.

Update to the integration test so bamboo doesn't look as though someone murdered it with a spork




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:04:01 +00:00
ebanks 70059a0fc9 Refactored joint estimation model to allow subclasses to overload PofD calculation over all frequencies. Pooled model now takes only 20% of time that it used to. 
Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2123 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:03:38 +00:00
rpoplin 7f947f6b60 Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2122 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 19:51:36 +00:00
ebanks 14bf6ce83c 1. Newest version of the joint estimation model. Faster than previous version and now qscores can get to be > 39.8 for hets. 
2. More sanity checks in annotations


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2119 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 17:05:50 +00:00
hanna ee2abd30c4 Count the best alignments and emit them to a file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2118 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 16:37:59 +00:00
rpoplin 1d46de6d34 The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2117 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 14:58:33 +00:00
ebanks dfe7d69471 1. VCF: don't print slod if it's never set 
2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 02:55:43 +00:00
ebanks 753cb100a3 Add checks for weird situations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2115 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 02:14:25 +00:00
ebanks 04d6ac940c Always print out VCF header - not just when there is genotype data present. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2114 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 01:44:10 +00:00
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
rpoplin b24240664f Reduced the number of calls to new ArrayList() in TableRecalibration. This results in a speed up of perhaps up to 6 percent (timed trials are hard). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2112 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-22 17:24:31 +00:00
hanna c9c4999354 BWA: odds and ends. Get rid of some spurious debug code that was accidentally 
checked in.  Add a better way to write out unmapped reads (thanks Kiran!)  Add 
a pre-built version of the shared library to the repository for early adoption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-22 15:26:07 +00:00
depristo 9c206abb97 removing unnecessary printing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2110 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-22 12:41:48 +00:00
chartl 59416ae06a This is an annotation adapted from one that Mark Daly suggested some time ago. Right now it calculates: 
- For all reference bases, the proportion of their second best bases that support the SNP

- the proportion of non-reference bases that support the SNP

and reports the difference between the two. Initially I was taking depth into account as well, but that did not appear to work as nicely as I'd like (even at 20,000x depth, if 95% of the non-reference bases are C, and 98% of the reference second-best-bases are C, then we would want to be suspicious of it; but perhaps slightly less so than if the depth were only 20...)

