4db2b13e9e
Rev tribble.
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Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
2011-07-17 13:05:04 -04:00
1af76736b9
Guarantees that the list of files will always be in the same order.
2011-07-17 11:41:34 -04:00
92a1c0c278
Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword.
2011-07-17 10:14:23 -04:00
eacf205f40
Tests needed to be updated to reflect the code reorg of tribble.
2011-07-16 09:22:34 -04:00
5cb5a4ec75
Merged bug fix from Stable into Unstable
2011-07-16 00:23:59 -04:00
dd92a14b40
Made extra indel VCF optional but DBSNP mandatory.
2011-07-16 00:23:35 -04:00
2fa5dbb0fe
Merged bug fix from Stable into Unstable
2011-07-16 00:15:19 -04:00
ed55182a4c
Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)
2011-07-16 00:09:00 -04:00
43bd45fcad
Merged bug fix from Stable into Unstable
2011-07-15 19:40:02 -04:00
fd1df31ef0
changing the output directory names for Analyze Covariates
2011-07-15 19:39:42 -04:00
dc7d1d2f08
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-15 17:49:13 -04:00
72f4cf9c0e
Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing)
2011-07-15 17:44:31 -04:00
aa30f416a3
Resolving conflicts
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Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
2011-07-15 16:21:42 -04:00
224d373997
No need to double overload the file constructor
2011-07-15 15:19:10 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
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Refactoring appropriately.
2011-07-15 14:34:50 -04:00
a670d6420a
Refactoring Qscript utils into queue general utils package.
2011-07-15 14:31:43 -04:00
9d59c2cb61
a) Made indel VQSR consensus script operational again, b) Made VariantsToTable more indel-friendly when printing out REF and ALT fields: strip out * from REF and print out alleles in the same way as the VCF so that offline processing is easier
2011-07-15 10:13:02 -04:00
10cf9245d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 19:18:05 -04:00
f19862a643
Fixing conflicts.
2011-07-14 17:13:31 -04:00
43c6a8565b
looks better now.
2011-07-14 17:10:44 -04:00
09ffe277ae
Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
2011-07-14 17:09:35 -04:00
4f8230c750
Merged bug fix from Stable into Unstable
2011-07-14 16:44:57 -04:00
9f5180ab05
Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
2011-07-14 16:42:17 -04:00
c0bbeb23ba
Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.
2011-07-14 15:12:28 -04:00
5ffeddd3b1
better to use _ instead of ., as this is a special case later.
2011-07-14 14:45:16 -04:00
9540df6998
Oops, forgot to update unit test
2011-07-14 14:00:19 -04:00
ed6beae1f3
Adding headers to diffable reading for VCFs
2011-07-14 13:55:35 -04:00
57a90173f3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 11:56:20 -04:00
66c652d687
Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions).
2011-07-14 11:56:10 -04:00
a4ab19d040
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 15:14:06 -04:00
0c54c796ed
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 14:57:33 -04:00
bb0e3a26fc
Added integration test for VCF writing. Also, bug fix for writing the GT-free records.
2011-07-13 14:57:21 -04:00
df996a1a73
more progress report for the Data Processing Pipeline.
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Bam lists can now have empty lines, comments and whitespaces anywhere.
2011-07-13 14:53:58 -04:00
6a431da554
Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.
2011-07-13 14:40:01 -04:00
e2f2917bd2
Merged bug fix from Stable into Unstable
2011-07-13 13:00:55 -04:00
ff4e31c554
Changing the file names as per Kris request.
2011-07-13 12:59:18 -04:00
74aa49e423
Merged bug fix from Stable into Unstable
2011-07-13 12:12:42 -04:00
fa3ff53508
Filters should only be applied to the new VC if the old VC had filters applied
2011-07-13 11:58:16 -04:00
969227c657
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 10:01:28 -04:00
797c50e689
Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore.
2011-07-13 10:01:23 -04:00
6007eea3ff
Allowing VCF records without GTs in vf4.1
2011-07-13 09:56:08 -04:00
1e81d521c0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 20:12:29 -04:00
837fb8f689
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:39:26 -04:00
5077c94d85
Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
2011-07-12 15:39:07 -04:00
01fd6a6949
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:20:44 -04:00
ccedd6ff4c
Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements.
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Added a size() function that calculates the number of elements tree from a DiffElement.
