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 We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this).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.
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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
3d055e3d16
Fail fast if users try to parallelize a read walker.
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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
7d79848f40
Better error message when bam file / list file with wrong extension is
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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
597b3744ab
Always use phasing info when converting genotypes to strings
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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
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
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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
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re-enabling regeneration of the tribble index if it's out of date.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).
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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
f0c379dde8
Unconsequential changes in report formatting
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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
3ab936181c
Supports the join feature of GenomicAnnotator
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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
f5f7217413
Implemented joins
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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
09c3b15af3
Implemented joins
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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
e14ae471a0
Refactored some of the small utility methods
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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
898a78e97d
Added toString()
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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
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
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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
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
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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
4a555827aa
Removing more toUpperCase sanity checks
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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
56e504789a
trivial change: toUpperCase no longer necessary
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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
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.
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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
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.
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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
21427211c0
Personal MD5 database system now live. WalkerTest now maintains a database of result files associated with MD5 results in integrationtest/, and provides command lines for diff-ing expected to current md5 results when encountering failed intergration tests. The suite currently takes 200Mb to store. Update and run intergrationtest to build your very own expectation database for future development work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3466 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-31 16:06:16 +00:00
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.
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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
eb25e41111
minor update to new tribble name
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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
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
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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
4e268ef6ac
Removing the Variant Recalibration Performance test because it isn't ready yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:27:25 +00:00
522dd7a5b2
Adding the variantrecalibration classes.
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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
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.
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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
871cf0f4f6
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
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@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
cc2bf549c8
Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time.
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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
a4d834cc01
fixing the test I broke
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3454 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 02:06:20 +00:00
6485e8383d
Trivial change to retrigger broken build that really isn't broken
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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
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.
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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
e1b0aefb29
fix for parallelism bug
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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
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.
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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
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).
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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
ff4a0764df
Read error rate is now parallelizable
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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
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.
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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
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.
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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
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.
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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
058441fa39
Trivial renaming of test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3441 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 16:56:42 +00:00
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)
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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
a2fab07258
fixed the build problem: there were two copies of the AnnotatorInputTable Codec and Feature in two different spots.
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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
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.
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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
88a06ad81f
Changes to Depth of Coverage:
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- 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
0607f76a15
commenting out this test until I can figure out what the hell is going on with the codecs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3436 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 01:12:10 +00:00
062b316881
Better Exception message when can't find annotation value in variant recalibrator.
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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
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.
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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
ae6c014884
Fixed UG parallelization bug. Better integration test to catch this in the future.
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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
434e920da9
Oops, forgot to update integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3431 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 20:37:45 +00:00
772f558ae0
Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.
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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
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.
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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
8db7c97c4d
Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
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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
aaron
hanna
ebanks
depristo
asivache
weisburd
rpoplin
chartl
delangel