Anyway it's now available. I'm not sure how useful it will be, but I spawned the FHS annotation jobs again, so we'll see.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2109 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-22 00:47:49 +00:00
rpoplin 98f921fe24 The refactored CountCovariates now hashes the read object into a HashMap which holds all the properties the covariates pull out of the read over and over again such as read group string, bases string and its complement string, quality scores, etc. This results in a big speed up. CountCovariatesRefactored is now just slightly slower than CountCovariates (perhaps 1.07x according to my latest time trial). Thanks to Alec for suggesting IdentityHashMap. CycleCovariate now warns the user that is is defaulting to the Solexa definition of cycle when the platform string pulled out of the read is unrecognized instead of halting with an Exception. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2108 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-21 20:38:17 +00:00
depristo 27122f7f97 Performance improvements for pooled caller. Now possible to actually run on real data in a finite amount of time. Minor changes to GL interface (making strandIndex public) to support cached calculations in pooled caller. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2107 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-21 15:07:40 +00:00
ebanks 797bb83209 New VariantFiltration. 
Wiki docs are updated.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 19:50:26 +00:00
hanna a78bc60c0f Minor tweak to improve ease-of-use of iterator system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 18:24:19 +00:00
hanna 4fbb6d05d0 Refactoring. Push the revisions to the common aligner interface down into 
the aligner base classes.  Hack the managed implementation to support the
new interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 17:08:09 +00:00
ebanks d84444200b The Unified Genotyper now sorts the sample names in the vcf that it outputs. 
[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 16:13:18 +00:00
hanna 38a030f2ba Finishing off data transfer conduits for single alignment generator. 
Misc bug fixes elsewhere.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 15:21:59 +00:00
ebanks 2a5349d886 VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied and it's not already set for a record 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2100 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 03:26:09 +00:00
ebanks b434c1c240 Check for null entries before adding 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2099 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 03:12:20 +00:00
depristo 82fd824c4d Continuing improvements to unified genotyper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2098 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 01:39:29 +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
rpoplin 22aaf8c5e0 Added the old recalibrator integration tests to the refactored recalibrator sitting in playground. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2096 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 22:43:28 +00:00
hanna a95302fe98 Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still 
needs to plumbed through and it may leak memory.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 21:20:03 +00:00
hanna a972b2769f Checkpoint. Add first phase of single alignment interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 19:03:43 +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
chartl b4babb82eb adding an extra bit of data to come out of CTT (number of chips with actual data) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2091 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:46:10 +00:00
alecw 7623b39927 Add rodPicardDbSNP 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2088 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:27:46 +00:00
alecw b2b4ff7eca Cache SAMReadGroup rather than get it twice 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2087 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:27:18 +00:00
depristo eeb3a3fffb comments for Aaron 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2081 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 12:56:04 +00:00
aaron 7997455f38 first go of the genotyper for the GATK paper. More testing and review tomorrow to call it done. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2080 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 07:55:24 +00:00
ebanks 7b957d3e2e Make the whining from Khalid's office stop already 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2079 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 03:04:48 +00:00
hanna 85bc9d3e91 (Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid 
off-by-one errors.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 23:33:27 +00:00
rpoplin 0fbd81766b CountCovariates now uses any rod of type VariationRod with the name dbsnp as the source of known variant sites to skip over. It also grabs the platform string out of the read group when deciding which algorithm to use to calculate machine cycle. In this way it can now handle multi-platform bams. I added a new covariate: PositionCovariate. This is simply the offset regardless of which platform the read came from. This will be useful for comparing between the two covariates. Finally, this message serves as a warning that I will be killing the old recalibrator tomorrow after I've updated and verified new integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2077 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 23:03:47 +00:00
ebanks f667bed7fc -Don't annotate allele balance or on-off genotype if there's no genotype data 
-If qscore is infinity (because of precision) make a best guess instead


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2076 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 22:01:32 +00:00
ebanks 087e01a439 minor changes for --noSLOD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2074 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 18:48:01 +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
chartl 405c6bf2c1 VariantEval genotype concordance for pools! Integration test coming soon 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2071 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 17:24:54 +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
rpoplin f0a234ab29 TableRecalibration is now much smarter about hashing calculations, taking advantage of the sequential recalibration formulation. Instead of hashing RecalDatums it hashes the empirical quality score itself. This cuts the runtime by 20 percent. TableRecalibration also now skips over reads with zero mapping quality (outputs them to the new bam but doesn't touch their base quality scores). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2069 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 16:47:44 +00:00
chartl be31d7f4cc Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it. 
This will output for hapmap variant sites:

chromosome  position  ref allele   variant allele   number of variant alleles of the individuals   depth of coverage   power to detect singletons at lod 3   number of variant bases seen   whether or not variant was called




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 15:47:52 +00:00
chartl b68d6e06b7 Rollback of the previous "fix" and implementation of the real fix. 
We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot.

Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 06:09:24 +00:00
chartl 95f1be94c0 Fix for the broken build: 
do **not** attempt to annotate if UnifiedGenotyper is called from another walker! Why this didn't break the build earlier I have no idea.

Ultimately, there should be a better way of interfacing UG with another walker -- what if some other walker wants the annotations from UG? But since we're calling map directly -- and the annotations don't get returned directly from map -- this needs to be handled differently, while the map function should ultimately return the LOD score or quality under the GCM alone.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2066 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 05:56:31 +00:00
ebanks 9fb50e9bd9 Further refactoring so that pooled calling will work. 
Okay, Mark, you should be all set.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2065 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 00:18:13 +00:00
chartl 539f6f15e5 Added -- 
Second base skew annotations and integration tests. Nothing need be given except -A SecondBaseSkew; the statistic it annotates calls with is a chi-square statistic given by the deviation of the observed proportion of reference second-best-bases from the expected 1/3. Future additions may be to ask that the deviation be instead from a given transition table.