2011-07-12 15:20:28 -04:00
a2597e7f00
This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
2011-07-12 14:11:53 -04:00
329c3d8050
Merged bug fix from Stable into Unstable
2011-07-12 13:55:51 -04:00
73735863b0
Fix for the case of requesting genotype for a sample that doesn't exist in a VariantContext
2011-07-12 13:55:21 -04:00
c4c145afb9
Merged bug fix from Stable into Unstable
2011-07-12 13:44:48 -04:00
cfe43e3971
Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations
2011-07-12 13:43:46 -04:00
bfbca8b194
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 12:11:58 -04:00
05212aea62
reader now takes an argument for the maximum number of elements to read from the file.
2011-07-12 08:53:19 -04:00
8056a3fe89
getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily.
2011-07-12 08:52:31 -04:00
f313e14e4e
Now deletes the dump directory on ant clean
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Moving diffengine tests from private to public
2011-07-12 08:50:58 -04:00
d7d15019dd
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
2011-07-12 01:16:21 -04:00
400b0d4422
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 23:38:57 -04:00
d5056ad899
Merge branch 'master' into diffit
2011-07-11 23:16:15 -04:00
893cc2e103
Making the package public, so there's no dependances from public -> private
2011-07-11 23:15:08 -04:00
5e593793af
DiffEngine utility function simpleDiffFiles
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printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
2011-07-11 23:10:27 -04:00
d11155ce2e
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 19:19:54 -04:00
e93052a51e
When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
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Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
2011-07-11 19:17:58 -04:00
e3748675db
Support for VCF 4.1 header counts
2011-07-11 17:40:45 -04:00
f54c2ae3b4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:26:27 -04:00
d6517adb42
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:16:37 -04:00
86890c6357
N and K (in binomial probability) got switched in RFA Walker with the last commit. No longer will NaNs be produced.
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Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
2011-07-11 16:16:15 -04:00
d587856f2d
Private feature to input a list of family descriptions from a file and to look for MV's on all of these. Feature can also output a detailed description of the violation into a separate file
2011-07-11 14:17:59 -04:00
a18380ab96
Merged bug fix from Stable into Unstable
2011-07-11 12:16:50 -04:00
8a78414432
Removed TileCovariate as a dependency for AnalyzeCovariates.jar
2011-07-11 12:10:11 -04:00
6e7b5e1e7a
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-08 21:19:45 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
224574424e
Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
2011-07-08 12:48:49 -04:00
2a4b3ae4a2
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
2011-07-08 12:48:33 -04:00
8add2a3866
Merge branch 'master' into diffengine
2011-07-08 09:15:54 -04:00
cc143493e3
Merged bug fix from Stable into Unstable
2011-07-07 23:01:24 -04:00
4cfe0dd857
Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
2011-07-07 23:01:03 -04:00
3d4f0e9dd7
Now supports the case where you have multiple AC values in the info field.
2011-07-07 17:21:15 -04:00
212e9a1a0c
Fixing unstable build after stable commit
2011-07-07 15:18:57 -04:00
11d9a0473a
Merged bug fix from Stable into Unstable
2011-07-07 15:03:58 -04:00
50111db2b7
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
2011-07-07 15:02:48 -04:00
4d565b0811
Merge branch 'incoming'
2011-07-07 06:21:05 -04:00
55c8c05060
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-07 06:18:29 -04:00
5ab2e83904
a) Cosmetic modifications to IndelType annotation. b) Add ability to select samples from a file in PrintReads, c) fixes to shaped AF random selection in SelectVariants
2011-07-07 06:15:10 -04:00
ccf34f7e45
(1) Added very useful helper class TestDataProvider to BaseTest that making creating data providers for TestNG far easier
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(2) DiffEngine now officially working with with summaries. Extensive UnitTests all around!
2011-07-06 21:57:22 -04:00
52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
bdef233d4d
Merged bug fix from Stable into Unstable
2011-07-06 10:05:02 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
8e8b901d12
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-06 09:57:55 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
407a0e535f
Merged bug fix from Stable into Unstable
2011-07-05 16:34:21 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
9124c84a7c
bug fixes
2011-07-04 21:10:44 -04:00
bb85f232b9
bug fixes
2011-07-04 21:04:49 -04:00
f26ffeaea0
bug fixes
2011-07-04 20:48:45 -04:00
04df153f47
bug fixes
2011-07-04 20:45:10 -04:00
7a04872a3f
bug fixes
2011-07-04 20:33:59 -04:00
08bc843d4c
SelectVariants can get a table to boost AF when choosing randomly
2011-07-04 20:23:22 -04:00
38740b0ff5
First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.
2011-07-04 16:11:42 -04:00
fac082de64
Report only highest AF and AC in multiallelic records in VariantsToTable or else R can't parse table
2011-07-03 14:32:12 -04:00
abe9480c6d
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 21:19:15 -04:00
fb315b5f8c
Merge branch 'incoming'
2011-07-02 18:10:48 -04:00
41d46059e7
fixing bad format statement
2011-07-02 18:09:17 -04:00
3804afeb8a
Merge branch 'incoming'
2011-07-02 17:55:39 -04:00
781c0c33a4
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
2011-07-02 17:55:10 -04:00
6b8af6afd8
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 17:15:56 -04:00
fdc2ebb321
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
2011-07-02 17:15:13 -04:00
09af6bbc6c
Ugh - backed out experimental code not for public consumption unintendedly committed
2011-07-02 16:58:57 -04:00
c6c0dba040
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 16:45:34 -04:00
4532a84314
Merged bug fix from Stable into Unstable
2011-07-02 10:48:55 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
17ff5bb094
Variant records coming out of the VQSR are now annotated with which input annotation was most divergent from the Gaussian mixture model. This gives a general sense for why each variant was removed from the callset.
2011-07-02 09:55:35 -04:00
c65e52f88a
Merged bug fix from Stable into Unstable
2011-07-01 20:50:56 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
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Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
0c9105ca22
Minor fix of description
2011-07-01 18:07:35 -04:00
444eae316c
Moving these supported perl scripts to public
2011-07-01 17:26:25 -04:00
546e7777fa
Re-fixing paths in pipeline tests after example qscripts got moved.
2011-07-01 16:39:10 -04:00
e9030a7bfd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 16:19:35 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
d647ea4fdc
Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache
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non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
2011-07-01 16:04:30 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
11d4af0e75
Path-related fixes to the private queue pipeline tests.
2011-07-01 13:41:34 -04:00
9644f104c4
Fixes to the queue pipeline tests to account for the new directory structure.
2011-07-01 13:13:24 -04:00
4b17f34640
Fixes to the packaging system to work with the new directory structure.
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Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
2011-06-30 18:27:17 -04:00
5786b51bcf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:26:28 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
75f93882c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 14:59:10 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
f4ae6edb92
Moving some of the released R scripts into public from private
2011-06-30 14:55:25 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
2011-06-30 14:29:21 -04:00
bb6b1d615b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 13:50:16 -04:00
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
352c38fc0b
Updated to reflect dbsnp conversion fix
2011-06-30 11:55:56 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
331b47afbd
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 08:29:11 -04:00
50c32ce52e
VariantsToTableFix
2011-06-29 21:39:53 -04:00
9b134f3b96
VariantsToTableFix
2011-06-29 21:33:41 -04:00
f18fffd625
Fixing broken paths to the testdata directory throughout the codebase.
2011-06-29 17:36:47 -04:00
2b88033ef4
Enable considering 454 reads, just lower GOP by 15
2011-06-29 16:12:55 -04:00
2ad4d2f0bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 16:06:14 -04:00
1085df8b7b
Making the BQSR pipeline publicly available and supported.
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this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.
2011-06-29 16:05:32 -04:00
dc4f63a1a8
a) consensus goes to week queue
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b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
2011-06-29 16:00:23 -04:00
70ba851478
Might as well check for the illegal state and throw an exception
2011-06-29 15:59:10 -04:00
1f19afe1d9
Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.
2011-06-29 15:54:09 -04:00
e91ae6b265
AF matching when selecting random variants
2011-06-29 15:00:26 -04:00
33c67a139c
Wrong package; this should have been moved when VC got moved in from Tribble
2011-06-29 14:56:02 -04:00
dee10140dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 13:58:04 -04:00
8586c86bc4
My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals.
2011-06-29 13:56:37 -04:00
f736a1d61b
Updated md5's from previous checkin
2011-06-29 13:37:15 -04:00
5b6d279a2e
Two bug fixes:
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a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.
2011-06-29 10:21:27 -04:00
139c6b84a1
Modified build.xml and the help extractor doclet to use the output of "git
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describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
2011-06-28 08:37:05 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Mark DePristo
Mauricio Carneiro
Menachem Fromer
Guillermo del Angel
Eric Banks
Ryan Poplin
Khalid Shakir
Christopher Hartl
David Roazen