A big note for all users: All IllegalStateExceptions from the variation ROD (e.g. the RodGeliText) are dealt with SILENTLY. I understand this isn't optimal, but I'd rather simply not annotate a non-bi-allelic site than fail completely (there are quite a few such sites even on the regions over which the integration test has been written).




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2064 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 00:11:13 +00:00
depristo 42a0bbaf46 Minor reformating for pooled calling 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2063 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 22:06:11 +00:00
rpoplin ec1a870905 Working with byte arrays is faster than working with Strings so the Covariates now take in byte arrays. None of the Covariates themselves used the reference base so I removed it. DinucCovariate now returns a Dinuc object which implements Comparable instead of returning a String because it was too slow. CountCovariates now uses a read filter to filter out unmapped reads and allows the user to specify -cov all which will use all of the available covariates, of which there are 7 now. If no covariates are specified it defaults to ReadGroup and QualityScore, the two required covariates. Initial code in place to leave SOLID bases alone if they have bad color space quality. TableRecalibration uses @Requires to tell the GATK to not give the reference bases since they weren't being used for anything. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2062 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 21:50:52 +00:00
ebanks 4d9c826766 Integration tests actually run on real data now. 
<tries to hide sheepish grin>


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2061 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 21:04:14 +00:00
ebanks a048f5cdf1 -Refactored JointEstimation code so that pooled calling will work 
-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 20:21:15 +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
asivache 21729d9311 Do not print debug message when debug mode is not requested!! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2056 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 20:28:41 +00:00
rpoplin 967215066d The old CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2055 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 19:16:46 +00:00
rpoplin eb07c7f7f8 CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2054 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 18:44:54 +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
hanna ce5034dc5d Finally reinstate the iterator-style interface. Get rid of some scaffolding code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 02:34:19 +00:00
kiran 103763fc84 An accessor for the VCF header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2051 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-15 09:28:25 +00:00
kiran 97ed945797 Example code for a bug in the VCF implementation. See JIRA entry at http://jira.broadinstitute.org:8008/browse/GSA-225 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2050 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-15 09:27:12 +00:00
rpoplin 88fd762436 The -rf argument is now being used for read filter and is colliding with my walkers. Changed mine to -recalFile 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2048 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-14 19:37:46 +00:00
rpoplin b05119987c Clarified some of the comments in the individual covariates now that things have been moved around to speed up the code. In general most error checking and adjustments to the data are done per read instead of per base. This means that functionality was moved out of the covariate modules and into CovariateCounterWalker and TableRecalibrationWalker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2047 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-14 18:44:05 +00:00
rpoplin 672472789e Added some documentation to the helper classes. Fixed an error case in TableRecalibrationWalker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2046 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-14 18:13:43 +00:00
hanna 15c14add4d Repackage the aligner for better partitioning. The C aligner, for example, is now 
partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 22:55:27 +00:00
rpoplin d1b525b428 Default window size for NQS covariate is 3 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2040 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 19:24:27 +00:00
rpoplin 394c839974 Implemented NQS covariate. Extended Cycle covariate to handle 454 and SOLID reads. Added a Primer Round covariate for SOLID reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2039 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 19:22:21 +00:00
ebanks bf451873ff 1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction 
2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 18:02:18 +00:00
asivache 1be36ca959 Bug fix: when cleanedReadIterator is initialized, it gets immediately set to the contig of the first cleaned read; when the first uncleaned read coming in is on the lower contig, this would trigger 'readNextContig' with that lower contig as an argument. As the result, the whole cleaned reads file would be read through the end and no cleaned reads would be ever seen by the code afterwards. Now we do not call readNextContig if the (uncleaned) read's contig is lower than the current contig already loaded into cleanedReadIterator. the 'readNextContig' method now also throws an exception if requested contig is less than the currently loaded one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2037 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 15:41:26 +00:00
rpoplin b1376e4216 structure refactored throughout for performance improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2036 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 15:41:09 +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 902cf84448 Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 04:10:32 +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
mmelgar 72825c4848 A walker that generates a table of secondary base counts in a bam file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2031 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 02:11:23 +00:00
hanna 8145ed4672 Take 2, updating picard with bug fix for bam files containing no reads. 
Just stomped on the existing md5s because that's what Eric told me to do.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:52:08 +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 0922400ca9 Don't try to calculate ratios when DoC is zero (which happens when calls are made by an LD-aware genotyper) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2025 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 02:51:44 +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
hanna 2ea85fb62b Fix some problematic command-line argument naming and descriptions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2023 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 02:12:26 +00:00
hanna 0c2a957ae0 Better configuration support. Now supports everything that people have expressed interest in except edit distance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2021 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 20:54:49 +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
ebanks 578dcc54a4 Don't create a record if ref=N 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2018 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 04:32:17 +00:00
hanna 8406325247 New Picard is breaking one of the integration tests. 
Revert until we find out whether the cause is legit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 03:59:32 +00:00
hanna 499e7d1d75 Push forward some more delicate merging routines. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2016 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 03:07:34 +00:00
hanna bae4d3f7ea Updated Picard with fix for Doug Voet. Thanks Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 02:01:08 +00:00
hanna 2e4782f202 Command-line arguments for SamReadFilters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2014 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 23:36:17 +00:00
rpoplin a13cbe1df0 The refactored recalibrator now passes the integration tests as well as my own validation tests. I'm ready to have other people start jamming on the files. I'll make an updated wiki page soon. The refactored recalibrator is currently a bit slower than the old one but there were a lot of great, easy ideas today for how to improve it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2013 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 22:20:06 +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
rpoplin 1e7ddd2d9f Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2010 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 15:55:56 +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
depristo d316cbad4c VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:24:58 +00:00
aaron f9819d5f13 a little clean-up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 06:18:34 +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 2fa2ae43ec Enough people have found this useful, so... 
Moving Callset Concordance tool to core and adding integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:59:18 +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
rpoplin 740a5484c4 Added some documentation to the code, mostly especially to CovariateCounterWalker but various comments added throughout. Also changed the HashMap data structure to accept an estimated initial capacity. This had a very modest improvement to the speed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2001 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:13:56 +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 ab705565cf Completely refactored the Callset Concordance code. Now, it takes in VCF rods and emits a single VCF file which has merged calls from all inputs and is annotated (in the INFO fields) with the appropriate concordance test(s). 
Still needs a bit of polish...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1999 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 05:03:13 +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
kiran 7fde6c0bf4 One more output tweak. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1996 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:42:55 +00:00
kiran 00a7113d7a Tweaks to formatting of output table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1995 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:33:36 +00:00
ebanks 7ce0df76f8 Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:25:39 +00:00
ebanks d07f3bb6f6 Added methods to get strand bias and to test if record has allele freq or bias fields set. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:20:35 +00:00
kiran 3313b0ddb4 Fixed a minor bug where the lodThreshold wasn't being printed in the header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:51:36 +00:00
kiran 95d381efe2 Optionally computes the error rate using the best base and a random base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:47:34 +00:00
kiran 567f5758d2 Optionally lists read depths by read group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:39:19 +00:00
kiran a679bdde18 FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear to be contaminants by searching for evidence of systematic underperformance at likely homozygous-variant sites. 
Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:36:39 +00:00
kiran 2225d8176e A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:34:35 +00:00
hanna 21c5f543fa Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an 
alignment start will confuse the sharding system and cause it to return duplicate reads.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 14:27:26 +00:00
rpoplin 84ba604611 Sequential quality score calculation is now in place in the refactored recalibrator and matches the quality scores calculated by the old recalibrator exactly; at least on the small sets of data used so far. Validation, documentation, and optimization work is on going. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1985 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-07 15:55:16 +00:00
depristo bf1bc94060 Fixes for PooledConcordance bugs and lack of safety checking 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-07 01:54:10 +00:00
rpoplin 66d4a995e6 Initial check in of refactored Recalibrator. The new walkers are called CountCovariatesRefactored and TableRecalibrationRefactored. More work is needed to finish up the sequential calculation and to document the code sufficiently. These files are not ready to be used by other people quite yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1982 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 22:33:55 +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
ebanks 0a55fa5bb1 Completely refactored the Genotype Concordance module(s). 
Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality).  Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 16:27:16 +00:00
ebanks d549347f25 Refactored GenotypeLikelihoods to use an underlying 4-base model. 
It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 21:59:25 +00:00
jmaguire 4d3871c655 don't flush anymore. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1977 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 19:11:51 +00:00
aaron aacd72854f a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads. 
Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1).  Updated and checked BamToFastqIntegrationTest MD5 sums.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 05:26:33 +00:00
hanna 43c3ee61d5 Fix minor mapping quality bug. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-04 14:33:23 +00:00
ebanks a545859c62 Joint Estimation model now emits a reasonable slod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 21:12:42 +00:00
ebanks 11d950abe0 No longer allow the lod_threshold argument - use confidence instead. 
Have UG output qscores in all cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:18:51 +00:00
asivache 2fb45dbd73 Make window size a command line argument 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:13:35 +00:00
asivache 55f61b1f88 Bug fix in adjustment of the shift position. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:08:11 +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
hanna c63af32fc7 The BWA/C bindings were triggering the local aligner to repeatedly reload the 
ref genome.  Make sure the reference genome is cached.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 00:01:55 +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
aaron ba67c7f02b added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 21:09:18 +00:00
aaron b71b66bd88 the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 20:22:25 +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
hanna 1896f334d9 Fixed collection of bugs in reads aligning to multiple locations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 04:02:09 +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
hanna b95165e39c Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-01 00:33:18 +00:00
asivache 4b0796ba58 After fixing a few glitches and bugs, this version finally works as intended 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-31 04:59:58 +00:00
depristo 7d0ac7c6f2 Fix for long-term VariantEval bug plus new intergration test to catch it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-31 00:00:33 +00:00
asivache ea8d5c7077 Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 17:50:51 +00:00
hanna a3da475c88 Documentation and cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1946 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 15:40:28 +00:00
hanna 2d15891719 Created walkers for alignment, validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1945 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 15:04:07 +00:00
ebanks 51fffc7f69 Comments for Ryan (which also apply to ReadQualityScoreWalker). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1944 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 14:44:04 +00:00
ebanks ccd7440730 We can actually make this a bit simpler (and faster) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1943 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 04:21:03 +00:00
ebanks 1b6333e4ab Enough people have asked for this that it just needed to get written. 
One can now split up any number of sets into an N-way Venn (although it doesn't check for discordance in the calls, so you'll still want to use SimpleVenn for 2-way comparisons).
Wiki docs are updated.

To do: update to use Ryan's generic hash map when it's ready for public use.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1942 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 04:08:45 +00:00
ebanks 4bdb5b03bd tell UnifiedGenotyper to return calls at all bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 03:10:44 +00:00
ebanks 4ee1d6f733 -Have the calculation models determine whether a call passes the lod/confidence thresholds (as opposed to returning everything and letting the UG decide); this way, walkers which call map() will get only the good calls. 
-Do the right thing in all models for all-base-mode (for Kiran).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 02:35:51 +00:00
ebanks 64ac956885 Okay, I caved in: 
CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 00:32:26 +00:00
hanna 1f0d852a48 Fix bug where alignments with indels would be busted because bwa reverses 
the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 21:33:13 +00:00
asivache e3b4d4cbed Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1936 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 19:09:16 +00:00